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B I O L O G Y

TABLE OF CONTENTS Chapter 1: The Science of Life .......................................................................................................2

Chapter 2: Chemistry......................................................................................................................7

Chapter 3: Biochemistry ...............................................................................................................11

Chapter 4: Structure and Function of the Cell ..............................................................................14

Chapter 5: Homeostasis and Transport.........................................................................................18

Chapter 6: Photosynthesis.............................................................................................................20

Chapter 7: Cellular Respiration ....................................................................................................24

Chapter 8: Cell Reproduction .......................................................................................................27

Chapter 9: Fundamentals of Genetics...........................................................................................32

Chapter 10: Nucleic Acids and Protein Synthesis ........................................................................35

Chapter 11: Gene Expression .......................................................................................................38

Chapter 12: Inheritance Patterns and Human Genetics ................................................................41

Chapter 13: DNA Technology......................................................................................................45

Chapter 14: The Origin of Life .....................................................................................................48

Chapter 15: Evolution: Evidence and Theory...............................................................................51

Chapter 16: The Evolution of Populations and Speciation...........................................................53

Chapter 19: Introduction to Ecology ............................................................................................56

Chapter 20: Populations................................................................................................................57

Chapter 22: Ecosystems and the Biosphere ..................................................................................59

Chapter 23: Environmental Science .............................................................................................61

PLEASE READ INSTRUCTIONS FOR USAGE:

! Chapters 7 – 23 have been proofread for accuracy. Exercise caution with chapters 1 – 7 which have not been reviewed. !

This is an outline of most chapters in Holt, Reinhart & Winston’s 2002 Modern Biology book, excluding Chapters 17 &18

which I never got to outlining. You can see that my note taking gets more in-depth as the chapters go on because at the time

this form of outlining was new to me. This document is in PDF format to make it easier to navigate. Please read the following

notes as they’ll help you comprehend the format and how to search for things.

• BOLD words are important non-vocabulary terms. COLORS do not mean anything specific unless otherwise noted,

they just look pretty. UNDERLINED words are words that are bolded in the textbook.

• ROMAN NUMERALS (I, II, III,…) indicate new chapters. CAPITAL LETTERS (A, B, C,…) are sections within

those chapters. NUMBERS (1, 2, 3,…) are subsections (subsections are in big, all caps blue letters in the book).

• Like bolded words, ITALICS are just there to put emphasis on certain things, such as examples.

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I. CHAPTER 1 – THE STUDY OF LIFE

A. Section 1 – Themes Of Biology

1. Primordial Earth

a. Formation of first life form on Earth dates back to approx. 3.5

Billion years ago.

b. Organism – a living thing.

c. Single-celled organisms were the only form of life on Earth for

several million years after genesis.

d. Cellular organisms gradually changed through time and lead to

Earth’s current diversity.

2. Biology – the science of life or all living things. Includes…

a. Microscopic structure of single cells;

b. Interactions between millions of species

c. History of individual organisms;

d. Collective history of life on Earth. 3. Cell Structure and Function

a. The cell is the basic unit of life; all organisms are made of and

develop from cells.

b. Unicellular Organisms – composed of only one cell.

c. Multicellular Organisms – composed of more than one cell.

d. All cells are surrounded by a membrane and contain genetic

information to help carry out internal processes.

e. New cells produced by unicellular organisms are identical to

the parent cell.

f. Differentiation – the process by which cells become different

each other as they grow to perform different tasks.

4. Stability and Homeostasis

a. Internal conditions such as food, water, and temperature need

to be controlled within an organism.

b. The average temperature of the human body is around 37 C

(98.6 F).

c. Homeostasis – a stable level of internal conditions that is found

in all living things) including unicellular organisms.

1. The Harp Seal utilizes the shape of its body, fat, and

circulatory system to survive in freezing water.

5. Reproduction and Inheritance

a. Reproduction – the process by which organisms produce new

organisms like themselves.

b. DNA – hereditary information. Deoxyribonucleic Acid.

1. In Multicellular organisms, DNA is enclosed within a

structure of membrane.

2. In Unicellular organisms, DNA exists as a loop.

c. Gene – short segment of DNA. Contains the instructions for

development of a single trait.

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d. The DNA in every cell in your body is exactly identical.

e. Sexual Reproduction

1. Half of the female genome as well as half of the male

genome combine to form a single cell (fertilized egg).

2. The cell divides repeatedly.

3. The new organism is made of cells containing

hereditary information from both parents.

f. Asexual Reproduction

1. A bacteria splits in two and hereditary information is

not combined.

2. The spider plant splits off vines to form offspring.

3. Each new cell is identical to the parent in every way.

6. Evolution – change over generations.

a. Natural Selection – organisms with more favorable traits will

be more successful at reproduction.

1. Driven by competition for resources.

7. Interdependence of Organisms

a. Ecology – the interactions of organisms between one another

and their environment.

b. Ecosystem – environmental community.

8. Matter, Energy, and Organization

a. Photosynthesis – the process by which plants capture energy from the sun and convert it to chemical food.

b. Autotrophs – organisms that make their own food.

c. Heterotrophs – organisms that get food from the outside

environment.

B. Section 2 – The World Of Biology

1. All organisms share certain features universal to all living things.

a. Cells – all living things are composed of cells.

b. Organization – living things are highly organized at the

molecular and cellular scale.

c. Energy Use (Metabolism) – the sum of all the chemical

processes that occur in an organism.

1. Greek metabole; i.e. to change

d. Homeostasis – all living things maintain stable conditions.

e. Growth – living and many nonliving things grow.

f. Reproduction – all species can reproduce.

2. The Living World

a. A gram of fertile soil may contain more than 2.5 Billon

unicellular organisms.

C. Section 3 – Scientific Methods

1. Observing

a. In 1976, a deadly pathogen appeared in the Congo. Doctors

observed symptoms and recorded locations of occurrences to

determine the cause.

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2. Asking A Question

a. All scientific investigations begin with one or more questions.

b. Questions are important to the scientific process as they

determine what aspects need to be investigated further and pick

out possible areas of further concern.

1. How is the disease transmitted?

2. Do all victims die?

3. What is the disease causing agent?

3. Collecting Data – the longest phase of a scientific investigation.

a. Data – any and all information that scientists gather in trying to

answer their questions.

b. Important aspects of collecting data include:

1. Observing i. It is the observations of something unusual that

raises the first question in a scientific

investigation.

ii. Observation – typically employs one or more of

the five senses to perceive objects or events.

2. Measuring i. Things are often measured in numbers.

ii. In Zaire, scientists recorded data including the

number of people who displayed symptoms of

the disease, among other key figures.

3. Sampling i. Sampling – the technique of using a sample to

represent an entire population.

ii. Samples must be large and random.

iii. In Zaire, scientists took hundreds of blood

samples from both infected and healthy people.

4. Organizing Data i. Organizing involves placing data in a logical

order, such as a graph, chart, table, or map.

ii. Flowcharts are also commonly used (Figure 1-

14, Pg. 16)

4. Hypothesizing

a. Hypothesis – a suggested explanation for what has been observed or recorded. A hypothesis can be tested.

b. Steps involves in hypothesizing: 1. Forming A Hypothesis

i. Cause-and-effect relationships can never be

assumed in an investigation.

ii. A statement is testable if evidence can be

collected that does or does not support it.

iii. A hypothesis can never be proved true beyond

all doubt.

2. Predicting

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i. Prediction – states the results that will be

obtained from testing a hypothesis.

ii. A prediction must always take the form of an if

then statement.

5. Experimenting

a. Experiment – the process of testing a hypothesis or prediction

by gathering data under controlled conditions.

b. Aspects of experimenting:

1. Conducting A Controlled Experiment i. Controlled Experiment – based on a comparison

of a control group with an experimental group.

ii. The control group and experimental group

are designed to be exactly the same except for

one factor called the independent variable.

iii. Dependant Variable – driven by or results from

the Independent variable.

2. Analyzing Data i. Analyzing data is the process of determining

whether data are reliable and support a

hypothesis.

ii. Scientists may use statistics to determine

relationships between variables.

6. Drawing Conclusions

a. Steps of drawing a conclusion: 1. Modeling

i. Model – an explanation supported by data.

ii. Scientists can use models to generate new

hypotheses or predictions.

2. Inferring i. Inference – a conclusion made on the basis of

facts or premises rather than on direct

observations.

ii. Unlike a hypothesis, an inference is not directly

testable.

3. Forming A Theory i. Theory – a broad and comprehensive statement

of what is thought to be true. A theory is

supported by considerable evidence and may tie

together several related hypotheses.

D. Section 4 – Microscopy And Measurement 1. Microscope – an instrument that produces an enlarged image of an

object.

2. Magnification – the increase of an object’s apparent size.

3. Resolution – the power to show details. Microscopes vary in power.

4. Compound Light Microscope (LM) – a lighter microscope used to

examine small organisms and cells. The specimen must be transparent.

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1. Stage – where the slide holding the specimen is placed.

2. Objective Lens – a variety of lenses through which

light passes through after the specimen. Objective

lenses enlarge the image of the specimen.

3. Ocular Lens – the lens in the in the eyepiece where the

image is magnified further.

4. Nosepiece – a rotating piece holding the objective

lenses in place.

5. Power Of Magnification – the factor of enlargement. A

typical light microscope produces an image 40 times

the actual size of the specimen.

6. Computing The Power Of Magnification i. The standard ocular lens magnifies 10x.

ii. The power of the strongest objective lens is

multiplied by the power of the ocular lens to get

the total power of the microscope.

5. Electron Microscope – a powerful microscope in which a beam of

electrons produces an enlarged image of the specimen.

a. Beyond 2,000x, the image of a specimen becomes blurry due to

the physical characteristics of light; therefore, another method

must be used.

b. Types of Electron Microscopes:

1. Transmission Electron Microscope (TEM) – transmits

a beam of electrons through a thinly sliced specimen.

TEM can magnify up to 200,000 times but cannot be

used to view living specimens.

2. Scanning Electron Microscope (SEM) – generates 3-D

images. The SEM operates by bouncing electrons off

an intact, metal-coated specimen. SEM can magnify up

to 100,000 times. Like the TEM, SEM cannot be used

to view living organisms.

6. Measurement In Science

a. The official name of the measurement system is Systèm

International d’Unités (Internal System of Measurements),

commonly called SI.

b. Base Units – fundamental base units that describe length, mass,

time, and other quantities.

c. The Seven Fundamental Base Units:

1. Meter (m) – length

2. Kilogram (kg) – mass

3. Second (s) – time

4. Ampere (A) – electric current

5. Kelvin (K) – thermodynamic temperature

6. Mole (mol) – amount of substance

7. Candela (cd) – luminous intensity

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d. Derived Unit – produced by the mathematical relationship

between two base or two derived units.

e. SI Derived Units: 1. Square Meter (m

2) – area

2. Cubic Meter (m3) – volume

3. Kilogram per Cubic Meter (kg/m3) – mass density

4. Cubic Meter per Kilogram (m3/kg) – specific volume

5. Degree Celsius (0C) – Celsius temperature

f. There are other units accepted for use with SI, concerning units

of time, volume, and mass including hours, days, and metric

ton.

II. CHAPTER 2 – CHEMISTRY

A. Section 2 – Composition Of Matter 1. Matter – anything that occupies space and has mass.

a. Mass is the quantity of matter an object has.

b. Mass and weight are NOT the same – the pull of gravity on an

object is what fives an object the property of weight.

c. Biologists study chemistry because all living things are made

of the same kinds of matter that make up nonliving things.

2. Elements – pure substances that cannot be broken down chemically

into simpler kinds of matter.

a. 118 elements on the periodic table.

1. <30 are vital to living organisms.

2. >90 of the mass of all kinds of living things are

composed of: Nitrogen, Oxygen, Carbon, Hydrogen,

Phosphorus, and Sulfur.

b. A chemical symbol consists of one or two letters of the

element’s name. Some element names branch off of Latin; for

example, Aurum and Ferrum.

3. Atoms – the simplest particle of an element that retains all the

properties of that element.

a. Masses of atoms are measured in Atomic Units (au). Protons

and Neutrons both equal 1 au while an electron is considered

insignificant.

b. Parts Of The Atom

1. Nucleus – the central core of the atom; consisting of

two kinds of particles.

2. Proton – one of the two varieties of particles present

within the nucleus with a positive charge.

3. Neutron – one of the two varieties of particles present

within the nucleus with a neutral charge.

4. Electron – a small, negatively charged particle. In a

normal atom, the number of protons is balanced by the

number of electrons to make a net electrical charge of

zero.

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c. Atomic Number – the number of protons in an atom. All atoms

of the same element have the same number of protons. If the

number of protons were to change, the atom would become

that of a different element.

d. The Energy Levels 1. Energy level “K” can contain up to two electrons and is the

closest to the nucleus.

2. Energy level “L” is the second energy shell and can contain

up to eight electrons.

3. Energy level “M” is the third shell from the nucleus and

can contain up to eight numbers. In the event that “M” is full,

more shells are introduced, each being named according to

the alphabet. Shell “N” can contain up to 18 electrons.

e. Electrons furthest away from the nucleus have more energy

than those closer.

4. Compound – a pure substance that is made up of atoms of two or more

elements.

a. Most elements do not exist by themselves, but combine with

other elements.

b. Physical and chemical properties of a compound defer from the

original characteristics of the elements composing it. For

example, H2 and O exist as gasses but water is a liquid.

c. Chemical Reactions – a combination between elements

ultimately resulting in atomic stability. During a reaction,

chemical bonds are broken.

d. Molecule – the smallest unit of a substance that keeps all of the

physical and chemical properties of that substance. They are

composed of at least two covalently bonded atoms.

e. Energy Reactions in Animals

1. Plants and animals both store glucose. Plants store it as

starch, while animals store it as glycogen.

2. Hydrolysis – the process of breaking down

hydrocarbons for energy.

3. Nucleic acids such as DNA are composed of:

i. Thymine

ii. Adenine

iii. Cytosine

iv. Guanine

4. Unsaturated fats are more reactive than saturated fats as

their molecular structure allows for enzymes to break

them down more efficiently.

f. Forms of Bonds 1. Covalent Bond – a form of bond between atoms that forms

when atoms share one or more pair of electrons. When two

atoms of a nonmetal bond, a large amount of energy are

needed for either atom to lose an electron. Instead, they

share the needed electron

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2. Ionic Bonds – a bond that forms when electrons are

transferred from one atom to another atom. During ionic

bonding, one or more valence electrons are transferred from

one atom to another.

B. Section 2 – Energy

1. Energy and Matter

a. Energy – the ability to do work and cause change. Energy can be converted from one form of energy to another, such as in a

light bulb.

b. Chemical energy, thermal energy, and mechanical energy are

all vital to the internal wellbeing of an organism.

c. Free Energy – the energy in a system that is available for work.

In a cell, free energy is the energy available to fuel cell

processes.

d. All atoms are in a state of constant motion. The precise amount

of motion between molecules determines the state of matter.

e. States of Matter

1. Solid – particles are tightly linked together in a definite

shape and volume and vibrate in place.

2. Liquid – particles are not as tightly linked together as

in a solid. A liquid has a definite volume but a shape

that varies.

3. Gas – particles of a gas have little or no attraction. A

gas has no definite shape and volume and fills to

completely encompass all available space.

2. Energy And Chemical Reactions

a. Reactants – the chemicals or elements being reacted with each

other to produce an outcome.

b. Products – the result of a reaction.

c. The number of each kind of atom must be the same on either

side of the � , as matter cannot be created or destroyed.

d. Most of the energy our bodies use comes from sugars from the

food we eat. To create energy, sugars are broken down to

carbon dioxide and water. The process results in the creation

of free energy.

e. Energy Transfer 1. Exergonic Reactions – reactions resulting in the release

of free energy.

2. Endergonic Reactions – reactions resulting in the

absorbance of free energy.

f. Activation Energy – the energy required to start Exergonic and

Endergonic reactions.

g. Catalysts – a chemical substance that reduces the amount of

activation energy needed for a reaction to occur.

h. Enzymes – an important class of catalysts present within the

cells of many living things.

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i. Reaction-Oxidation Reactions

1. Redox Reactions – reactions during which electrons are

transferred between atoms.

2. Oxidation Reaction – a reaction during which a

reactant loses one or more electrons, becoming positive

in charge.

3. Reduction Reaction – a reaction during which a

reactant gains one or more electrons, becoming

negative in charge.

C. Section 3 – Solutions 1. Describing Solutions

a. Solutions:

1. Solution – a mixture that appears to be a single substance

but is actually a mixture. A solution must be composed of

substances that are in the same phase (combining two or

more liquid/gases). Solutions have the same appearance and

properties throughout the mixture.

2. Solute – the substance that is dissolved into the mixture

(such as adding a spoonful of sugar to a cup of tea).

3. Solvent – the substance in which the solute is dissolved in

(the cup of tea). In order for the solute to be able to dissolve

into the solvent, it must be soluble.

b. Concentration – the measure of the amount of solute dissolved into

the solvent. Expressed in g/mL.

c. Aqueous Solution – solutions in which water is the solvent. They are very important to living things. Examples include sea

water, intracellular fluid, and tea.

2. Acids And Bases

a. In water, the force of attraction between molecules that the

oxygen atom can remove a hydrogen atom from another water

molecule.

b. Disassociation – the breaking apart of a water molecule into

two ions of opposite charge.

H2O ↔ H+ + OH

-

c. In the above equation: 1. OH

- is the Hydroxide Ion.

2. H+ can react with other water molecules through this

equation:

H+ + H2O ↔ H3O

+

3. H3O+ is known as the Hydronium Ion.

d. Acidity or alkalinity is a measure of the relative amounts of

hydroxide ions and hydronium ions dissolved into a solution.

e. Relationship Between Hydroxide And Hydronium Ions

1. If the number of hydroxide ions in a solution equals the

number of hydroxide ions, the solution is neutral.

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2. If the number of hydronium atoms in a solution is

greater, the solution is an acid.

3. If the number of hydroxide atoms in a solution is

greater, the solution is a base. The word alkaline refers

to bases

f. pH Scale – a scale for comparing the relative concentrations of

hydroxide and hydronium ions in a solution. It ranges from 0 to

14; 0 being the most acidic and 14 being the most alkaline.

g. Buffers – chemical substances that neutralize small amounts of

either an acid or a base added to a substance.

III. CHAPTER 3 – BIOCHEMISTRY

A. Section 1 – Water 1. Polarity

a. The electrical layout of a water molecule is unevenly

distributed due to the deeper charge of the Oxygen atom.

b. The region that the two hydrogen atoms are located has a slight

positive bias.

c. Polar – refers to the dipole-dipole intermolecular forces

between the slightly positive ends of one molecule to the

negative end of another or the same molecule.

1. Water shares hydrogen atoms unevenly; hence, the

presence of only two hydrogen atoms leaves one side of

the atom predominantly negative. In Methane

hydrogen atoms are distributed evenly, hence the

compound is non-polar.

d. The polar nature of Water makes it a prime candidate for the

dissolution of other polar substances, such as sugars, proteins,

and ionic compounds.

2. Hydrogen Bonding

a. Hydrogen Bond – the type of attraction that holds two water molecules together. A hydrogen bond has energy comparable

to that of a weak covalent bond, but is easily breakable.

b. Attractive forces: 1. Cohesion – the attractive force between particles of the

same kind. Cohesive forces resulting from water’s

hydrogen bond cause water to act as if it has a “skin”

due to surface tension.

2. Adhesion – the attractive force between unlike

substances. Water droplets, for example, stick to

cobwebs and blades of grass.

i. Capillarity is the ability of a substance to draw

another substance into it.

c. The temperature of water does not experience any significant

change until after hydrogen bonds have fallen apart.

d. Temperature moderation – water molecules can absorb a lot of

energy before its temperature changes.

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B. Section 2 – Carbon Compounds 1. Organic compounds – compounds containing carbon atoms that are

covalently bonded to other carbon atoms and to other elements as well.

2. Carbon Bonding

a. Carbon’s tendency to bond with itself and other elements

results in an enormous variety of organic compounds, hence

the term carbon-based life form.

b. A single Carbon atom can form up to four covalent bonds with

other atoms, as it has four valence electrons.

3. Functional groups – clusters of atoms that influence the properties of

the molecules they are part of. For example, the hydroxyl group.

a. Alcohol – an organic compound with a hydroxyl attached to

one of its carbon atoms.

1. Ethanol causes cell death in the liver and brain.

2. Methanol is wood alcohol, and causes blindness or

death.

3. Glycerol is needed by humans to assemble some

molecules.

b. Because hydroxyl is polar, alcohol has the ability to form

hydrogen bonds with other molecules.

4. Large Carbon Molecules

a. Forms of Carbon molecules:

1. Monomers are smaller, simpler molecules built up

from Carbon. They can bond with one another to form

more complex compounds.

2. Polymers consist of repeated, linked units. They may

be identical or related to each other.

3. Macromolecules are larger, more complex polymers.

b. Condensation reaction (“dehydration synthesis”) – a chemical

reaction in which two molecules combine to form one single

molecule.

c. Hydrolysis – the process by which some large molecules, such

as polymers, break down. Hydrolysis is a reversal of a

condensation reaction.

1. The addition of water to some complex molecules can

cause them to break down the bonds that hold them

together.

d. Adenosine Triphosphate (ATP) – the universal energy

“currency” for all living things. ATP contains a large amount

of energy in its overall structure.

1. Three linked Phosphate groups (PO4-) are attached to

one another by covalent bonds. When these bonds

break, more energy is released than was require

breaking them.

C. Section 3 – Molecules Of Life

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1. Carbohydrates – organic compounds composed of carbon, hydrogen,

and oxygen in a ration of about 2 hydrogen atoms to 1 oxygen. They

are the most abundant of the four biomolecules.

a. Monosaccharides – are the most basic unit of carbohydrates

(monomers). They are simple sugars.

1. General Formula = (CH2O)n

2. The most common monosaccharides are glucose,

fructose, and galactose

i. Glucose is the main energy source for cells.

ii. Fructose is found in fruits and is the sweetest

monosaccharide.

iii. Galactose is found in milk and is usually

combined with the other two.

3. Isomer – compounds with the same molecular formula

but different structural formulae.

b. Disaccharide – two monosaccharides combined through a

condensation reaction. Sucrose is a disaccharide.

c. Polysaccharide – a complex molecule composed of three or

more monosaccharides. Glycogen is a polysaccharide.

1. Starch and Cellulose are other polysaccharides.

2. Animals such as cows can digest cellulose because of

the presence of microscopic organisms inside.

2. Proteins – organic compounds composed mainly of carbon, hydrogen,

nitrogen, and oxygen. The two types are structural proteins and

enzymes.

a. Amino acids – the monomer building blocks of proteins. There

are 20 amino acids.

b. Dipeptide – a molecule consisting of two amino acids joined by

a single peptide bond. Peptide bonds form through

condensation reactions.

c. Polypeptide – short polymers formed from the linking, in a

defined order, of amino acids.

d. Substrate – a molecule upon which an enzyme acts.

e. Enzyme – organic molecules that act as catalysts. Enzymes

work by adding pressure to bonds (twisting), reducing the

amount of activation energy needed.

f. Proteins change shape with shifts in the environment. For

example, the proteins in an egg reshape when fried.

3. Lipids – large, nonpolar organic molecules that do not dissolve in

water. Lipids have a higher ratio of carbon to hydrogen atoms than

carbohydrates. They store more energy than C – O bonds.

a. Fatty acids – unbranched carbon chains that make up most

lipids. Fatty acids have a COOH group on one end.

b. Reaction to Water

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1. Hydrophilic substances are “water-loving” and tend to

stay close to and form hydrogen bonds with water

molecules.

2. Hydrophobic substances do not interact with water

and are repelled by it. Nonpolar substances, or groups,

are generally hydrophobic.

c. Complex Lipids

1. Triglyceride – composed of three molecules of fatty

acids joined to one molecule of the alcohol glycerol.

i. Saturated Fatty Acids have high melting

points, and are therefore solid at room temp.

ii. Unsaturated Fatty Acids are liquid at room

temp.

2. Phospholipids – have two fatty acids joined by a

molecule of glycerol.

3. Wax – consists of a long fatty-acid chain joined to a

long alcohol chain. They are highly waterproof and can

serve as structural lipids.

4. Steroids – four fused carbon rings with various

functional groups attached. Cholesterol is a steroid.

4. Nucleic acids – very large and important complex organic molecules

that store information within cells.

a. Forms of Nucleic Acids

1. Deoxyribonucleic Acid (DNA) - nucleic acid that

contains the genetic instructions used in the

development and functioning of all known living

organisms.

2. Ribonucleic Acid (RNA) – stores and transfers

information that is essential for the manufacturing of

proteins.

b. Nucleotides – linked monomers composing both DNA and

RNA. DNA and RNA themselves are polymers. They are

composed of three primary parts:

1. A Nitrogen-containing “base”,

2. A 5 Carbon sugar,

3. And a Phosphate group.

IV. CHAPTER 4 – STRUCTURE AND FUNCTION OF THE CELL

A. Section 1 – Introduction To The Cell 1. Discovery Of The Cell

a. History of Observation

1. In 1665, Robert Hooke used a microscope to examine

a slice of cork, noting multiple little porous boxes. He

called them “cells” after the small chambers in which

Monks lived.

2. Anton van Leeuwenhoek was the first person to

observe living cells, in 1673.

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b. Cell Theory – a unified theory stating that: 1. All living things are composed of one or more cells.

2. Cells are the basic units of structure and function in

an organism.

3. Cells only come from the reproduction of existing

cells.

c. Proof of Cell Theory

1. 1838 – Matthias Schleiden (botanist) confirms that all

plants are composed of cells.

2. 1839 – Theodor Schwann (zoologist) finds that all

animals are composed of cells.

3. 1855 – Rudolf Virchow (physician) discovers that cells

come only from other cells.

2. Cell Diversity

a. A typical human body contains over 200 different types of cells.

b. Size – cells are limited in size by the ratio between their outer

surface area and their volume.

c. Shape – the diversity in a cell’s shape reflects the diversity of

different functions. Nerve cells exhibit extensions, while skin

cells are flat.

d. Organelle – a cell component that performs vital functions for

the cell. Cells are split into two kingdoms based on the

structure of its organelles:

1. Eukaryote:

i. Cell Membrane – a thin membrane surrounding

the entire cell. Organelles also are surrounded

by membranes.

ii. Nucleus – contains a majority of the cell’s

genetic information and directs most of the

activities of a cell.

2. Prokaryote:

i. A prokaryote is always unicellular.

ii. Has an outer cell membrane, but no membranes

surrounding organelles.

iii. There is no membrane-bound nucleus in a

prokaryote.

B. Section 2 – Parts Of The Eukaryote Cell 1. Cell Membrane

a. Semipermeable Membrane (selective permeability) – a

membrane that will only certain molecules or ions to pass

through it.

b. Phospholipids compose cell membranes. They are aligned so

that the hydrophilic head is facing outwards while the

hydrophobic tail is facing inwards.

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c. Since cells are both surrounded and filled with water, cell membranes are composed of a lipid bilayer; two parallel

layers of phospholipids facing opposite directions.

1. Steroids – fit between tails of phospholipids.

2. Cholesterol is the standard steroid in animals. It gives

cells strength and rigidity.

d. Membrane Proteins

1. Peripheral proteins (PMP) can be located on either

surface of the cell membrane; bonded weakly. They are

not permanently attached.

2. Integral proteins (IMP) are protein molecules that are

permanently embedded in the bilayer.

i. They act as channels and can extend all the way

through the bilayer.

ii. Those exposed to the outside often have

carbohydrate chains attached, which old

adjoining cells together and can anchor

viruses/hormones to the cell.

e. Fluid Mosaic Model – states that the lipid bilayer behaves more

like a fluid than a solid.

2. Organelles

a. Cytoplasm – a watery substance that keeps organelles in place.

b. Cytosol (intracellular fluid) – an gelatin-like fluid that

surrounds a cell on the outside.

c. Mitochondrion – known as the cell’s “power plant” as they

produce most of the cell’s supply of ATP.

d. Ribosome – makes protein for the cell, and adds to the cell’s

structure. They have no membranes.

e. Endoplasmic reticulum (ER)

1. Rough ER – prepares proteins for export and is studded

with a number of ribosomes.

2. Smooth ER – synthesizes steroids, regulates calcium

levels, and breaks down toxins.

f. Golgi apparatus – processes and packages substances

produced by the cell.

g. Lysosome – digests molecules, old organelles, and foreign

substances.

h. Cytoskeleton – a network of long protein strands located in the

cytosol. They support movement and division.

1. Microfilaments – made of a protein called actin. They

are the shortest strand.

2. Microtubules – extend outward from a central point

near the nucleus to near the cell membrane. They aid in

cell division by forming spindle fibers.

i. Cilia & Flagella – propel cells through the environment, move

materials over the cell’s surface.

17

j. Nucleus – stores hereditary information in DNA; manufactures

ribosomes and RNA.

1. Nuclear Matrix – a protein skeleton controlling the

nucleus’ shape.

2. Nuclear Envelope – a double membrane surrounding

the nucleus.

3. Chromatin – strands composed of a combination of

DNA and proteins.

4. Chromosomes – densely packed structures formed

when chromatin bundles up doing cell division.

5. Nuclear Pores – small holes in the nucleus through

which RNA can pass.

6. Nucleolus – where ribosomes are synthesized and

partially assembled.

k. Cell Wall – supports the structure of and protects a cell.

l. Vacuole – stores enzymes and waste products.

m. Plastid – stores food or pigments.

1. Chloroplasts transfer light energy from the sun to

organic compounds.

2. Thylakoids – a system of flattened, membranous sacks

within chloroplasts.

C. Section 3 – Multicellular Organization

1. Tissues, Organs, and Organ Systems

a. Tissues – groups of cells that carry out a specific function. 1. Muscle tissue causes movement.

2. Epithelial tissue sheets of closely-packed cells that

form surface coverings.

3. Connective tissue holds tissues/organs together.

4. Nervous tissue transmits messages back and forth

between the tissue and brain.

b. Organ – several types of tissues that interact to form a specific

function. The Stomach is an example of an organ.

c. Organ System – a group of organs that work together to

perform a common task. The Digestive system is an example

of an organ system.

d. Plants also have tissues and organs, but their arrangement

differs from that of animals.

1. A dermal tissue system forms the outer layer of a

plant.

2. A ground tissue system makes up the bulk of the roots

and stems.

3. A vascular tissue system transports water throughout

the plant.

4. The four plant organs are: 1) roots,

2) stems,

3) leaf, and

4)

flower.

2. Evolution Of Multicellular Organization

18

a. Step 1: fossils suggest the earliest cells on Earth were simple

prokaryotes similar to some present day bacteria.

b. Step 2: Colonial Organisms – several organisms of the same

species working together for survival.

1. Volvox is a perfect example; a hollow Volvox sphere

contains 500 to 60,000 cells, each of which continues

to exist individually but carry out specific functions

that benefit the whole colony.

c. Step 3: animals, plants, and fungi likely evolved from different

varieties of colonial organisms hundreds of years ago. Cells

became less capable of functioning by themselves as

multicellular colonies became the norm.

V. CHAPTER 5 – HOMEOSTASIS & TRANSPORT

A. Section 1 – Passive Transport – the movement of substances across a cell

membrane without any input of energy. 1. Diffusion – the movement of molecules from an area of higher

concentrations to an area of lower concentrations.

a. Concentration Gradient – the difference in the concentration between molecules across open space.

b. Diffusion is driven by kinetic energy. Molecules are in constant

motion.

c. Molecules tend to move “down” their concentration gradient;

or from areas of higher pressure to lower pressure.

d. The ability of a particle to diffuse depends on: 1. The size of the molecule;

2. The type of the molecule;

3. The chemical nature of the membrane.

e. Ex. There are 50 students crammed in uncomfortably into a

room. The students will try to get out into open space; or from

an area of high concentration to low concentration.

f. Equilibrium – when the concentration of molecules is the same

throughout a space.

2. Osmosis – the process by which water molecules diffuse across a cell

membrane from an area of higher concentration to an area of lower

concentration.

a. The direction of osmosis depends on the relative concentration

of solutes on the two sides of the membrane.

1. Hypotonic solutions occur when the concentration of

molecules outside the cell is lower than the

concentration in the cytosol.

2. Hypertonic solutions occur when the concentration of

molecules outside the cell is higher than the

concentration in the cytosol.

3. Isotonic solutions occur when a cell is surrounded by

an environment that has the same solute concentration

as the cell.

19

b. Contractile Vacuole – organelles that remove water. Cells

usually need a lower concentration of water in the cytosol to

function, and therefore must work against osmosis by

eliminating unneeded water.

c. Turgor Pressure – the pressure that water molecules exert

against the cell wall.

d. Cell Disruption through Osmotic Imbalance

1. Plasmolysis occurs in a hypertonic environment, where

cells shrink away from the cell wall, and turgor

pressure is lost. This is the reason plants wilt if

dehydrated.

2. Cytolysis occurs in a hypotonic environment, where

water diffuses into cells, causing them to swell and

eventually burst.

3. Facilitated Diffusion – a form of passive transport facilitated by carrier

proteins.

a. Carrier Proteins – specific types of integral proteins that assist the movement of molecules across the cell membrane.

b. The cell does not have to supply additional energy to promote

osmosis, as molecules automatically move down their

concentration gradient.

c. Facilitated diffusion is used for molecules that cannot diffuse

rapidly enough and are not fat-soluble.

4. Diffusion Through Ion Channels

a. Ion Channels – regulate the flow of ion across cell membranes.

Ions cannot travel through the lipid bilayer without assistance.

They are ion-specific.

b. Ions requiring ion channels include Na+, K

+, Ca

+, Cl

+

c. While some ion channels are always open, other have “gates”

which can open and close to allow or prohibit ion movement.

d. These “gates respond to three kinds of stimuli:

1. Stretching of the cell membrane,

2. Electrical signals (i.e. nerve impulses),

3. Chemicals in the cytosol or external environment.

B. Section 2 – Active Transport – the process of moving across a biological

membrane against a concentration gradient. Active transport requires

added energy from the cell to occur. 1. Cell Membrane Pumps

a. Sodium-potassium Pump – a carrier protein in animal cells that

transports Na+ and K

+ up their concentration gradients.

b. To function normally, many cells must have a higher

concentration of Na+ outside and a higher concentration of K

+

within.

c. Operation of the Sodium-potassium Pump:

20

1. First, three Na+ ions bind to the carrier protein on the

cytosol side of the membrane.

2. At the same time, the carrier protein splits a phosphate

group from a molecule of ATP and binds with it.

3. Next, the energy from the ATP molecule changes the

shape of the carrier protein; releasing the three Na+.

4. Fourthly, two K+ ions from the outside environment

attach to the carrier protein.

5. The phosphate group is released, changing the shape of

the protein again.

6. Lastly, the two K+ ions are released into the cell and the

cycle is ready to repeat again.

7. At maximum speed, Sodium-potassium Pumps can

transport about 450 Na+ and 300 K

+.

2. Endocytosis And Exocytosis

a. Endocytosis – the process by which cells ingest external fluids, macromolecules, and large particles, including other cells.

b. External materials are enclosed by a portion of the cell, which

folds into itself, forming a pouch known a vacuole.

c. There are two types of endocytosis. 1. Pinocytosis is a process involving the transport of

solutes or fluids.

2. Phagocytosis is a process involving the movement of

large particles or whole cells.

i. Phagocytes are cells which allow lysosomes to

fuse with vesicles that contain bacteria and

viruses.

d. Exocytosis – essentially the reverse of endocytosis; where cells eject waste or unwanted materials.

e. During exocytosis, vesicles in the cytoplasm fuse with the cell

membrane, releasing their contents into the environment.

VI. CHAPTER 6 – PHOTOSYNTHESIS

A. Section 1 – Capturing The Energy In Light 1. Photosynthesis – the process by which plants capture part of the

energy in light and store it within organic compounds.

2. Energy For Life Processes

a. Heterotrophs are not capable of manufacturing their own food.

They obtain their food by eating Autotrophs or other

Heterotrophs.

b. Autotrophs are capable of manufacturing their own food.

c. Biochemical Pathway – a complex series of chemical reactions

occurring within a cell; in which the product of one reaction is

consumed in the next reaction.

3. Light Absorption In Chloroplasts

a. Light Reactions – the initial phases of photosynthesis, beginning with the absorption of light in chloroplasts.

21

b. Composition of a Chloroplast:

1. Grana – a stack of thylakoids disks.

2. Stroma – a solution that fills the interior of the

chloroplast and surrounds the thylakoids.

c. Visible Spectrum – the array of colors resulting from the

splitting of a beam of white light.

d. Wavelength – the distance between crests in a wave.

e. Pigment – a compound that absorbs light. Certain pigments

absorb more light than others.

f. Chlorophyll – the most important of the many varieties of

pigments in the membranes of thylakoids. The two most

common forms are chlorophyll a and chlorophyll b.

1. Chlorophylls a and b are slightly different, causing

them to absorb different amounts of light.

2. Chlorophyll a absorbs less blue light but more red light

than b. Green light is reflected, making the leaf look

green.

3. Only chlorophyll a is directly involved in light

reactions.

g. Accessory Pigment – light absorbing compounds that work in

conjunction with chlorophyll a. They enable plants to capture

more of the energy in light. They include:

1. Chlorophyll b;

2. Carotenoids are other pigments present in plants that

largely absorb blue light. They appear orange, brown,

and yellow.

4. Electron Transport

a. Photosystem – a cluster of pigment molecules. Chlorophylls

and cartenoids are grouped into clusters of a few hundred

molecules in the thylakoids membrane. There are two –

Photosystem I and II.

b. Step 1: Light energy forces electrons to enter a higher energy

level within the two chlorophyll a molecules of Photosystem II.

c. Step 2: The excited electrons leave the molecules. Because

they have lost electrons, the chlorophyll a molecules have

undergone an oxidation reaction.

1. Primary Electron Acceptor – substance that accepts the

two lost electrons.

d. Step 3: The primary electron acceptor then donates the

electrons to the first of a series of molecules located in the

thylakoids membrane.

1. Electron Transport Chain – a series of molecules that

transfers electrons from one molecule to the next.

e. Step 4: At the same time light is absorbed by photosystem II,

light is also absorbed in photosystem I. The electrons from P-I

that have been lost are replaced by the electrons from P-II.

22

f. Step 5: The primary electron acceptor of P-I donates electrons

to a different chain. Here, they combine with a proton and

NADP+.

1. NADP+ - an organic molecule that accepts electrons

during redox reactions.

g. NADP+ is reduced to NADPH.

h. Step 6: Electrons supplied from the splitting (or photolysis) of

water restore the oxidized chlorophyll a molecules.

5. Chemiosmosis – the synthesis of ATP through the diffusion of protons

across a membrane.

a. The concentration gradient of protons represents potential energy, harnessed by a protein called ATP synthase.

b. ATP synthase makes ATP by adding a phosphate group to

adenosine diphosphate, or ADP.

c. The ATP synthase acts as both an enzyme and carrier protein.

d. Energy is being converted from potential to chemical energy. A

higher concentration of protons inside the thylakoid is

responsible for high potential energy.

B. Section 2 – The Calvin Cycle 1. Calvin Cycle – a series of biochemical reactions that takes place in the

stroma of chloroplasts. It produces organic molecules using the energy

stored in ATP and NADPH.

2. Carbon Fixation By The Calvin Cycle

a. Carbon Fixation – the incorporation of CO2 into organic

compounds.

b. In the Calvin Cycle, carbon atoms from CO2 are bonded into

organic compounds.

c. Step 1 (Carbon Fixation): CO2 diffuses into the stroma from

the cytosol. An enzyme combines a CO2 molecule with a 5

carbon carbohydrate called RuBP (Ribulose Biphosphate)

which decays into a pair of 3 carbon PGA molecules.

d. Step 2 (Reduction): Each PGA molecule receives a phosphate

group from a molecule of ATP. The resulting compound then

receives a proton from NADPH and releases a phosphate group,

producing PGAL. ADP, NADP+, and a phosphate are also

produced which can be used again in light reactions.

e. Step 3 (Regeneration of Ribulose): Most of the PGAL is

converted back to into RuBP in a complex series of reactions;

requiring a phosphate group from another molecule of ATP,

which is changed to ADP. This allows the Calvin cycle to

continue operating. However, some PGAL molecules are not

converted into RuBP and leave the cycle, where they can be

used to make other organic compounds.

f. Molecules used for each turn (it takes three turns to produce a

molecule of PGAL):

1. In Step 1, one CO2 molecule is needed.

23

2. In Step 2, two ATP and two NADPH molecules are

used, one for each PGAL molecule.

3. In Step 3, one ATP molecule is used.

g. Products of the Calvin cycle, including PGA, can be built up into a variety of organic compounds, including carbohydrates,

lipids, and amino acids.

h. The simplest overall equation for both light dependant and

independent cycles can be written as

CO2 + H20 + light energy ���� (sugar) + O2

i. Glucose itself is not produced by the pathways of

photosynthesis. Instead, it is there to emphasize the relationship

between photosynthesis and cellular respiration.

3. Alternative Pathways

a. C3 Plants – a plant species that fixes carbon exclusively

through the Calvin cycle. It is named so because of the PGA 3

carbon compound that is initially formed.

b. Certain other plant species fix carbon through alternative pathways before releasing it to the Calvin cycle. These plants

generally exist in extreme, arid climates.

c. Stomata – small pores which are usually located on the

undersurface of leaves. Water loss occurs through these.

d. List of Alternative Pathways: 1. C4 Pathway – enables certain plants to fix CO2 into

four carbon compounds. In C4 plants, stomata are

partially closed during the hottest part of the day;

however, they contain an enzyme which can fix CO2 to

into four carbon chains. Steps are separated spatially.

i. Examples include sugar cane, corn, and

crabgrass.

2. CAM Pathway – a variation in which stomata open at

night and close during day. At night, they take in CO2

and fix it into organic compounds. During the day, CO2

is released from these compounds and put through the

Calvin cycle. They grow more slowly but lose less

water than C3 and C4 plants. Steps are separated by

time of day. i. Examples include pineapple and cacti.

4. Rate of Photosynthesis

a. The rate at which a plant performs photosynthesis is affected

by the surrounding environment.

1. An increase in light energy causes photosynthesis to

accelerate and level off at a maximum rate, as plants

can only replenish lost electrons so fast.

2. An increase in CO2 levels would also stimulate the rate

of photosynthesis.

24

3. An increase in temperature would initially cause

hasten chemical reactions involved in photosynthesis.

A very high temperature would cause many of the

enzymes and proteins to become unstable.

VII. CHAPTER 7 – CELLULAR RESPIRATION

A. Section 1 – Glycolysis And Fermentation 1. Harvesting Chemical Energy

a. Cellular Respiration – a series of redox reactions in which cells make ATP by breaking down organic compounds.

b. Glycolysis – a biochemical pathway that begins cellular

respiration and yields a small amount of ATP. The other

products of glycolysis can follow one of two pathways:

1. Anaerobic Pathway – yields additional ATP from

oxygen lacking products.

2. If oxygen is present, products enter aerobic

respiration. Aerobic respiration produces a much

larger amount of ATP than glycolysis alone.

2. Glycolysis

a. Glycolysis is a pathway in which one six-carbon molecule of

glucose is oxidized to produce two three-carbon molecules of

pyruvic acid.

b. Reactions of glycolysis take place in the cytosol and are catalyzed by enzymes.

c. Step 1 (Energy Investment): Two phosphate groups are

attached to glucose, forming a new six-carbon compound. The

phosphate groups are supplied by two molecules of ATP,

which are converted into molecules of ADP in the process.

d. Step 2 (Cleavage of Sugar): The six-carbon compound

formed in Step 1 is split into two three-carbon molecules of

PGAL.

e. Step 3: The two PGAL molecules are oxidized, and each

receives a free-floating phosphate group. This produces two

molecules of a new three-carbon compound. Two molecules of

NAD+ are reduced to NADH after accepting the electrons from

the oxidation reaction.

f. Step 4 (Energy Generation): The phosphate groups added in

Steps 1 and 3 are removed from the three-carbon compounds.

This produces two molecules of pyruvic acid. Each of the four

phosphate groups combine with ADP to make four molecules

of ATP.

g. Because 2 ATP molecules are required to transport NADH into

the mitochondria, the net product of glycolysis is 2 ATP.

3. Fermentation – the combination of glycolysis with additional pathways

to convert pyruvic acid into other compounds in the lack of oxygen.

a. These additional pathways do not produce ATP. Instead, they regenerate NAD

+ which can be used to power glycolysis.

25

b. Lactic Acid Fermentation – the process by which an enzyme

converts pyruvic acid into another three-carbon compound,

called lactic acid. NADH is oxidized back to NAD+. It occurs

in muscle cells.

1. When oxygen is once again available, the liver can

convert lactic acid back into pyruvate.

c. Alcoholic Fermentation – the process by which cells convert

pyruvic acid into ethyl alcohol. Yeast uses this pathway; and

hence they form the basis for the wine and beer industry.

1. Organisms can only use alcoholic fermentation at

concentration of alcohol at or below 14%. Otherwise,

the organism could die.

4. Energy Yield

a. Kilocalorie (kcal) – a value used to obtain the efficiency of anaerobic pathways.

b. The complete oxidation of a standard amount of glucose

released 686 kcal.

c. The efficiency of glycolysis can be calculated using this formula:

Energy required making ATP

Energy released by oxidation of glucose

B. Section 2 – Aerobic Respiration 1. Overview Of Aerobic Respiration

a. Mitochondrial Matrix – a space inside the inner membrane of a

mitochondrion. The pyruvic acid that is produced in glycolysis

diffuses across the mitochondrion’s double membrane into the

matrix.

b. Acetyl CoA (acetyl coenzyme A) – the product of a reaction

involving pyruvic acid and coenzyme A.

c. One carbon atom is lost during the reaction, which combines

with two oxygen molecules to form CO2. The reaction also

reduces a molecule of NAD+ to NADH.

2. The Krebs Cycle – a biochemical pathway that breaks down acetyl

CoA, producing hydrogen atoms and ATP.

a. The reactions that comprise the cycle were discovered in 1937

by Hans Adolf Krebs.

b. Step 1: A two-carbon molecule of acetyl CoA combines with a

four-carbon compound, oxaloacetic acid, to produce a six

carbon compound, citric acid.

1. This reaction regenerates coenzyme A, which moves

back out to carry and change more pyruvic acid.

c. Step 2: Citric acid releases a CO2 molecule and a hydrogen

atom to form a five-carbon compound. By losing a hydrogen

atom with its electron, citric acid is oxidized. The hydrogen is

transferred to NAD+, reducing it to NADH.

26

d. Step 3: The five-carbon compound formed in Step 2 also

releases a CO2 molecule and a hydrogen atom, forming a four-

carbon compound. Again, NAD+ is reduces to NADH. A

molecule of ATP is also synthesized from ADP.

e. Step 4: The four-carbon compound formed in Step 3 releases a

hydrogen atom to form another four-carbon compound. This

time, the hydrogen atom is used to reduce FAD to FADH2.

1. Like NAD+, FAD accepts electrons during redox

reactions.

f. Step 5: The four-carbon compound formed in Step 4 releases a

hydrogen atom to regenerate oxaloacetic acid, which keeps the

Krebs cycle operating. They hydrogen atom reduces NAD+ to

NADH.

g. Molecules used for each turn (one molecule of glucose causes

two turns of the Krebs cycle, as one glucose molecule can form

two molecules of acetyl CoA):

1. 6 NADH

2. 2 FADH2

3. 4 CO2;

4. 2 ATP. Hence, both the Krebs cycle and Glycolysis

produce two ATP molecules each.

3. Electron Transport Chain – constitutes the second stage of aerobic

respiration.

a. The electrons in the hydrogen atoms from NADH and FADH2

are in a high energy level. These electrons pass through a series

of molecules, and lose a portion of their energy in the process.

b. Energy shed off of electrons is used to pump protons from the

mitochondrial matrix to the other side of the inner membrane.

The concentration of protons becomes greater on the outside

the matrix.

c. The concentration gradient drives chemiosmosis via the ATP

synthase, located in the inner membrane. Energy harnessed

from protons moving back into the matrix synthesizes ATP

from ADP.

d. The last molecule in the chain transfers electrons to oxygen

atoms, which combine with four protons supplied by NADH

and FADH2 to form two molecule of water.

O2 + 4e- + 4H

+ � 2H2O

4. Energy Yield

a. In total, the sum of all chemical reactions in aerobic respiration

generate the following amounts of NADH, FADH2, and ATP:

1. 10 NADH – each molecule that supplies to the electron

transport chain can make up to 3 ATP.

2. 2 FADH2 – each FADH2 molecule can generate 2 ATP.

3. The Krebs cycle and Glycolysis generate a product 4

ATP.

27

4. 38 ATP molecules are produced. However, the actual

number of ATP molecules made can vary from cell to

cell.

5. Summarizing Cellular Respiration

a. The oxidation of glucose in aerobic respiration can be summarized using the following equation:

C6H12O6 + 6O2 � 6CO2 + 6H2O + energy

b. The equation above is the general opposite of photosynthesis. However, aerobic respiration is not the exact reverse of

photosynthesis.

c. Cellular respiration provides the ATP that all cells need to support the activities of life.

VIII. CHAPTER 8 – CELL REPRODUCTION

A. Section 1 – Chromosomes 1. Chromosome Structure

a. As a cell prepares to divide, its DNA coils around proteins and twists into rod-shaped chromosomes.

b. Each chromosome is a single DNA molecule associated with

proteins.

c. Histones – proteins within the chromosomes around which

DNA wraps tightly. They maintain the shape of chromosomes

and aid in the tight packing of DNA.

d. Nonhistone – involved in controlling the activity of specific regions of the DNA.

e. Chromatid – one of the two halves of chromosomes. The two

halves are identical to each other.

1. Chromatids form as the DNA makes a copy of itself

before beginning cell division.

2. When the cell divides, each of the two new cells will

receive one chromatid from each chromosome.

f. Centromere – holds the two chromatids together until they

separate during cell division.

g. Between periods of cell division, DNA is uncoiled so that information can be more easily read. The less tightly packed

DNA cluster is called chromatin.

h. DNA is simpler in prokaryotes than in eukaryotes. It consists

of only one chromosome which is attracted to the inside of the

cell membrane. Chromosomes consist of a circular DNA

molecule and additional proteins.

2. Chromosome Numbers

a. Each species contains different numbers of chromosomes.

Humans contain 23 pairs, giving a total of 46. Some species,

however, have the same amount of chromosomes (i.e. both

plums and chimpanzees have 48).

b. Human and animal chromosomes are categorized as either sex

chromosomes or autosomes.

28

1. Sex Chromosomes – chromosomes that determine the

sex of an organism. In humans, sex chromosomes are

either X or Y.

i. XX, or two “X” chromosomes, denotes a

normal female human.

ii. XY, or one “X” and one “Y” chromosome,

denotes a normal male human.

2. Autosomes – the remaining 22 pairs of chromosomes.

c. Every cell produced by sexual reproduction has two copies of each autosome. The organism receives one copy of each

autosome from each parent.

d. Homologous Chromosomes (homologues) – the two copies of

each autosome.

e. Homologues are the same size and shape and carry genes for

the same trait.

f. Karyotype – a photomicrograph of the chromosomes in a

dividing cell found in a normal human.

g. Diploid – cells having two sets of chromosomes.

1. Diploid cells have both chromosomes for each

homologous pair. They also have two reproductive

chromosomes.

2. All normal human cells, except reproductive cells, are

diploid cells.

3. Diploid is commonly abbreviated as 2n.

h. Haploid – contain only one set of chromosomes.

1. Human sperm and egg cells are haploid. They have half

the number of chromosomes present in diploid cells.

2. Human haploid cells only have one chromosome of

each homologous pair and one sex chromosome.

3. Haploid is commonly abbreviated as 1n.

4. When a sperm and egg cell combine, the result will be

a diploid cell.

5. If the reproductive cells were diploid, the new cell

would have too many chromosomes and would not be

able to function.

B. Section 2 – Cell Division 1. Cell Division In Prokaryotes

a. Binary Fission – the division of a prokaryote cell into two different offspring cells.

b. Binary Fission consists of three generalized steps. 1. Step 1 (DNA Replication): The chromosome, which is

attached to the inside of the cell membrane, copies

itself, resulting in two identical chromosomes attached

to the inside of the prokaryote’s inner membrane.

2. Step 2 (Chromosome Segregation): The cell

continues to grow until it is roughly two times the size

29

of the original. A cell wall forms between both

chromosomes.

3. Step 3 (Cytokinesis): The cell splits into two cells.

Each of the cells contains one of the chromosomes that

resulted from the copying of the original.

2. Cell Division In Eukaryotes

a. In eukaryotic cell division, both the cytoplasm and the nucleus

divide.

b. Mitosis – results in new cells with genetic material that is

identical to that of the original cell. Mitosis occurs in the

reproduction of unicellular organisms as well as the addition of

cells to a tissue or organ.

c. Cell Cycle – the repeating set of events that make up a cell’s

life. It consists of:

d. Interphase – the time between cell division, divided into three

phases:

1. G1 Phase is the first stage of interphase. Offspring cells

grow to mature size.

2. S Phase (synthesis phase) is the second stage; in which

chromosomes are replicated.

3. G2 Phase is the third stage; during which cells prepare

for cell division. It is the last stage of interphase before

mitosis begins.

4. G0 Phase is an “exit” phase in which a cell can leave

the cell cycle.

i. These cells do not copy their DNA and do not

undergo cell division.

ii. Cells composing the central nervous system

stop dividing at maturity and never divide again.

e. Prophase – begins with the tight coiling and shortening of

DNA into rod-shaped chromosomes.

1. The two chromatids stay connected by the centriole.

2. At this time, the nucleolus and nuclear membrane break

down and disappear.

3. Centrosomes – two pairs of dark spots that appear next

to the deteriorating nucleus. Each centrosome contains

a pair of small bodies called centrioles.

4. The centrosomes move toward opposite poles of the

cell, dragging spindle fibers with them.

i. Kinetochore Fibers – attach to a protein in the

centromere of each chromosome.

ii. Polar Fibers – extend from centrosome to

centrosome.

iii. Mitotic Spindle – the array of spindle fibers

which serves to equally divide the two

chromatids between the two offspring cells.

30

f. Metaphase – the second phase in which chromosomes are

easiest to identify. During metaphase, kinetochore fibers move

chromosomes to the center of the cell.

1. Karyotypes are taken from cells in metaphase.

g. Anaphase – the chromatids of each chromosome separate and

slowly move, centromere first, toward opposite ends of the cell.

1. When chromatids separate, they are considered to be

individual chromosomes.

h. Telophase – the fourth phase in which the chromosomes reach

opposite ends of the cell and the spindle fibers disassemble.

1. A nuclear envelope and nucleolus form around each set

of chromosomes.

2. The chromosomes return to a less tightly coiled

chromatin state.

i. Cytokinesis – the process by which the cytoplasm of a cell

divides.

1. In animal cells, the cell membrane pinches inward and

separates midway between the cell’s two poles.

i. Cleavage Furrow – the area of the cell that

pinches in and eventually separates the two cells.

2. In plant cells, vesicles formed by the Golgi apparatus

fuse at the midline of the dividing cell.

i. Cell Plate – a membrane-bound cell wall which

will separate the two cells.

3. Each offspring cell receives approximately 1/2 of the

original cell’s cytoplasm and organelles.

C. Section 3 – Meiosis 1. Meiosis – reduces the chromosome number by half in new cells. The

new cells join later in the organism’s life to produce cells with a

complete set of chromosome.

a. Gametes – haploid reproductive cells produced by meiosis in

humans.

b. Human gametes are sperm and egg cells, each of which

contains 23 (1n) chromosomes.

c. The fusion of a sperm and an egg results in a zygote which

contains 46 (2n) chromosomes.

2. Stages of Meiosis

a. Because cells undergoing meiosis divide twice, diploid cells

that divide meiotically result in four haploid cells.

b. The stages of the first cell division are called meiosis I, and

that of the second meiosis II.

c. Meiosis I 1. Prophase I – DNA coils tightly into chromosomes.

i. As in the prophase of mitosis, spindle fibers

appear and the nuclear membrane dissolves.

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ii. Each chromosome lines up next to its

homologue.

iii. Synapsis – the pairing of homologous

chromosomes.

iv. Homologues are aligned lengthwise so that

genes are adjacent to their correspondents.

v. Tetrad – each pair of homologues.

vi. Crossing-Over – when chromatids within a

homologous pair break off and attach to

adjacent chromosomes.

vii. Crossing-over results in genetic recombination.

2. Metaphase I – tetrads line up randomly alone the

midline of the dividing cell. Fibers from each pole

attach to one of the two homologous chromosomes.

3. Anaphase I – each homologous chromosome moves to

an opposite side of the dividing cell.

i. Independent Assortment – the random

separation of the homologous chromosomes.

ii. Independent assortment results in genetic

variation.

4. Telophase I – chromosomes reach opposite ends of the

cell, and cytokinesis begins. The new cells contain a

haploid number of chromosomes.

5. Each new cell actually contains two copies of a

chromosome because its parent cell copied its DNA

before meiosis I.

d. Meiosis II 1. In some species, meiosis II begins after the nucleus

reforms. In some, it occurs directly after meiosis I.

2. Prophase II – fibers form and begin to move the

chromosomes towards the middle of the cell.

3. Metaphase II – the chromosomes move to the midline

of the dividing cell. They face opposite poles of the

dividing cell.

4. Anaphase II – the chromatids separate and move

towards opposite poles of the dividing cells.

5. Telophase II – a nuclear membrane forms around the

chromosomes in each of the four new cells. Cytokinesis

occurs.

3. In humans, meiosis occurs in the testes and ovaries.

4. Spermatids – haploid cells resulting from meiosis II during

spermatogenesis. Each spermatid matures into a sperm cell.

5. Spermatogenesis – the production of sperm cells.

6. Oogenesis – the production of mature egg cells, or ova.

a. During cytokinesis I and II, the cytoplasm is divided unequally.

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b. One cell, the mature egg cell, receives most of the cytoplasm.

As a result, meiosis produces one egg.

1. Polar bodies – the other three products, which

degenerate.

c. There are two forms of reproduction of life on earth:

1. Asexual Reproduction – the production of offspring

from one parent.

i. Unicellular organisms are created by binary

fission or mitosis.

ii. Multicellular organisms are created by budding

off of the original body.

2. Sexual Reproduction – the production of offspring

through the union of a sperm and egg cell.

i. Except in the case of identical twins, offspring

contain unique combinations of their parent’s

genes.

3. It enables species to rapidly adapt to changes in their

environment.

IX. CHAPTER 9 – FUNDAMENTALS OF GENETICS

A. Section 1 – Mendel’s Legacy 1. Genetics – the field of biology devoted to understanding how

characteristics are transmitted from parent to offspring.

2. Gregor Mendel

a. In 1842, Gregor Johann Mendel moved into a monastery in

Brunn, Austria.

b. His task of tending the garden gave him time to think and

observe the growth of many plants. He is remembered for his

experiments involving Pisum sativum, or garden peas.

c. Heredity – the transmission of characteristics from parent to

offspring.

d. Mendel observed seven characteristics of pea plants. Each

characteristic occurred in two contrasting traits:

1. Plant height (long or short stems),

2. Flower position along stem (axial or terminal),

3. Pod color (green or yellow),

4. Pod appearance (inflated or constricted),

5. Seed texture (smooth or wrinkled),

6. Seed color (yellow or green),

7. Flower color (purple or white).

e. Mendel was able to document the traits of each generation’s

offspring by controlling how the pea plants were pollinated.

f. Pollination – occurs when pollen grains produced in the

anthers (male) of a flower are transferred to the stigma

(female).

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g. Self-Pollination – occurs when pollen is transferred from the

anthers of a flower to the stigma of either the same flower or a

flower on the same plant.

h. Cross-Pollination – involves flowers of two separate plants.

i. Pea plants normally reproduce through self-pollination.

j. Mendel encouraged cross-pollination by removing the anthers

from a flower and transferring them to flowers on another plant.

3. Mendel’s Experiments

a. Mendel began by growing plants that were pure for each trait.

b. Pure – plants that always produce offspring with their same

traits.

c. Strain – denotes plants that are pure for a specific trait. Mendel

produced strains by allowing his plants to self-pollinate for

several generations.

d. Mendel eventually obtained 14 strains, one for each of the 14

he observed.

e. P1 Generation – a parental generation; Mendel’s name for each

of his 14 plants.

f. Mendel cross-pollinated these strains by transferring the pollen

of one plant to the stigma of plants possessing the contrasting

trait.

g. F1 Generation – the first filial generation, or the offspring of

the P1 generation.

h. F2 Generation – the second filial generation or the offspring of

the first filial generation.

4. Mendel’s Results And Conclusions

a. Mendel’s observations led him to hypothesize that something

within the pea plants controlled the characteristics he observed.

He called these factors.

b. Because the characteristics he studied had two alternative forms, he reasoned that there must be a pair of factors

controlling a single trait.

c. Dominant – a factor that masks, or dominates, the other factor

for a specific characteristic.

d. Recessive – the factor that is being masked.

e. Law of Segregation – states that a pair of factors is

segregated, or separated, during the formation of gametes.

f. Law of Independent Assortment – states that factors for

different characteristics are distributed to gametes

independently.

5. Chromosomes And Genes

a. Molecular Genetics – the study of the structure and formation

of chromosomes and genes.

b. Pleitropy – the ability of a gene to affect more than one trait.

c. Polygenic – one trait being controlled by more than one gene.

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d. The characteristics of an organism can be altered by

environment, regardless of whatever genes they may carry. For

example, the hair of an organism may appear lighter in sun-rich

environments than in darker ones.

e. Allele – each of the several alternative forms of a gene. They

are the same as Mendel’s factors.

f. Letters are used to represent alleles.

1. Capital letters refer to dominant alleles.

2. Lower case letters refer to recessive alleles.

g. Mendel’s law is supported by the fact that chromosomes

segregate independently to gametes during meiosis.

B. Section 2 – Genetic Crosses 1. Genotype And Phenotype

a. Genotype – the genetic makeup of an organism.

b. The genotype consists of the alleles that the organism inherits

from its parents.

c. Phenotype – the appearance of an organism as a result of its

genotype. Human phenotypes can appear to be altered by

behavior.

d. The two alleles of a pair can be alike or different. 1. Homozygous – when both alleles of a pair are alike.

2. Heterozygous – when the two alleles of a pair are

different.

2. Probability – the likelihood that a specific event will occur. A

probability may be expressed as a decimal, percentage, or fraction.

a. Probability is expressed by the following equation: Number of times an event is expected to happen

Number of opportunities for an event to happen

b. Probability tells us that there are three chances in four that an offspring of two heterozygous individuals will have the

dominant trait and a one in four chance it will have the

recessive trait.

3. Predicting Results of Monohybrid Crosses

a. Monohybrid Cross – a cross between individuals that involves

one pair of contrasting traits.

b. A cross between a pea plant that is pure for purple flowers and one for white flowers is an example of a monohybrid.

c. Punnett Square – a diagram which biologists use to aid in

determining the probability of an offspring inheriting a trait.

Examples include:

1. Homozygous x Homozygous – there is a 100%

probability the offspring will have the same genotype

(Ex. Pp).

2. Homozygous x Heterozygous – two types of offspring

can result: PP and Pp. The probability of each is 50%.

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3. Heterozygous x Heterozygous – three types of

offspring can result: PP, Pp, and pp. 50% will carry

genotype Pp; 25% PP, and 25% pp.

i. Genotypic Ratio – the ratio of genotypes that

appear in the offspring.

ii. Phenotypic Ratio – the ratio of the offspring’s

phenotypes.

4. Testcross – a test to determine the genotype of an

organism, in which the individual in question is crossed

with a homozygous recessive individual.

5. Incomplete Dominance – occurs when two or more

alleles influences the phenotype, resulting in a

phenotype intermediate between the dominant and

recessive traits.

i. Ex. if two four o’clock flowers, one red and one

white, are crossed; the F1 generation will have

pink flowers.

6. Codominance – occurs when neither allele is dominant

or recessive. Alleles do not blend.

4. Predicting Results Of Dihybrid Crosses

a. The four blood types of a human are A, B, AB, and O. Type O

is the recessive blood type, and all other blood types except AB

have a copy of the O gene. Therefore, O is known as the

universal donor.

b. Dihybrid Cross - a cross between individuals that involves two pairs of contrasting traits. Examples include:

1. Homozygous x Homozygous – independently assorted

alleles from each parent are listed along the left and top

of the square. The genotypes of all offspring will be

heterozygous.

2. Heterozygous x Heterozygous – is likely to result in

nine different genotypes and four different phenotypes.

X. CHAPTER 10 – NUCLEIC ACIDS & PROTEIN SYNTHESIS

A. Section 1 – DNA (Deoxyribonucleic acid) 1. Structure Of DNA

a. A DNA nucleotide has three parts: 1. Deoxyribose – a five-carbon sugar.

2. Phosphate group – contains one phosphorous atom

surrounded by oxygen atoms.

3. Nitrogen-containing base – a molecule containing a

nitrogen atom.

b. The four nitrogen-containing bases in DNA molecules are

Adenine (A), Guanine (G), Thymine (T), Cytosine (C).

c. The bases are divided into two groups, determined by the

number of rings they contain.

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1. Purines – bases that have two rings (Adenine and

Guanine).

2. Pyrimidines – bases that have one ring (Thymine and

Cytosine).

d. Double Helix – the structure of DNA. Two nucleotide chains wrap around each other to form a double spiral.

e. Complimentary Base Pairs – the pairing of base pairs in a

spiral of DNA. They are:

1. Adenine ↔ Thymine (2 Hydrogen Bonds)

2. Guanine ↔ Cytosine (3 Hydrogen Bonds)

f. Base-Pairing Rules – describe the pairing behaviors of bases.

They state that cytosine bonds with guanine and thymine

bonds with adenine.

2. Replication Of DNA

a. Replication – the process of copying DNA in a cell. During replication, the two nucleotides separate by unwinding.

b. Step 1: the two nucleotide chains separate at the replication

fork. The chains are separated by enzymes called helicases. As

the helicase enzymes move along the molecule, they break

down the hydrogen bonds connecting complements. The chains

then separate.

c. Step 2: enzymes called DNA polymerase (DNA polymerase

III holoenzyme) bind to the separated chains. As polymerases

move along the chains, new chains of DNA are assembled

using nucleotides in the surrounding medium.

d. Nucleotides are joined by covalent bonds between sugars and phosphate groups, and to the original chain by hydrogen bonds.

e. Step 3: at the end of replication, there are two identical copies

of the original molecule. Each DNA molecule is made of one

new chain and one old from the original.

f. Mutation – a change in the nucleotide sequence which may

have a serious effect in new cells. Causes include UV radiation.

B. Section 2 – RNA (Ribonucleic Acid) 1. Structure Of RNA

a. Although both RNA and DNA are made up of nucleotides,

RNA has a differing structure from DNA:

1. Ribose – the sugar molecule of every RNA molecule.

In contrast, DNA molecules contain deoxyribose.

2. Uracil (U) is a nitrogen-containing base that takes the

place of thymine within RNA.

3. RNA is single stranded and smaller than DNA.

b. RNA exists in three forms; each with a different function:

1. Messenger RNA (mRNA) consists of RNA molecules

in the form of a single uncoiled chain. It carries

information from the nucleus to the cytosol.

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2. Transfer RNA (tRNA) a single, hairpin shaped chain

of about 80 RNA nucleotides that bind to specific

amino acids.

3. Ribosomal RNA (rRNA) is the most common RNA. It

consists of RNA nucleotides in a globular form. rRNA

and proteins compose ribosomes.

2. Transcription – the process by which genetic information is copied

from DNA to RNA.

a. One function of RNA is to transport genetic information from

the nucleus to the cytosol.

b. Step 1: RNA copies are synthesized by the RNA polymerase.

RNA polymerase bonds to specific regions of DNA called

promoters; marking the beginning of the DNA chain. The DNA

strands in that region separate; only one of them, called the

template, is used.

c. Step 2: RNA polymerase adds complementary RNA

nucleotides to the new RNA molecule. Except for the addition

of uracil, the base-pairing rules are the same as in DNA.

d. Step 3: transcription continues until the polymerase reaches a

termination signal, a sequence of nucleotides marking the end

of a gene.

e. All three forms of RNA are transcribed in this process.

C. Section 3 – Protein Synthesis 1. Protein Synthesis – the production of protein.

2. Protein Structure And Composition

a. Proteins are polymers, made of one or more polypeptides, each

of which consists of a sequence of amino acids linked by a

peptide bond.

b. The function of a protein depends on its three-dimensional

structure and how that will allow it to bind.

3. The Genetic Code

a. During protein synthesis, the sequence of nucleotides in an mRNA transcript is translated into amino acids.

b. Genetic Code – an association between a nucleotide sequence and an amino acid sequence which is used to translate mRNA

transcripts into proteins.

c. Codon – each combination of three mRNA nucleotides. Each

codes for a specific amino acid.

d. The near-universality of the genetic code supports the idea that all organisms are evolutionarily related.

e. A few codons do not code for amino acids. Instead, they signal

for a translation to start and stop:

1. Start codons (AUG), which also codes for methionine,

signals a ribosome to start translating an mRNA

transcript.

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2. Stop codons (UAA, UAG, UGA) cause the ribosome

to strop translating a transcript.

4. Translation

a. Translation – the process of assembling proteins form

information stored in mRNA.

b. Free amino acids are transported to the ribosomes by tRNA

molecules.

c. Anticodon – a unit made up of three nucleotides that

correspond to the bases of an mRNA codon.

d. Ribosomes are composed of rRNA and proteins. They are

usually both free in the cytosol and attached to an endoplasmic

reticulum.

1. Free Ribosomes produce proteins that will be used

within the cell.

2. Attached Ribosomes produce proteins that will be

exported for use outside of the cell.

e. Ribosomes have three binding sites: one that holds an mRNA

transcript so that its codons are accessible to rRNA, and two

which hold tRNA which pair with mRNA.

f. Protein Assembly:

1. Step 1: a polypeptide attaches to the start codon on an

mRNA transcript. The start codon pairs with its

corresponding anticodon on a tRNA.

2. Step 2: each mRNA codon is sequentially paired with

its tRNA anticodon. The pairing causes the specified

amino acid to form a peptide bond with a previously

translated amino acid.

3. Step 3: the ribosome eventually reaches a stop codon,

ending translation. The mRNA is released and the

polypeptide chain is complete.

XI. CHAPTER 11 – GENE EXPRESSION

A. Section 1 – Control Of Gene Expression 1. Role Of Gene Expression

a. Gene Expression – the activation of a gene that results in the formation of a protein. A gene is said to be expressed when

transcription occurred.

b. In order to conserve energy, certain genes are expressed only when the proteins they code for are needed.

c. Genome (portmanteau of gene and chromosome) – the

complete genetic material contained within an organism.

d. Gene expression occurs in two steps, transcription and translation.

2. Gene Expression In Eukaryotes

a. Francois Jacob and Jacques Monod were responsible for

discovering lactose in E. coli.

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b. The production of an enzyme or protein is controlled by three

regulatory elements.

1. Structural Genes are genes that code for a particular

polypeptide.

2. Promoters are regions of DNA that serve as the

binding site for RNA polymerase.

3. Operators are DNA segments that serve as a binding

site for an inhibitory protein that blocks transcription.

c. Operon – a series of genes that code for specific products and the regulatory elements that control them.

d. Lac Operon – the chosen name for the operon studied by Jacob

and Monod. Its structural genes coded for the enzymes that

regulated lactose metabolism.

e. Jacob and Monod’s research showed that gene expression in

the lac operon exhibits two forms: repression and activation.

1. Repression – the blockage of transcription by the

action of a repressor protein; a protein which inhibits

a specific gene from being expressed.

i. The attachment of the repressor to the operator

prohibits RNA polymerase from binding.

ii. Regulator Gene – the gene which codes for the

repressor protein.

2. Activation – the initiation of transcription by the

removal of a repressor protein. The removal of the

repressor allows RNA polymerase to transcribe the

structural genes of an operon.

i. Inducer – a molecule that activates, or induces,

transcription. In E. coli, lactose is an inducer.

f. Because lactose acts as an inducer, the lac operon is

transcribed only when lactose is present.

3. Gene Expression In Eukaryotes

a. Not all genes in a eukaryotic cell are expressed at the same

time.

b. Eukaryotes can control gene expression at multiple levels.

c. Different cells produce different types of proteins.

d. So far, no operons have been recorded in eukaryotes.

e. Euchromatin – the uncoiled, lightly-packed form of DNA

which is the active site of RNA transcription.

f. Some portions of the chromatin are permanently coiled so their

genes cannot be transcribed (called heterochromatin).

g. In eukaryotic genes, there are two kinds of segments beyond

the promoter:

1. Introns – sections of a structural gene that do not code

for amino acids.

2. Exons – the sections of a gene that code for amino

acids, and therefore proteins.

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h. Unlike prokaryotes, eukaryotes can control gene expression by modifying RNA after transcription.

i. Pre-mRNA – a form of messenger RNA that contains both

introns and exons.

j. Enzymes remove the introns from pre-mRNA, and the

remaining exons are spliced together to form a mature mRNA

strand.

k. Enhancer – noncoding control sequences that facilitate transcription. It must be activated for its associated gene to be

expressed.

l. Transcription Factor – additional proteins that bind to

enhancers and RNA polymerase and regulate transcription.

B. Section 2 – Gene Expression And Development 1. Cell Differentiation – the development of cells having specialized

functions.

a. Morphogenesis – the development of form in an organism.

b. Homeotic Gene – regulatory genes that determine where

certain anatomical structures will develop in an organism

during morphogenesis.

c. Homeobox – the specific DNA sequence within a homeotic

gene that regulates patterns of development.

d. Regulatory proteins are formed when homeoboxes are

transcribed and translated.

2. Cancer

a. Tumor – an abnormal growth of cells that result from

uncontrolled cell division.

1. Benign Tumor ☺☺☺☺ - generally pose no threat to life.

Their cells remain within a mass. Ex. Fibroid cysts,

warts.

2. Malignant Tumor ���� - (cancer) the uncontrolled

dividing cells invade and destroy healthy tissues

elsewhere in the body.

3. Metastasis – the spread of cancer cells beyond their

point of origin.

b. Malignant tumors can be categorized according to the types of

tissues they infect:

1. Carcinoma: grows in the skin and the tissues that line

the organs of the body. Ex. Lung cancer, breast cancer.

2. Sarcoma: grows in bone and muscle tissue.

3. Lymphomas: solid tumors that grow in the tissues of

the lymphatic system.

i. Leukemia – the uncontrolled production of

white blood cells.

c. The frequency of cell division is governed by several factors; including adequate nutrition and attachment to another cell

or membrane.

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d. Growth Factors – regulatory proteins that ensure that the events of cell division occur in the proper sequence and correct rate.

e. Carcinogen – any substance that increases the risk of cancer. Ex. Tobacco, asbestos, ionizing radiation.

f. Mutagens – agents that cause mutations to occur within a cell.

g. Oncogene – a gene that causes cancer. They begin as proto-

oncogenes that control a cell’s growth and differentiation.

h. Tumor-suppressor Gene – codes for proteins that prevent

uncontrolled cell division. When they mutate, the proteins for

which they code are either defectively expressed or not

expressed at all, which can lead to cancer.

i. A person’s likelihood of developing cancer depends on:

1. Their genetic makeup,

2. Amount of exposure to a carcinogen,

3. Amount of a carcinogen in each exposure,

4. Mutations in gametes,

5. Their age.

XII. CHAPTER 12 – INHERITANCE PATTERNS & HUMAN GENETICS

A. Section 1 – Chromosomes And Inheritance 1. Sex Determination

a. Early 1900’s – Thomas Hunt Morgan began breeding

experiments with Drosophila, the fruit fly.

1. He named the chromosome that was the same in both

male and female the X chromosome.

2. He named shorter, hook-shaped chromosome the Y

chromosome.

b. Since chromosomes segregate into separate cells in meiosis II,

the resulting gametes will either have one X or one Y

chromosome.

c. X -linked Genes – genes found on the X chromosome.

d. Y -linked Genes – genes found on the Y chromosome.

e. Sex Linkage – the presence of a gene on a sex chromosome.

f. Morgan crossed a white-eyed male fly with a red-eyed female.

After crossing members of the F1 generation, the result was the

expected ration of 3 red to 1 white. However, all white-eyed

flies were male.

g. Morgan concluded that eye color in Drosophila was X-linked.

2. Linkage Group – a set of genes on a chromosome that tend to be

inherited together.

a. In Drosophila, the allele for grey body is dominant over black

body; the allele for long wings is dominant over short.

b. After crossing homozygous grey, long winged flies with

homozygous black, shot winged flies, Morgan produced an F1

generation of heterozygous grey, long winged flies.

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c. He crossed members of this generation, strangely producing an

F2 generation with several grey, short winged flies and black,

long winged flies.

d. Morgan concluded that alleles must have been rearranged

through crossing-over.

e. Crossing-over changes the locations of genes among the

chromosomes that carry them, producing new blends.

3. Chromosome Mapping

a. Chromosome Map – a diagram that shows the linear sequence

of genes on a chromosome.

1. The farther apart two genes are, the likelier they are to

be separated by crossovers.

2. Map Unit – two genes that are separated by crossing

over 1% of the time.

4. Mutation

a. Germ cell mutation – a mutation that occurs in an organism’s

germ cells (gametes). They do not affect the organism they are

produced in but may affect offspring.

b. Somatic mutation – take place in an organism’s body cells.

c. Lethal mutation – a mutation that can cause death.

d. Some mutations can be beneficial and assist the process of

evolution.

e. Chromosome mutations are either changes in the structure of

a chromosome or the loss of an entire chromosome:

1. A deletion involves the loss of a piece of a

chromosome. All of the information carried by the lost

piece may be lost.

2. An inversion involves a chromosomal section breaking

off then reattaching in reverse to the same chromosome.

3. A translocation involves a chromosome piece

breaking off and reattaching to different chromosome.

4. A nondisjunction involves the failure of a

chromosome to separate from its homologue during

meiosis. One gamete receives an extra chromosome,

and another lacks it entirely.

f. Gene mutations may involve large segments of DNA or a

single nucleotide within a codon.

1. A point mutation involves the substitution, addition,

or removal of a single nucleotide.

i. Substitutions – one nucleotide replaces another.

ii. Ex. sickle cell anemia, where a substitution of

adenine for thymine in a single DNA codon

results in defective red blood cells.

iii. Nucleotide deletion mutations – one or more

nucleotides in a gene are lost.

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iv. Insertion mutations – one or more nucleotides

are added to a gene.

2. A frame shift mutation results from the incorrect

grouping of codons after the addition or deletion of

nucleotides.

B. Section 2 – Human Genetics 1. Studying Human Inheritance

a. Pedigree – a family record that shows how a trait is inherited

over several generations.

b. Patterns of Inheritance – the repetition of certain phenotypes in a pattern from one generation to the next.

c. Carriers – individuals who have one copy of a recessive autosomal allele.

2. Genetic Traits And Disorders

a. Genetic Disorders – diseases that have a genetic basis.

b. Genetic Marker – a short section of DNA that is known to have

a close association with another gene.

c. Single-allele Traits – traits controlled by a single allele. 1. More than 200 traits are governed by a single allele.

i. Huntington’s disease (HD) is caused by a

dominant allele located on an autosome.

ii. HD is said to show an autosomal-dominant

inheritance pattern.

2. More than 250 traits are governed by homozygous

recessive alleles.

i. Ex. Cystic fibrosis, sickle cell anemia,

albinism, phenylketenuria, deafness.

ii. Cystic Fibrosis and sickle cell show an

autosomal-recessive inheritance pattern.

d. Multiple-allele Traits – traits controlled by three or more

alleles of the same gene that code for a single trait.

1. The ABO blood groups are controlled by the three

alleles IA, I

B, and i.

2. Each individual’s genotype consists of two of these

alleles, which determines blood type.

3. The alleles IA and I

B are codominant.

4. There are six possible ABO blood genotypes, and four

possible blood types:

i. IAIA � A

ii. IAi � A

iii. IBIB � B

iv. IBi � B

v. IAIB � AB

vi. ii � O

e. Polygenic Traits – traits that are controlled by two or more

genes. Most human traits are polygenic.

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1. Ex. skin, eye color, hair color.

2. The expression of many genes is influenced by the

environment. Ex. height

f. X-linked Traits - traits that are passed on from parent to

offspring on the X chromosome.

1. Colorblindness is a recessive X-linked disorder in

which an individual cannot distinguish between certain

colors.

2. Hemophilia impairs the ability of blood to clot

following an injury. It largely occurs in males.

3. Duchenne muscular dystrophy is a defect which

weakens and progressively destroys muscle tissue.

g. Sex-influenced Traits – traits influenced by the presence of sex hormones.

1. Even though females and males may share the same

genotype, they display different phenotypes.

2. Ex. pattern baldness is controlled by an allele which is

dominant in males but recessive in females.

h. If nondisjunction occurs during egg formation, one egg will

have 22 chromosomes and another 24, resulting in an embryo

with 45 (monosomy) or 47 (trisomy) chromosomes when

fertilized.

1. Monosomy – a zygote with 45 chromosomes only has

one copy of a particular chromosome.

2. Trisomy – a zygote with 47 chromosomes has one

additional copy of a particular chromosome.

i. Many anomalous chromosome counts are lethal. However,

some are able to develop. Ex. Down Syndrome = Trisomy 21,

results in mental retardation, muscle weakness, etc.

j. Nondisjunction also affects sex chromosomes. Males with an

extra X chromosome have Klinefelter’s syndrome; and females

with one X chromosome Turner’s syndrome.

3. Detecting Human Genetic Disorders

a. Genetic Screening – an examination of a person’s makeup

which may involve a karyotype or blood test.

b. Genetic Counseling – a form of medical guidance that reveals

problems that may affect offspring.

c. Physicians can diagnose more than 200 genetic disorders in the

fetus using a variety of tools and techniques.

1. During amniocentesis, the physician removes a small

amount of amniotic fluid to analyze fetal cells.

2. During chorionic villi sampling, a sample of the

chorionic villi growing between the uterus and placenta

is used to produce a karyotype.

d. Phenylketonuria (PKU) – a genetic disorder in which the body cannot metabolize the amino acid phenylalanine.

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XIII. CHAPTER 13 – DNA TECHNOLOGY

A. Section 1 – The New Genetics 1. Genetic Engineering – the application of molecular genetics for

practical purposes. It can be used to identify specific traits or transfer

them from one organism to another.

2. Manipulating Genes

a. DNA Technology – the technology involved in genetic engineering.

b. DNA technology can be used to: 1. Treat genetic disorders,

2. Improve food crops,

3. Improve upon and prolong human life.

c. Restriction Enzyme – a bacterial enzyme used to cut a DNA

molecule at specific locations.

1. “Sticky” Ends – single chain tails of DNA created on

each cut DNA segment

2. Sticky ends that have been cut by the same enzyme can

readily bond together to form a new sequence.

d. Cloning Vector – a carrier that is used to clone a gene and transfer it from one organism to another.

e. Plasmid – a ring of DNA found in a bacterium in addition to its

main chromosome.

f. Donor gene; a specific gene isolated from another gene.

g. Gene Clone – an exact copy of a gene. 3. Transplanting Genes

a. Plasmids may be used to transfer a gene to bacteria so that the

bacteria will produce a specific protein, such as insulin:

b. Step 1 (Isolating a Gene): to isolate the human insulin gene, a

restriction enzyme is used to cut the DNA into many pieces;

which are spliced into plasmids to create a genomic library.

c. Step 2 (Producing Recombinant DNA): a recombinant DNA

molecule is created by inserting a donor gene (insulin) into a

cloning vector.

d. Step 3 (Cloning DNA): the plasmid containing recombinant

DNA is inserted into a bacterium, called the transgenic

organism. The bacterium is placed in an environment

favorable for reproduction. As the gene for insulin is copied

with every division, massive amounts of insulin can be

produced.

4. Expression Of Cloned Genes

a. A donor gene is transcribed and translated in its host as if it were still in its original cell.

b. To induce a host cell to express a certain gene, methods such as

transferring promoters and modifying gene location.

B. Section 2 – DNA Technology Techniques

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1. DNA Fingerprints – a pattern of bands made up of specific fragments

from an individual’s DNA.

a. DNA fingerprints can be used to determine similarities

between two individuals or species.

b. The method for preparing a DNA fingerprint is called

restriction fragment length polymorphism (RFLP).

1. Step 1: DNA is extracted from a specimen of blood or

other tissue and cut into pieces using restriction

enzymes.

2. Step 2: gel electrophoresis separates fragments

according to their size and charge. Samples of the DNA

are placed in gel wells, which are run through an

electric current.

3. Step 3: the DNA fragments that have been separated

are split into single chains and blotted onto filter paper.

Probes (radioactive segments that are complementary

to the segments being compared) are added. They form

visible bands when exposed to photographic film.

c. If little DNA is available, the polymerase chain reaction (PCR)

can be used to make copies of segments.

1. PCR requires the presence of 1)

a supply of four

nucleotides, 2) DNA polymerase,

3) primers,

4) a

fragment

2. Primer – an artificial single-stranded sequence of DNA

required for the initiation of replication.

3. When combined, the selected regions of DNA quickly

multiply. The new copies can be used to obtain a

fingerprint.

2. Human Genome Project – a project with the goal of determining the

sequence of nucleotides which make up human DNA.

a. Gene Therapy- the act of treating a genetic disorder by introducing a gene into a cell or correcting a defect.

C. Section 3 – Practical Uses Of DNA 1. Producing Pharmaceutical Products

a. Some proteins can be produced far more inexpensively using

DNA technology, such as Insulin. More examples:

1. Colony-stimulating factors – stimulates the

production of white blood cells.

2. Erythropoietin – used to treat anemia by stimulating

the production of red blood cells.

3. Growth Factors – used to promote the healing of

wounds by stimulating the growth of different types of

cells.

4. Human Growth Hormone – used as a treatment for

dwarfism.

47

5. Interferons – used to treat viral infections and some

cancers by preventing the replication of viruses.

6. Interleukins – used to treat a variety of conditions by

activating and stimulating different kinds of white

blood cells.

7. Tissue Plasminogen Activator – used to prevent heart

attacks and strokes by dissolving blood clots.

8. Atrial Peptides – used to treat high blood pressure and

kidney failure.

2. Genetically Engineered Vaccines

a. Vaccine – a solution that contains a harmless version of a virus

or a bacterium.

1. Pathogens – disease causing agents.

2. DNA technology can produce more effective, less risky

vaccines.

3. Increasing Agricultural Yields

a. DNA technology has been used to develop new strains of diseases and pest proof crops.

1. Ex. transferring genes that are harmful to hornworms

into tomato plants, making the plants toxic to

hornworms.

b. Herbicides – weed-controlling chemicals. Strains of plants

have been produced that are unaffected by herbicides.

c. Researchers are working towards transplanting the nitrogen-fixing gene from bacteria into plants, which would eliminate

the need for fertilizers.

4. Safety And Environmental Issues

a. In the United States, genetic engineering is regulated by: 1. Food and Drug Administration (FDA)

2. National Institutes of Health (NIH)

3. US Department of Agriculture (USDA)

4. Environmental Protection Agency (EPA)

b. Concerns with Genetically Engineered Foods:

1. Concern: Foods produced by genetic engineering could

contain toxic proteins or allergens.

2. Response: FDA requires manufacturers of genetically

engineered foods to provide evidence that allergens

have not been transferred to new foods.

c. Concerns with Genetically Engineered Crops

1. Concern: Genetically engineered crops could spread

into the wild and wipe out native species.

2. Concern: Transgenic crop plants could transmit their

new genes to neighboring species, creating a

“superweed”.

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3. Response: Regulatory agencies require labels on the

packages of transgenic plants to indicate their proper

uses and risks.

XIV. CHAPTER 14 – THE ORIGIN OF LIFE

A. Section 1 – Biogenesis 1. Biogenesis – the current model, which states that all living things

come from other living things.

2. Spontaneous Generation – states that living things arise from nonliving

things.

3. Redi’s Experiment

a. Francesco Redi questioned the commonly held belief that flies

were generated spontaneously from rotting meat.

b. Redi devised an experiment to test his hypothesis that meat

kept away from flies would not get maggots.

1. Experimental ���� consisted of net-covered jars that

contained meat.

2. Control � consisted of uncovered jars containing

meat.

c. Result ���� maggots swarmed only over meat in open jars.

d. Conclusion ���� flies come only from eggs laid by other flies.

4. Spallanzani’s Experiment

a. Lazzaro Spallanzani tested the hypothesis of spontaneous

generation of microorganisms.

b. Spallanzani reasoned that boiling broth in a flask would kill any microorganisms.

1. Experimental ���� consisted of sealed flasks full of

boiled clear, fresh broth.

2. Control ���� consisted of unsealed flasks full of boiled

clear, fresh broth.

c. Result ���� the broth in the sealed flasks remained clear, while

that in the open flasks became cloudy due to contamination

with microorganisms.

d. Conclusion ���� the broth became contaminated only when

microorganisms entered with the air.

5. Pasteur’s Experiment

a. Louis Pasteur devised an experiment in which a flask with a

curved but open neck prevented microorganisms from entering.

b. Broth boiled in the flasks became contaminated by

microorganisms only when the necks were removed.

c. Conclusion ���� the contamination was due to microorganisms

in the air.

B. Section 2 – Earth’s History 1. The Formation Of Earth

a. The solar system formed from a mass of gas and dust at the

center of a giant molecular cloud.

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b. Most of this material fell inward, forming a stellar core that

would eventually achieve hydrogen fusion and become the Sun.

c. The remainder of the material circled as a protoplanetary disk.

The terrestrial planets formed as solid debris accumulated, and

the gas planets formed from large rocky cores that had enough

gravitational attraction to pull in gas from the surrounding disk.

d. The estimated age of Earth is 4.5 billion years.

e. Radioactive Dating – methods of establishing the age of

materials.

f. Isotopes – atoms of the same element that differ in the number

of neutrons they contain.

1. The mass number of an isotope is the total number of

protons and neutrons.

2. Isotopes are designated by their chemical name

followed by their mass number, ex. carbon-12.

g. Radioactive Decay – the release of particles or radiant energy from unstable nuclei. (through beta decay)

1. Radioactive Isotopes – isotopes that are radioactive and

are undergoing decay.

2. Half-life (represented by λ) – the length of time it takes

for ½ of an isotope to decay.

3. The age of a material can be determined by measuring

the amount of a radioactive isotope it contains.

h. The age of Earth was estimated by using a method based on the

decay of uranium and thorium in rock crystals.

2. The First Organic Compounds

a. Alexander Oparin (1894-1980) suggested that the atmosphere

of the primitive Earth was composed of:

1. Ammonia (NH3)

2. Hydrogen Gas (H2)

3. Water Vapor (H2O)

4. Methane (CH4)

b. These chemicals may have rearranged under the searing heat to

form organic molecules.

c. Lightning and UV radiation may have catalyzed the formation

of molecules essential to life.

d. Stanley L. Miller and Harold C. Urey built an apparatus to

test Oparin’s hypothesis.

1. Their apparatus included a chamber containing the

gases Oparin assumed were present in the young

atmosphere.

2. As the gases circulated in the chamber, electric sparks

drove chemical reactions.

3. Result ���� the production of a variety of organic

compounds, including all amino acids.

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e. Organic compounds are present in the atmospheres of most of

the planets and in interstellar space.

3. From Molecules To Cell-Like Structures

a. Cell-like structures have formed from solutions of simple

organic molecules.

1. Microspheres – spheres composed of protein molecules

organized as a membrane.

2. Coascervates – collections of droplets that are

composed of molecules of different types, such as

amino acids and sugars.

C. Section 3 – The First Life-Forms 1. The Origin Of Heredity

a. The t shape of tRNA is dictated by hydrogen bonds between particular nucleotides.

b. This observation led to speculation that RNA molecules may

behave like enzymes.

2. The Roles of RNA

a. Ribozyme (portmanteau of ribosome and enzyme) – a type of

RNA that can act as an enzyme.

b. Life may have started with self replicating molecules of RNA.

3. The First Prokaryotes

a. The first cells were probably anaerobic heterotroph

prokaryotes, since there was little oxygen.

b. The next generation was probably autotroph prokaryotes.

c. Archaebacteria – living organisms that may be similar to the

first organisms. They are unicellular organisms that thrive in

seemingly inhospitable places.

d. Photosynthetic life appeared about 3 billion years ago.

e. Cyanobacteria – a group of photosynthetic unicellular prokaryotes possibly related to the first photosynthetic life.

f. It took about one billion years for the O2 in the atmosphere to

reach current levels.

g. O2 can be split into 2O by high energy light. Each reacts with

O2 to form O3, or ozone. Ozone is toxic but is responsible for

absorbing UV in the upper atmosphere.

4. The First Eukaryotes

a. About 2.0-1.5 billion years ago, a small aerobic prokaryote

began to live and reproduce inside larger, anaerobic

prokaryotes.

1. It is thought that it gave rise to mitochondria.

2. A relative of photosynthetic cyanobacteria gave rise to

the chloroplast.

b. Endosymbiosis – a successful, mutually beneficial relationship.

51

XV. CHAPTER 15 – EVOLUTION: EVIDENCE AND THEORY

A. Section 1 – The Fossil Record 1. Nature Of Fossils

a. Fossil – a trace of a long-dead organism. They are often found

in layers of sedimentary rock.

1. Sediment such as dust, sand, or mud is deposited by

wind or water.

2. There are two principal forms of fossil:

i. Mold is an imprint in rock in the shape of an

organism.

ii. Cast is a rocklike model of an organism.

3. Robert Hooke concluded that fossils are the remains

of plants and animals.

2. Distribution Of Fossils

a. Nicolaus Steno made an important contribution toward a

modern understanding of Earth’s biological history.

1. Law of Superposition – stated that successive layers, or

stratum, of rock or soil were deposited by wind or

water.

2. Using Steno’s law, observers could establish:

i. The relative age of a fossil (one fossil is

younger/older than the other).

ii. The absolute age of a fossil (age in years),

which could involve radiological dating.

3. Fossil-bearing strata show that species appeared,

existed for a while, and then disappeared.

i. Extinction – the permanent disappearance of an

entire species from earth.

ii. Mass Extinctions – brief periods during which

large numbers of species vanish.

4. Biogeography – the study of the geographical

distribution of fossils and living organisms.

5. A comparison of fossil types shows that new organisms

arise in areas where similar ones lived.

B. Section 2 – Theories of Evolution 1. Lamarck’s Explanation

a. Jean Baptiste de Lamarck proposed that similar species

descended from a common ancestor.

1. He hypothesized that acquired traits were passed on to

offspring.

2. Acquired Trait – a trait that is not determined by genes.

It arises as a result of an organism’s experience or

behavior.

3. Ex. Lamarck believed that the webbed foot of shore

birds resulted from repeated stretching of membranes

between toes.

52

i. Offspring of birds with webbed feet would

acquire that trait from their parents.

ii. If an organism did not use a certain part of its

body, a smaller version of that part would be

passed on.

4. His hypothesis was easily disproved, but laid out the

foundations for the eventual work of Charles Darwin.

2. The Beginning Of Evolutionary Thought

a. Natural Selection – organisms best suited for their environment

reproduce more successfully.

1. Population – a group of organisms of the same species.

2. Over time, the proportion of organisms with more

favorable traits increases.

b. Charles Darwin was born in 1809 to a wealthy British

physician.

1. In 1831, Darwin sailed aboard the H.M.S. Beagle as the

ship’s naturalist for five years.

i. Uniformitarianism – the geological structure of

Earth results from cycles. Detailed in Principles

of Geology by Charles Lyell.

ii. In Chile, Darwin observed fossil shells in rock

beds more than 4 km above ground. He

reasoned that the formation of mountains slowly

changed habitats.

c. Alfred Wallace approached Darwin with his own paper on

natural selection, prompting Darwin to publish his own work.

1. Both their hypotheses were presented to the Linnean

Society of London in 1858.

2. A year later, Darwin published On the Origin of

Species.

3. Darwin’s Theories

a. Darwin’s ideas about evolution and natural selection are summed up in two theories:

1. Descent with modification – newer forms appearing in

fossil records are actually the modified descendants of

older species.

2. Modification by natural selection – states how

evolution occurs. Darwin was influenced by Thomas

Malthus.

b. Adapt – an organism becomes better suited to its habitat.

c. Fitness – a single organism’s genetic contribution.

C. Section 3 – Evolution in Process 1. Evidence Of Evolution

a. Homologous Features – similar features that originated in a

shared ancestor.

53

1. Ex. beaks of birds, similar forelimbs of penguins,

alligators, bats, and humans.

b. Analogous Features – serve identical functions and look somewhat alike.

1. They have very different embryological development

and may differ in anatomy.

2. Ex. A hummingbird and a humming moth both hover to

feed off of flower nectar, but do not share anatomy or

embryological structure.

c. Vestigial Features – features that seem to serve no useful

function in an organism.

1. A vestigial feature in a modern organism is evidence

that the structure was used in some ancestor.

2. Ex. humans tailbones, appendix, whale pelvis.

d. The early stages of different vertebrate embryos are strikingly

similar to each other.

e. Ernst Haeckel stated that embryological development repeats

evolutionary history.

1. His statement was over exaggerated; as during no stage

of development does a fish resemble a gorilla.

2. All vertebrate embryos are similar, but those

similarities fade as development continues.

f. Darwin hypothesized that more similar forms of organisms

have a more recent common ancestor than less-similar forms.

2. Patterns Of Evolution

a. Coevolution – the change of two or more species in close

association with each other. Ex. plants and pollinators.

b. Convergent Evolution – organisms that appear to be similar

are not related at all. Ex. sharks and dolphins.

c. Divergent Evolution – two or more related populations or

species become increasingly dissimilar.

1. Adaptive Radiation – many related species evolve from

a single ancestral species. Ex. Galápagos finches,

which diverged in response to food availability.

2. Artificial Selection – selection for reproductive success

in plants and animals that is directed by humans. Ex.

domestic dogs are all members of the same species but

come in multiple “breeds”.

XVI. CHAPTER 16 – THE EVOLUTION OF POPULATIONS AND SPECIES

A. Section 1 – Genetic Equilibrium 1. Variation Of Traits In A Population

a. Population Genetics – the study of the genetic aspect of evolution.

b. Variations are influenced by environmental factors and

heredity.

c. Variations in genotype arise in three main ways:

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1. Mutations result from faulty copies of individual genes.

2. Recombinations occur during meiosis through

independent assortment and crossing-over.

3. Random fusion of gametes is driven by probability.

Out of millions of sperms, only one will fertilize an egg,

ensuring that offspring vary from their parents.

2. Allele Frequencies And The Gene Pool

a. Gene Pool – the total amount of genetic information available

in a population.

b. Allele Frequency – a measure of the genetic frequency of an

allele within a population. Can be determined with the formula:

Number of a Particular Allele

Total Number of All Alleles in the Population

c. Phenotype Frequency – a measure of the frequency of

phenotype in a population. Can be determined with the formula:

Number of Individuals with the Phenotype

Total Number of Individuals in the Population

3. Hardy-Weinberg Genetic Equilibrium – allele frequencies within a

population remain the same from generation to generation.

a. In a non-evolving ideal population under in equilibrium:

1. Allele frequencies do not change because of mutation.

2. Individuals neither enter nor leave the population.

3. The population is very large.

4. Individuals mate randomly.

5. Natural selection does not occur.

B. Section 2 – Disruption of Genetic Equilibrium 1. Mutation

a. Mutations can influence genetic equilibrium in a species by

producing new alleles for a trait.

b. Beneficial mutations, in the long term, play a vital role in

ensuring the survival of a species.

2. Migration

a. Immigration and emigration can affect gene frequencies in a

species.

b. Gene Flow – the process by which genes are transferred from

one population of a species to another.

3. Genetic Drift – a shift in allele distribution due to random changes in

individual allele frequency.

a. Abnormal rates of reproduction in small populations can easily

disrupt allele distribution, leading to genetic drift.

55

b. This can result in all organisms in a population having the

same allele, which can endanger the species since there is no

variation for natural selection to act on.

4. Nonrandom Mating

a. Mating of related individuals can lead to the anomalous

amplification of certain traits, leading to disorders.

b. Assortative Mating – individuals seek out mates that have

similar physical characteristics/genes.

5. Natural Selection

a. Any of the 4 forms of natural selection can lead to evolution:

1. Stabilizing Selection – individuals with the normal

form of a trait are the most successful. Ex. lizards of a

certain color and size evade predators more efficiently.

2. Directional Selection – favors individuals with traits at

one extreme of the phenotypic range. Ex. anteaters

with longer tongues can reach into deeper ant nests.

3. Disruptive Selection – favors individuals with traits at

either extreme of the phenotypic range. Ex. white and

dark shelled limpets blend in better than grey shells.

4. Sexual Selection – based on the selection of a mate

because of certain distinguishing features. Ex. female

peacocks pick their mate based on their plumage.

C. Section 3 – Formation of a Species 1. The Concept Of Species

a. Speciation – the process of the formation of a new species.

Existing species are basically altered versions of older ones.

b. Morphology – the internal and external structure/appearance of

an organism. It was originally used to define a species.

c. Biological Species Concept – proposed by Ernst Mayr; states

that “species are groups of interbreeding natural populations

that are reproductively isolated from other such groups”.

2. Isolating Mechanisms

a. Isolation involves two populations that cease interbreeding. Two forms of isolation drive speciation:

1. Geographic Isolation – the physical isolation of two

different populations.

2. Reproductive Isolation – groups within a population

can become genetically isolated from the rest. There

are two types:

i. Prezygotic Isolation – occurs before fertilization.

ii. Postzygotic Isolation – occurs after fertilization.

3. Rates Of Speciation

a. Speciation can occur quickly; on the order of thousands of years rather than millions.

56

b. Punctuated Equilibrium - holds that evolutionary change in the

fossil record came in fits rather than a steady process of slow

change.

XVII. CHAPTER 19 – INTRODUCTION TO ECOLOGY

A. Section 1 – Ecology 1. Ecology – the study of the interactions between organisms and living

and nonliving components of their environment.

2. Today’s Environment

a. Our ancestors obtained their food by hunting animals and

gathering plants.

b. The world’s human population has tripled from 2 billion in

1930 to 6 billion in 1999.

c. Humans are out competing and outnumbering other species,

driving many to extinction (sixth mass extinction?)

1. Many are eliminated by habitat destruction,

overhunting, and introduced predators and diseases.

2. Extinction is occurring most rapidly in the tropics.

d. Scientists estimate that about 1/5 of species may disappear by

2100.

e. Greenhouse Effect – the process by which CO2 and H2O trap

reflected heat and prevent it from escaping into space.

3. Levels Of Organization

a. Scientists have a system of different levels or organization

within organisms.

b. 1) Biosphere – the thin volume of Earth and its atmosphere

that supports life. All organisms are found within the biosphere.

c. 2) Ecosystem – all of the organisms and environment of a

particular place, including nonliving things.

d. 3) Community – all the organisms living in an area.

e. 4) Population - includes all the members of a species that live

in one place at one time.

f. 5) Organism – development of adaptations that allow a species

to evolve and overcome challenges of their environment.

4. A Key Theme In Ecology

a. No organism is isolated.

b. Many populations are interrelated; an increase in one can lead

to an increase in another.

5. Ecological Models

a. Ecologists use models to help understand the environment and

to make predictions about change.

b. Models may be in form of graphs, diagrams, or equations.

B. Section 2 – Ecology of Organisms 1. Habitat – where an organism lives.

2. Biotic And Abiotic Factors

a. There are two classes of influential environmental factors:

57

1. Biotic factors are living components, including all

living things that affect organisms.

2. Abiotic factors are nonliving components, including

chemical and physical characteristics. Examples:

i. Temperature

ii. Humidity

iii. pH

iv. Salinity

v. Oxygen Concentration

vi. Amount of Sunlight

vii. Availability of Nitrogen

viii. Precipitation

b. Tolerance Curve – a graph of performance vs. values of an

environmental variable.

c. Acclimation – the process of adjusting tolerance to Abiotic

factors.

d. There are two ways in which organisms deal with changes in

their environment.

1. Conformers do not regulate their internal conditions,

but change as their external environment changes.

2. Regulators use energy to control some of their internal

conditions.

e. Dormancy – a state of reduced activity to survive unfavorable

environmental conditions.

f. Migration – moving to a more favorable habitat.

g. Resources – the energy and materials a species needs.

3. Niche – a species’ way of life or involvement in its environment.

a. Fundamental Niche – the range of conditions that a species can

tolerate and the range of resources it can potentially use.

b. Realized Niche – the range of resources a species actually uses.

c. A species’ niche can change within a single generation. 1. Generalists have broad niches and can tolerate a

variety of conditions and use a variety of resources.

2. Specialists have narrow niches and have a limited

array of resources. Ex. koala.

XVIII. CHAPTER 20 – POPULATIONS

A. Section 1 – Understanding Populations 1. Properties Of Populations

a. A population is a group of organisms of the same species that

live in a particular place at once. Boundaries may be imposed

by a feature of the environment such as a shore.

1. Size is the number of individuals a population has. It

can be determined by counting or estimating.

2. Density measures how crowded a population is;

expressed as the number of individuals per volume.

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3. Dispersion is the distribution of individuals within a

population. It can be clumped, even, or random.

2. Population Dynamics

a. All populations experience change in size and composition

over time. Some figures used to understand change include:

1. Birth rate, the number of births in a period of time.

2. Death rate (mortality rate), the number of deaths in a

period of time.

3. Life expectancy, how long an individual is expected to

live.

b. Age Structure – the distribution of individuals of different ages in a population.

c. Survivorship curves – the likelihood of survival at different ages throughout an organism’s life.

1. Type I curves occur when the chance of death is small

until later in life.

2. Type II curves occur when the probability of death is

relatively constant throughout organism’s life.

3. Type III occurs when the greatest chance of death is in

an organism’s youth.

B. Section 2 – Measuring Populations 1. Population Growth Rate

a. Growth Rate – the amount of change a species’ population

experiences.

b. Whether a population grows, shrinks, or stays the same

depends on four processes:

1. Birth

2. Death 3. Immigration, or the movement of individuals into a

population.

4. Emigration, or the movement of individuals out of a

population.

c. Birth, death, and growth rates are usually expressed per capita

(per individual).

d. The per capita growth rate can be found with the following formula:

Birth rate – death rate = growth rate

2. Exponential Model – describes that a population grows quickly after a

few generations. The larger the population, the faster it grows.

a. It is assumed that birth and death rates remain constant,

regardless of how large population becomes.

b. On a graph, an exponential growth is marked by a J-shaped

curve.

c. Limiting Factor – a factor that limits the growth of a population.

Ex. competition, leading to lower birth and higher death rates.

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3. Logistic Model – builds on the exponential model but takes limiting

factors into consideration.

a. Carrying Capacity (represented by K) – the number of species

the environment can support over a large length of time.

b. On a graph, logistic growth is marked by a warped S-shape.

4. Population Regulation

a. Two kinds of population size-limiting factors have been

identified.

1. Density-independent factors reduce population by the

same amount, regardless of population size.

2. Density-dependent factors include resource

limitations and are triggered by increasing density.

b. Inbreeding – matting with relatives; this can occur within a

small population.

C. Section 3 – Human Population Growth 1. History Of Human Population Growth

a. Hunter-gatherer Lifestyle – the way of life of the first nomadic

humans.

b. Humans learned to domesticate animals and use certain plants

for food about 10,000 years ago, leading to the agricultural

revolution.

c. Better sanitation, disease control, and economic conditions led

to a decline in mortality rates after the Middle Ages.

d. Developed countries contain about 20% of the world

population, including all industrialized nations.

e. Developing countries contain about 80% of the populous,

including most Asian countries and all of Central America,

South America, and Africa.

XIX. CHAPTER 22 – ECOSYSTEMS AND THE BIOSPHERE

A. Section 1 – Energy Transfer 1. Producers

a. Autotrophs, which include plants and some kinds of protists

and bacteria, manufacture their own food.

b. Producers – organisms that capture energy and use it to make

organic molecules. Autotrophs are producers.

c. Most producers are photosynthetic.

1. In terrestrial ecosystems, plants are normally the

major producers.

2. In aquatic ecosystems, photosynthetic protists and

bacteria are normally the major producers.

d. Some autotrophic bacteria do not use sunlight as an energy

source.

e. Chemosynthesis – the process by which these bacteria produce

carbohydrates by using energy from inorganic molecules.

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f. Gross Primary Productivity – the rate at which producers in an

ecosystem capture energy.

g. Biomass – the organic material in an ecosystem. Producers add

biomass to an ecosystem by making organic molecules.

1. Only energy stored as biomass is available to other

organisms in the ecosystem.

2. Net Primary Productivity (kcal/m2/y) – the rate at

which biomass accumulate.

h. Variations in light, temperature, and precipitation account

for most of the variation in productivity among terrestrial

systems.

i. In aquatic ecosystems, productivity is usually determined only

by light and the availability of nutrients.

2. Consumers

a. All animals, most protists, all fungi, and many bacteria are

heterotrophs. They cannot manufacture their own food.

b. Consumers – another name for heterotrophs. They obtain

energy by consuming organic molecules made by other

organisms.

c. Consumers can be grouped according to the type of food they

eat.

1. Herbivores eat producers.

2. Carnivores eat other consumers.

3. Omnivores eat both producers and consumers.

4. Detritivores are consumers that feed on the waste of an

ecosystem.

i. Decomposers, which include bacteria and fungi,

cause decay by breaking down the molecules in

waste and dead tissue into simpler molecules.

ii. Some of the molecules are absorbed by

decomposers, while others are returned to the

soil or water.

3. Energy Flow

a. Trophic Level – indicates an organism’s position in the

sequence of energy transfer.

b. Most ecosystems only contain three or four trophic levels.

c. All organisms that feed on the same kind of food are on the

same trophic level.

d. Food Chain – a single pathway of feeding relationships among

organisms in an ecosystem that results in energy transfer.

e. The feeding relationships in an ecosystem are usually too

complex to be represented by a single food chain.

1. Many consumers eat more than one type of food.

2. More than one species of consumer may feed on the

same type of organism.

f. Food Web – the interrelated food chains in an ecosystem.

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g. Roughly 10% of the total energy consumed in one trophic

level is incorporated into the organisms of the next.

1. Thus, there is not enough energy in the highest trophic

level to support another level.

2. Organisms in the lowest trophic level are normally

more abundant than those in the highest.

h. Organisms that have many energy-consuming processes will

transfer less energy to the next trophic level than organisms

that do not.

i. No transformation of energy is 100% efficient. Every time

some energy is transformed, some is lost as heat.

XX. CHAPTER 23 – ENVIRONMENTAL SCIENCE

A. Section 1 – Humans And The Environment 1. Environmental Science – a field of study which uses biology to look at

the relationships between humans and the planet Earth.

2. A Global Connection

a. Convection cell – regions of rising, warm air and falling, cold

air.

b. Upwelling – a rising current of cold water which replaces warm water at the surface, bringing organic materials and

nutrients with it.

c. El Niño – a warm-water anomaly that develops off of the

Peruvian coast in December, due to absent east-to-west trade

winds.

3. Human Influences On Global Systems

a. Chlorofluorocarbons (CFCs) – an ozone depleting chemical

which is used as refrigerator and air conditioner coolant.

b. A single CFC molecule can destroy up to 100,000 ozone

molecules.

c. Correlation – a corresponding relationship. Temperature

changes match up to changes in CO2 concentration.

d. Cause-and-Effect Relationship – a relationship in which the occurrence of one event leads to another.

B. Section 2 – The Biodiversity Crisis 1. Biodiversity – the variety of organisms in an area.

a. Evenness – a method of comparing the different number of a

species’ individuals that are present in an area.

b. Genetic Diversity – the amount of genetic variation in an area.

2. Measuring Earth’s Biodiversity

a. The most confident estimate is that there are at least 10 million

species on Earth. Fewer than 3 million have been documented.

b. Debt-for-Nature Swap – a system in which organization

gradually pay off the debts of a developing country in

exchange for preservation of biodiversity.

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c. Ecotourism – tourism involving a national park or other natural

destination.

3. The Importance Of Biodiversity

a. Utilitarian Value – a way of measuring the importance of

biodiversity that takes economic benefit into account.

b. Nonutilitarian Value – the value an organism can have because

it exists.

C. Section 3 – Taking Action 1. Conservation And Restoration Biology

a. Biologists are developing plans to protect and manage

remaining biodiversity-rich areas.

1. Conservation biology seeks to identify and maintain

natural areas.

2. Restoration biology involves rebuilding a heavily

damaged ecosystem.

2. Conserving Migratory Birds

a. Migratory Birds – travel long distances to remain in a favorable

environment.

b. Flyways – generally north-south routes along major land

features followed by migratory birds.

3. Getting Involved

a. Urban Ecology – involves people who are interested in the challenge of increasing biodiversity in urban areas.