campbellessentialbiology4th ch.notes

8/3/2019 CampbellEssentialBiology4th Ch.notes

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1. Order - order and organization

2. Regulation - within appropriate limits

3. Growth & Development - genes; instructions

4. Energy Utilization

5. Response to environment

6. Reproduction7. Evolution

Biosphere - all the environments on earth that support life; Earth.

- the whole is greater than the sum of its parts

Biosphere:

1. Biosphere

2. Ecosystem

3. Communities

4. Populations

5. Organisms

6. Organ systems & organs

7. Tissues

8. Cells

9. Organelles

10. Molecules & Atoms

Ecosystems - interaction between organisms & their environment

a. Process 1 - cycling of nutrients

b. Process 2 - gains and looses energy constantly

Cells and DNA:

Cells are the level which properties of life emerge

All organisms are composed of cells

2 types of cells

Prokaryotic - simpler and smaller, i.e. - bactieria

Eukaryotic - Plants, Animals, Fungi and protists. DNA holding nuclear

membrane.

DNA - composed of 4 different molecules (A, G, C, T)

human cell DNA is 3 billion chemical letters long

Biodiversity:

290,000 types of plants

52,000 types of vertebrates

Three domains:

1. Bacteria - or Eubateria; all true bacteria


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2. Archaea - Least evolved forms of life on earth, very similar to bateria

3. Eukarya - Animals, Plants, Fungi and Protists.

Bacteria & Archaea areprokeryotic

Evolution:

Charles Darwin 1859 - Origin of Species decent with modification

Natural Selection:

Darwins Observations:

1. Overproduction & competition

2. Individual variation

3. Unequal reproductive success

Steps of Natural Selection:

1. Population with varied inherited traits

2. Elimination of individuals

3. Reproduction of Survivors

4. Increasing frequency of traits of survivors

Scientific Method:

1. Observation

2. Question

3. Hypothesis

4. Prediction

5. Experiment

6. Result / Predicted result

Discovery Science: Observation and measurements are the data of discovery science

A Controlled Experiment has two groups:

Experimental group

Control group - the group which the experimental group is compared.

Theory is bigger in scope from hypothesis. Theory describes a general behavior and is

widely accepted

Culture in Science:

1. Dependence on observations & measurements others can varify

2. Requires that ideas are testable & repeatable.

Scientists build on each other byremaining scepticaland byseeking reproducible

evidence.


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Chapter 2 matter - anything that occupies space and has mass

elements - substances that cannot be broken down into other substances

92 naturally occurring elements

25 essential to life

O, C, H, P, K, S, Na, Cl, Mg, Ca

Trace: B, Cr, Co, Cu, F, I, Fe, Mn, Mo, Se, Si, Sn, V, Zn

Atomic # = number of protons

Mass # = sum of protons and neutrons in nucleus

Isotopes - have different number of protons and neutrons, differ in mass (ex:

Carbon 13; 6 protons, 7 neutrons)

Radioactive Isotope - isotope whos nucleus is decaying and giving off energy

due to instability (ex Carbon 14; 6 protons, 8 neutrons) compounds - substances containing 2 or more elements

atom - smallest unit of matter

Composed of Proton (+), Electron (-), and Neutron (neutral)

ion - electrically charged atom

ionic bond - bond formed from two oppositely charges ions

covalent bond - 2 or more atoms sharing outer shell electrons (e-) to form molecule to

better fulfill the octet rule.

hydrogen bond - weak attraction in polar molecules

Water

The polarity of water molecules and hydrogen bonding that results explain most

of waters life-supporting properties

cohesion - tendency for molecules to stick together. Responsible forsurface

tension and capillary action.

ice floats - crystal stucture of ice is less dense than liquid water.

Water is a solvent - solution = solvent + solute (aqueous solution)

evaporative cooling - loss of heat through evaporation of water.

water regulates the temperature of the biosphere.

Heat - amount of energy associated with the movement of the atoms and molecules in a

body of matter.

Temperature - measure of heat Acids & Bases & pH

Acids - release H+ in to solution

Base - release OH- (hydroxide ion) into solution

pH scale - logarithmic scale of the concentration of H+ ions. 0(acid) - 14(base); 7

neutral

Slight changes in pH can be very harmful to an organism


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Buffers - substances in biological fluids that prevent harmful changes in pH by

accepting or donating H+ when there is and excess or depletion of H+ ions

CO2 is absorbed by oceans when it combines with seawater which produces an

acid.

Chapter 3 Lactose - milk sugar (many people have a lack of lactase enzyme)

Organic Compounds organic compound - carbon based molecules

hydrogen, oxygen, and nitrogen are commonly found in organic compounds

hydrocarbons: carbon-hydrogen molecules

methane (CH4) is the simplest hydrocarbon

Functional Groups - groups of atoms that perform chemical reactions

hydroxyl group (-OH)

carboxyl group (-COOH)

polymers - large moleculesmade by stringing together smaller molecules called

monomers

dehydration reaction - chemical reactionthat removes a molecule of H2O

Hydrolysis - to break with water ; reverse of dehydration reaction

Carbohydrates - sugars or sugar polymers

monosaccarides - simple sugars that cannot be broken down by

hydrolysis (ex: glucose, fructose) [Glucose = C6H12O6 (fructose has same

chemical formula)]

isomers - molecules that have same molecular formula but different

structure (like glucose and fructose)

The shape of molecular structure is important

monosaccharides - the main fuel for cellular work

dextrose - aqueous solution of glucose

disaccharide - double sugar, contructed from 2 monosaccharides through

dehydration reaction (ie - lactose, maltose, sucrose)

sucrose - disaccharide; table sugar (glucose+fructose)

polysaccharide - long chains of sugar units. Polymers ofmonosaccharides.

glyocogen - animal polysaccharide, more extensively branched than

starch

cellulose - ploysaccharide used by plants for structure (animals this plant

fiber for dietary fiber or roughage)

Lipids - hydrophobic organic molecule; neither


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macromolecules nor polymers

fat - glycerol molecule + 3 fatty acid molecules via dehydration reaction

forming triglycerides

hydrocarbons (fatty acid) store a lot of energy

Omega 3 has double bond in certain spot.

stored in adipose cells

unsturated - do not contain maximum # of hydrogen atoms;

unstarurated fats tend to be solid at room tempurature. One fatty

acid is bent due to double bond.

atherosclerosis - lipid containing deposits in blood vessels.

hydrogenation - adding hydrogen, causes trans fats

steroids - hydrophobic molecules that behave like hormones like

testosterone and estrogen

Cholesterol Testosterone & type of estrogen

THG - synthetic steriod

Proteins - polymers of amino acids amino acid - central carbon with 4 covalent partners (monomer)

Amino Group

Carboxyl Group

Side group

Hydrogen

polypeptide - polymer

peptide bond - bond of amino acid

protiens are made up of one or more polypeptides.

leucine - hydrophobicamino acid

styrine - hydrophillicacid

hemoglobin - 146 amino acid chain

Primary Structure

Alpha helix

pleated sheet

Protein Shape

3D shape determines function

denaturation is loss of proper shape

Nucleic Acids

Nucleotides are monomers

Nitrogen base

sugar

phosphate group

DNA & RNA

DNA sugar is deoxyribose nucleic acid

RNA sugar is ribose

DNA - (A,G,C,T)

A - Adenine


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G - Guanine

T - Thynine

C - Cystocine

Adenine partners with Thynine

Guanine partners with Cystine

RNA - (A,G,C,U) U - Uracil

DNA RNA Amino Acid

Inability to make sufficient amounts of Lactase (enzyme that brakes down

lactose) is genetic; one letter change (C to T) causes this.

Chapter 4 - Tour of a Cell Intro

Antibiotics - drugs that disable or kill bacteria (penicillin, 1928)

ribosomes of humans and bacteria are sufficiently different that antibiotics only

bind to bacterial ribosomes

Microscopy

Resolving power- the ability of an optical instrument to show two objects as

separate

resolving power of human eye is about 0.1 millimeter apart

Light Microscopy (LM) - surface features, low resolving power, though much

better then human

Scanning Electron Microscopy (SEM) - surface features, high resolving power

Transmission Electron Microscopy (TEM) - Inner features, high resolving power

Robert Hooke in 1665 first described cells

Prokaryotic Cells - Domains Bacteria and Archaea

prokaryotic cells are said to be older in evolutionary sense (3.5 billion years

ago)

prokaryotic cells are generally much smaller then eukaryotic cells; about 1/10th

the length.

Eukaryotic Cells - Domains Protists, Plants, Fungi, andAnimals

eukaryotic cells are about 2.5 billion years

have organelles. All cells have:

A plasma membrane - thin outer membrane that regulates traffic of molecules

between the cell and its surroundings

DNA

Ribosomes - tiny structures that build protiens according to the instruction of

DNA


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Eurkaryoticcells have organelles

Nucleus - houses mose of a eukaryotic cells DNA

prokaryotic cells dont have a nucleus, DNA is bunched together in a region

called the nucleoid.

Someprokaryoticcells have a capsule, a sticky outer layer that surrounds the cell wall

some prokaryotes have pili and flagella that allow them to attach to surfacesand propel them through a fluid environment, repectively.

Eukaryotic Cells Organelles:

Mitochondrion

Nucleus

Rough Endoplasmic Reticulum

Smooth Endoplasmic Reticulum

Ribosomes

Golgi Apparatus

Plasma Membrane

Cytoskeleton

Only in Plant cells:

Central Vacuole

Cell Wall

Chloroplast

Only in Animal cells:

Centriole

Lysosome

Flagellum

Plasma Membrane

Composed of lipids and protiens

lipids belong to special category called phospholipids

phospholipids have 2 (hydrophobic) fatty acid tails and one (hydrophilic)

phosphate group head.

phosphate group is electrically charges making it hydrophilic (likes water),

but fatty acids are hydrophobic (fears water) making one end like water

and the other end avoids water

phospholipid bilayer, hydrophilic on outside and hydrophobic on inside

protiens float around phospholipid bilayer creating a fluid mosaic and

protiens regulate traffic across membrane.

Cell Walls

Plants have cell walls made of rigid cellulose fibers.

Animal cells secrete a sticky coat called an extracellular matrix instead of a cell

wall, and most have cell junctions, structures that connect to other cells.

Nucleus and Ribosomes

Structure and Function of Nucleus:

nuclear membrane - double layer membrane encasing nucleus

chromatin - long DNA molecules and associated proteins that form long


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fibers

chromosome - each long organized structure of chromatin fiber (humans

have 46)

nucleolis - where the components of ribosomes are made

Ribosomes

small dots in cell floating in cytoplasm and attached to endoplasmicreticulum.

responsible for protein synthesis

How DNA Directs Protein Production

1. DNA transfers information to mRNA (messenger RNA)

2. mRNA exits nucleus into cytoplasm though pores in nuclear

membrane

3. Ribosome moves along mRNA, generating a protein.

Endomembrane System: Manufacturing and Distributing Cellular

Products

Endoplasmic Reticulum (ER) - labyrinth of tubes and sacs that run throughoutcytoplasm. Rough & Smooth

Rough ER -ribosomes are attached, producing proteins into ER. ER forms

transport vesicles around proteins

Smooth ER - Part of endoplasmic reticulum that is responsible for detoxifying

cell and creates lipids

Transport Vesicles travel along the cytoskeleton, moving protiens to the Golgi

Apparatus

Golgi Apperatus - refinery, warehouse, shipping center

Transport vesicles from the ER come to the receiving side of the Golgi apparatus

and turn into pancake shapes and release proteins. Golgi produces digestive enzymes, waste or secretory proteins, and cell products

that are moved from the Golgi by the Golgi budding around the enzymes, waste,

or products.

Lysosomes - capsules that hold digestive enzymes that bud off golgi

digest macromolecules and old organelles

lysosomes burst in apoptosis releasing digestive enzymes into

cytoplasm causing the cell to digest itself and die.

Vacuoles - storage cells

Bud off the ER, Golgi Apparatus, or Plasma Membrane

Some are contractile to regulate chemistry

Central Vacuole - holds water for plant cells

Transport Vesicles

Also bud from Golgi (not just ER) to transport secretory proteins

out of the cell.

Chloroplasts and Mitochondria

Chloroplasts - where plant cells produce sugars

Inner and outer membrane


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Stroma - thick fluid inside inner membrane

Granum - stacks of thylakoids

Mitochondria - sites of cellular respiration

2 components:

1. Intermembrane Space2. Matrix

Inner membrane has folding called cristea that increase surface area.

Cytoskeleton

Maintains cell shape

Enables cell movement (amoebas, cilia, and flagella)

microtubles - highways of the cell

different types of fibers

Cilia and Flagella

Cilia are shorter and wiggle; little hairs

cilia lining of respitory tract moves mucus

Flagella whip around a bit like a screw, longer and tail-like

Chapter 5 - The Working Cell

Conservation of Energy Potential Energy (Stored) Kinetic Energy (moving working energy) Entropy (S)

amount of disorder always positive (increasing)

Chemical Energy (Potential Energy) Examples; Hydrocarbons

Octane + O2 Heat + Energy + CO2 + H2O (~30% efficiency) Fat + O2 Heat + Energy + CO2 + H2O (~40% efficiency) (Heat is a form of energy)

Calorie 1 calorie = the heat to raise (1 ml) of H2O (1 degree) Celsius. 1 Calorie = 1 kilocalorie

ATP and Cellular Work ATP - adenosine triphosphate

Each phosphate group is negatively charged Crowding of negative charges gives ATP its potential energy Energy is released when last phosphate is released off of the

triphosphatet tail creating ADP (adenosine diphosphate)


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ATP provides energy for three kinds of cell work: Mechanical Work Transport Work (transport molecules across plasma membrane) Chemical Work (making large molecules)

ATP Cycle Renewable resource

ATP ADP + Energy for Cell ADP + cellular respiration + P ATP

Enzymes metabolism - the tota of all the chemical reactions in an organism enzymes - protiens that speed up chemical reactions

enzymes lower activation energy activation energy - energy required to trigger a chemical reaction;

energy barrier

Induced Fit substrate - enzymes ability to recognize a certain reactant molecule; the

molecule that fits in the enzymes active site. (Lactose is the substrate of

Lactase)

active site - region of an enzyme that has the shape and chemistry thatfits a substrate molecule

induced fit - the change in shape of an enzyme slightly, making the fitbetween the substrate and the active site tighter.

Enzymes functions repeatedly, accepting and releasing substrates more thanonce

Many enzymes are named for their substrate with and -ase ending. (i.e. -lactose and lactase) Enzyme Inhibitors - substrate impostors that plug up the active site of andenzyme, disrupting its function

some inhibitors regulate metabolism penicillin and nerve gas are examples of enzyme inhibitors feedback regulation - keeps cell from wasting resources by using

inhibitors

Membrane Function Transport proteins - transport materials in and out of the cell, through the

plasma membrane

Membrane Protein Functions Cell signaling - binding cite of chemical messanger Attachment to cytoskeleton and extracellular matrix to help maintain

shape

Enzymatic activity - active sites that fit substrates; some proteins mayteam up to carry out steps of a pathway

Transport - provide channel for a solute (integral protein) Intercellular joining - proteins that link adjacent cells (integral protein)


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Cell recognition - proteins with chains of sugars serve as identificationtags recognized by other cells. (peripheral protein)

Diffusion - movement of molecules to spread out into available space passive transport - cell does not expend energy to transport materials

with diffision

facilitated diffusion - a type of passive transport concentration gradient - region where the density of a substancechanges. Concentration represented with square brackets [ ] (i.e.-

concentration of hydrogen ions is [H+].

Osmosis and Water Balance osmosis - diffusion of water across a selectively permeable membrane hypertonic - side with higher concentration of solute hypotonic - side with lower concentration of solute (higher H2O

concentration)

Water moves from hypotonic side to hypertonic side. isotonic - equal concentration osmoregulation - regulation of water balance so to not burst (lysis) or

dehydrate.

plasmolysis - when the under hydrated plant cells plasma membranepulls away from its cell wall

Active Transport Active transport - pumping of molecules across membranes; this

requires energy. Pumping a solute against its concentration gradient.

Energy Source: ATP

Exocytosis and Endocytosis - bulk shipment traffic of large molecules (macromolecules) macromolecules are too large to travel through the plasma membrane membrane forms sacs, packaging larger molecules into vesicles Exocytosis - transport vesicles inside cell fuse to plasma membrane,

secreting proteins out of cell (like from Golgi)

Endocytosis - reverse of exocytosis. Takes material into cell withinvesicles that bud inward. 3 types:

pinocytosis - (nonspecific) cellular drinking; gulping fluid droplets phangocytosis - (nonspecific) cellular eating; engulfs particle and

forms food vacuole.

receptor-mediated endocytosis - triggered by certain molecules(specific) binding to the outside of plasma membrane. (like in

neurotransmitters)

Cell signaling signal transduction pathway - passing a signal through relays that turn

into chemical reactions. (i.e. - adrenaline triggers glycogen glucose

without entering cell)


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Chapter 6 - Cellular Respiration Intro

Marathon runners slow-twitch use O2 (aerobic) to make ATP

Sprinters fast-twitch no O2 (anaerobic) to make ATP

Energy Flow and Chemical Cycling Photosythesis - using light to build organic molecules Producers and Consumers

Autotrophes - self-feeders, organisims that make their own orgainicmatter (carbohydrates, lipids, protiens, & nucleic acids) from inorganic

sources (CO2, H2O, minerals). (producers)

Heterotrophs - other-feeders, organisims that cannot make organicmolecules from inorganic ones. Eat organic material (consumers)

Chemical Cycling Between Photosynthesis and Cellular Respiration photosynthesis needs CO2 and H2O

chloroplasts use light energy to rearrange atoms to producesugars (glucose C6H12O6) and other organic molecules

byproduct is O2 Cellular respiration uses O2 and energy extracted from organic sources

(like glucose) to make ATP

production of ATP in plants and animals occurs mainly inorganelles called mitochondria

By product is CO2 and H2O, same as whats needed forphotosynthesis.

Cellular Respiration: Aerobic Harvest of Food Energy

aerobic - requires oxygen The overall equation for cellular respiration

C6H12O6 + 6 O2 6 CO2 + 6 H2O + ATP The main function of cellular respiration is to generate ATP One glucose molecule can produce up to 38 ATP molecules Cellular respiration transfers H atoms from glucose to O, forming H2ORole of Oxygen in Cellular Respiration

During cellular respiration, hydrogen and its bonding electrons change partnersfrom sugar to oxygen, forming water as a byproduct

Redox Reactions

redox reaction - oxidation-reduction reation oxidation - loss of electrons


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reduction - acceptance of electrons (reduce the amount of positive charge) Oxygen is reduced during cellular respiration, accepting election (and oxygen)

lost from glucose

C6H12O6 oxidation 6 CO2 6 O2 reduction 6 H2O

When water is produced in a redox reaction, energy is released (potentialchemical energy is released)

NADH & Electron Transport Chain

1. First carrier of electrons is NAD+ (nicotinide adine dinucleotide)

2. NAD+ is reduced to NADH

3. NADH travels to the electron transport chain eventually forming H2O

Each link in the electron transport chain is a molecule, usually a protein.

Series of redox reaction first accepts then donates electrons

Each transfer releases a small amount of energy used indirectly to form ATP

NADH carries electrons from glucose (and other fuel molecules) and deposits

them at the top of the electron transport chain electrons cascade down the chain, molecule to molecule. Molecule at the bottom

drops the electrons to oxygen forming H2O.

glucose NADH Electron transport chain H2O

The stepwise release of chemical energy in the electron transport chain produces

most of the ATP

Oxygen, the electron grabber makes this all possible. Fuctions as gravity

pulling object downhill.

An overview of Cellular Respiration

1. Glycolysis - molecule of glucose is split into two molecules of pyruvic acid.Enzymes for glycolysis are located in the cytoplasm, outside the mitochondria

2. Citric Acid Cycle - Pyruvic acid enters mitochondria after being split byglycolysis. The Citric Acid Cycle completes the breakdown of glucose all the way

down in to CO2 inside the mitochondria matrix.

3. Eletron Transport Chain - electrons are captured from food (glucose, pyruvicacid, etc.) by NADH formed in the first two stages fall down the Electron

Transport Chain, to oxygen. Electron transport from NADH to oxygen releases

the energy your cells use to make most of their ATP.

The Three Stages of Cellular Respiration

1. Glycolysis - splitting of sugar1. 6-carbon glucose molecule is broken in half forming two 3-carbon

molecules (Pyruvic acid)

2. The 3-carbon molecules donate electrons to NAD+ forming NADH

3. Glycolysis also makes 2 ATP molecules directly when enzymes transfer

phosphate groups from fuel molecules to ADP and two pyruvic acid

molecules.

2. Citric Acid Cycle - pyruvic acid from glycolysis ispreppedfor the Citric AcidCycle forming acetic acid and then down to CO2. This process happens twice


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per glucose molecule (2 Pyruvic acid molecules 2 ATP, 6 NADH, 2 FADH2)

Preparation for Citric Acid Cycle

1. Pyruvic acid loses a carbon forming acetic acid and CO22. Oxidation forms NADH, (NAD+ take two electrons)3. Acetic acid attaches to Co-enzyme A (CoA) to form acetyl CoA.

CoA escorts acetic acid to the Citric Acid Cycle.2. Acetic acid joins 4-carbon acceptor to form 6-carbon citric acid for every

one acetic acid that enters the cycle as fuel

3. Two CO2 molecules exit as waste, citric acid cycle harvests energy from

fuel.

4. Some energy is used to produce ATP directly.

5. NADH is formed 3 NADH

6. FADH2 is formed (flavenoid)

7. All carbons that enter as fuel are accounted for as CO2, and 4-carbon

acceptor molecule is recycled

3. Electron Transport Chain - uses the energy released by the fall of electronsto pump H+ across the inner mitochondrial membrane, then [H+] gradient is

used to produce ATP (square brackets are used to indicate concentration of a

substance, here concentration gradient of H+ ions)

1. NADH transfers 2 electrons to an electron carrier in the first protein

complex, pumping H+ from in the matrix across the inner mitochondrial

membrane

2. FADH2 transfers electrons to a carrierthat transfers H+ to the second

protein complex.

3. Electrons fall through second protein complex pumping out more H+

ions across the inner mitochondrial membrane and a second carrier

moves the electrons from the second protein complex to the third proteincomplex.

4. Oxygen pulls the electron down the chain out of the third protein

complex, combining with H+ in matrix forming H2O, in the process

pumping more H+ across the membrane as well.

5. All of the H+ stored on the outside of the inner wall falls downhill

through the ATP synthase protein. This spins a component of the ATP

synthase.

6. The rotation of the ATP synthase actives part of the synthase molecule

that attach phophate groups to ADP molecules to generate ATP. ATP

synthase produces most of a cells ATP in aerobic cellular respiration (~34

ATP produced)

The Versatility of Cellular Respiration

Cellular respiration can burn many different kinds of molecules, not just

glucose.

Adding up ATP form cellular repiration

Glycolysis and Citric Acid Cycle each directly produce 2 ATP (Totalling 4

ATP)


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ATP synthase produces the rest, to total up to 38 ATP molecules per

glucose molecule.

Fermentation: Anaerobic Harvest of Food Energy

anaerobic - without oxygen fermentation - anaerobic process that cells use for short periods to produce energy

Fermentation in Human Muscle Cells

Blood provides cells with O2

Anaerobic process occurs when body is burning ATP faster than it can deliver O2

for electron transport chain.

Fermentation relies on glycolysis

glycolysis does not require O2, and produces 2 ATP for every molecule

broken down to pyruvic acid.

Cells have to consume more glucose fuel per second, because less ATP per

glucose is being generated NAD+ must be present as an electron acceptor

in aerobic conditions, NAD+ regenerates when NADH drops electron

cargo down electron transport chain

In Anaerobic conditions, NADH disposes electrons by adding them to pyruvic

acid producing a waste product lactic acid.

lactic acid is transported to liver

Fermentation in Microorganisms

2 ATP per glucose is enough energy to sustain many micoorganisms

sharp flavors (like in cheese) are due to lactic acid

Yeast is capable of both cellular respiration and fermentation when forced to be anaerobic, they are forced to fermentation, producing

ethyl alcohol instead of lactic acid. (as well as CO2)

Human heart can use lactic acid as fuel.

Chapter 7 - Photosynthesis: Using Light

to Make Food Intro

biomass - living material

biofuels - fuel from living material

The Basics of Photosynthesis


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Photosynthesis - a process by which plants, algae (protists), and certain bacteria

transform light energy in to chemical energy.

Autotrophs

Chloroplasts: Sites of Photosynthesis

Chloroplasts - light absorbing organelles

Chlorophyll - Light absorbing pigment the chloroplasts (often green) that plays acentral role in converting solar energy to chemical energy

chloroplasts are concentrated on the interior of cells of leaves

Stomata - where CO2 enters the O2 exits; tiny pores

H2O absorbed by plants roots

chloroplasts have double membrane like mitochondria

Stroma - thick fluid that fills the inner membrane of chloroplasts

Thylakoids - interconnected membrane sacs suspended in stroma

Grana - concentrated stacks of thylakoids.

chlorophyll molecules are built into the thylakoid membranes

The Overall Equation of Photosynthesis 6 CO2 + 6 H2O + Light Energy C6H12O6 + 6 O2

Photosynthesis take exhaust from cellular respiration

Electrons are boosted and added to CO2 to produce sugar

Hydrogen moved with electrons to H2O and CO2 in a redox reaction

chloroplasts must split H2O to perform this reaction

A Photosynthesis Road Map

Photosynthesis happens in 2 stages: Light Reaction and Calvin Cycle

Light reaction - chlorophyll in the thylakoid membrane absorbs solar energy,

which is then converted to the chemical energy of ATP and NADPH

NADPH - electron carrier light drives electrons from H2O to NADP+ (oxidized form of carrier) to form

NADPH (reduced form of carrier)

H2O is split providing source of electrons and O2 is released

Calvin Cycle - uses products of light reaction to produce sugar from O2

enzymes for Calvin Cycle stored in stroma

ATP provides energy for sythesis of sugar

NADPH provides electrons for reduction of CO2 to sugar (glucose)

The Light Reactions: Converting Solar Energy to

Chemical Energy

The Nature of Sunlight

radiation energy

Wave and Particle energy

wavelength - distance between crests of 2 adjacent waves

electromagnetic spectrum - full range of radiation. Gamma rays to radio waves,


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visible light is a very small fraction of this spectrum

The wavelengths not absorbed are reflected

green is poorly absorbed by chloroplasts and is reflected and transmitted

toward the observer

Chloroplast Pigments

Chlorophyll-a - absorbs mainly blue-violet and red light; participates directly inlight reactions

Carotenoids - absorbs blue-green light

some energy is passed to chlorophyll-a

carotenoids protect by absorbing and dissipating excessive light that

could damage chlorophyll

Carrots, fall colors

Chlorophyll-b - absorbs blue and orange.

How Photosystems Harvest Light Energy

particle light

Photons - fixed quatities of light energy shorter the wavelength of light, the greater the energy of photon

photon of violet is nearly twice the energy of red photon

When pigment molecule absorbs a photon, the pigments electrons gain energy to

an excited state (higher orbital), which is highly unstable.

Electron falls back to ground state almost immediately releasing heat and

sometimes light (floresence). In photosystems, this excited electron is grabbed

instead of falling back down.

Photosystem - a cluster of a few hundred pigment molecules (chlorophyll-a,

chlorophyll-b, and carotenoids)

photosystems function as a light gathering antennae.

Reaction center - a chlorophyll-a molecule that sits next to aprimary electron

acceptor

Primary Electron Acceptor- traps light-excited electron from chlorophyll-a in

the reaction center

How the Light Reactions Generate ATP and NADPH

1. Photons excite electrons in chlorophyll of water-splitting photosystem. Electrons

are trapped by primary electron acceptor. The H2O splitting photosystem

replaces its light-excited electrons by extracting the electrons form H2O. O2 is

released

2. Energized electrons from H2O splitting photosystem pass down an electron

transport chain to the NADPH-producing photosystem. The chloroplast uses the

energy released by this electron fall to make ATP.

3. The NADPH-producing photosystem transfers its light-excited electrons to

NADP+, reducing it to NADPH

ATP production is very similar to cellular respiration, using [H+] gradient to power

ATP synthase in thykaloid membrane

The Calvin Cycle: Making Sugar from Carbon Dioxide


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Sugar factory within stroma of cholorplasts. Uses ATP and NADPH

Like Citric Acid Cycle, starting material is regenerated (3-carbon sugar)

CO2 + ATP + NADPH G3P

G3P - glyceraldehyde 3-phosphate

G3P is raw material to make glucose and other organic compounds

(cellulose, starch, etc.) CO2 (from air) is added to RuBP (5-carbon sugar)

ATP & NADPH form two 3-carbon sugars ( ADP and NADP+ for electron

transport chain)

Every three CO2 molecules added makes one 3-carbon (G3P) sugar to use (two

3-carbon molecules makes one glucose)

One extra G3P from Calvin cycle is taken to make glucose and other molecules,

the rest is recycled into the Calvin Cycle.

Solar Driven Evolution

C3 Plants - plants that use CO2 directly

When weather is hot, stomata close holding in H2O but also do not allow CO2 in,halting sugar production

C4 Plants orCAM plants - use alternative modes of incorporating carbon

(shuttle cells) from CO2 to allow them to save water without giving up sugar

production. (sugarcane and corn (C4), pineapple and cacti (CAM))

Chapter 8 - Cellular Reproduction: Cells

from Cells (Part A)

What Cell Reproduction Accomplishes

Cell Division - two daughter cells that are genetically identical

chromosomes - structures that contain most of an organisms DNA. Daughter cells

receive identical sets of chromosomes

Millions of cells must divide every second to replace damaged or lost cells in ones body

Cell division is also vital for reproduction of an organism

Asexual Reproduction - does not involve fertilization of and egg by sperm. Reproduceby dividing in half and offspring are genetic replicas of the parent, inheriting all of their

chromosomes from a single parent

Mitosis - the type of cell division that is responsible for asexual reproduction and the

growth and maintenance of multicellular organisms

Sexual Reproduction - requires fertilization of an egg by sperm

Meiosis - special type of cell division which occures on in reproductive organs (such as


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testes and ovaries in humans)


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Sexual organisms require both mitosis for growth and development and meiosis for

reproduction

The Cell Cycle and Mitosis

Almost all Genes of a eukayotic cell - around 21,000 in humans - are located in thechromosomes in the cell nucleus.

Eukaryotic Chromosomes

Each eukaryotic chromosome contains on very long DNA molecule, typically

bearing thousands of genes

Chromatin - combination of DNA and protein molecules that make

chromosomes

protein molecules help organize the chromatin and help the activity of

genes

Most of the time, the chromosomes exist as a diffuse mass of fibers that are

much longer that the nucleus they are stored in. Stretched out, DNA would belonger than a person

As a cell prepares toe divide, its chromatin fiber coil up, forming compact

chromosomes. When the cells are not dividing chromosomes are too thin to be

seen with a Light Micrograph

Histones - found only in eukaryotes, small proteins that help DNA pack into

small packages

Nucleosome - small beads of DNA wrapped around histones; appear as small

beads on a string in an electron micrograph

When preparing to divide, the beaded string packs into a tight helical fiber, this

fiber coils further into a thick supercoil

Looping and folding further compact DNA

Before cell begins division process, the DNA molecules of each chromosome

is copied through a process call DNA replication producing 2 copies call sister

chromatids

Centromere - the narrow waist where two sister chromatids are joined.

Once seperated from its sister, each chromatid is considered a full fledged

chromasome

The Cell Cycle

Cell cycle - the ordered sequence of events that extends from the time a cell is

first formed from a dividing parent cell until it own division into two cells

Interphase - most of the cell cycle; the time when a cell performs its normalfunctions within the organism. Lasts at least 90% of cell cycle.

During interphase, a cell roughly doubles everything in its cytoplasm.

It increases supply of proteins, organelles (such as mitochondria and

ribosomes), and grows in size.

From the standpoint of cell reproduction, the most important event of

interphase is chromosome duplication


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G1 phase - (G for gap) occures before S phase

S phase - (S for DNA synthesis) approximately in the middle of the

interphase, this is the phase when chromosomes duplication occures

G2 phase - occurs after S phase, cell is preparing to divide.

M phase - (Mitotic Phase) part of the cell cycle when the cell actually dividing

Includes two overlapping processes: mitosis and cytokinesis Cytokinesis - cytoplasm is divided in two. Begins before mitosis is

completed

Combination of mitosis and cytokinesis produces 2 genetically identical

daughter cells, each with its own nucleus, organelles, cytoplasm, and

plasma membrane.

Mitosis and Cytokinesis

Mitosis is a continuum divided into 4 main stages (P.M.A.T.):

1. Prophase - chromatin fibers coil and appear as two identical chromatidsjoined at the centromere. Mitotic spindle begins to form

mitotic spindle - football shaped structure of microtubles thatguides the separation of the two sets of daughter chromatids.

Microtubles connect to proteins located at the centromere.

2. Metaphase - mitotic spindle fully formed and centromeres line up onimaginary plate

3. Anaphase - When sister chromatids separate. Each considered a fullfledged (daughter) chromosome.

4. Telephase and Cytokinesis - 2 groups of chromosomes have reachedopposite ends of cell. Telephase opposite of prophase, nuclear envelopes

form and chromosomes uncoil.

cleavage furrow - indentation at equator of cell. A ring of

microfillaments in the cytoplasm contracts just under the plasma

membrane. Used in cytokinesis of animal cells.

cell plate - the beginning of a new cell wall. Used in cytokinesis of

plant cells. Transport vesicles bring material to make cell wall to

equator of cell and release material. The material forms together

to produce a cell plate.

Cancer Cells: Growing out of control

Cell cycle control system - system of specialized protiens that integrate information

form the environment and form other body cells and sent STOP and go-ahead signalsat certain key points during the cell cycle using transduction pathways

Muscle and brains cells never receive signal to go beyond G1.

What is Cancer?

Disease of cell cycle

Cells divide excessively and can invade other tissues

Cell is transformed because of genetic change (mutation) in one of more genes


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that encode proteins in the cell cycle control system

Tumor- if bodys immune system fails to destroy the cell. (All it takes is one cell)

Benign Tumor- if the abnormal cells remain at the original site. Usually can be

completely removed by surgery

Malignant Tumor- a tumor can spread to neighboring tissues and other parts of

the body through blood stream. Cancer- a disease of an individual with a malignant tumor.

Cancer Treatment

Slash, burn, and poison

Remove tumor slash

Radiation Therapy - burn

side effects nausea, hair loss.

Chemotherapy - drugs that disrupt dell division poison

paclitaxil - from the Pacific Yew tree

Metastasis - The spread of cancer cells beyond their original site.

Cancer Prevention and Survival Not smoking

Excercise

High-fiber diet

Low fat diet

Chapter 10: The Structure and Functionof DNA

Intro

flu vaccine

influenza virus

virus - nucleic acid and protien

DNA: Structure and Replication

molecular biology - study of heredity at the molecular level.

Discovery of DNA led to a race to discover how the structure of this molecule could

account for its role in heredity

DNA and RNA Structure

DNA and RNA are nucleic acids

Nucleotides - monomers of DNA


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Polynucleoties - nucleotide polymer

polynucleotides tend to be very long and can have any sequence of

nucleotides, so a large number of polynucleotide chains are possible

nucleotides are joined together by covalent bonds between the sugar of one

nucleotide and the phosphate of another nucleotide

Sugar-phosphate backbone - repeating pattern of sugar - phosophate - sugar -phosphate that form the backbone of polynucleotides

nitrogenous bases are arranged like ribs that project from the backbone.

Each nucleotide has three components:

a. Phosphate group - with phosphorus atom at center, the source of

the acid in nucleic acid

b. Sugar - 5 carbon atoms, 4 in its ring and one extending above the ring.

(Deoxyribose is missing an oxygen atom that ribose has)

c. Nitrogenous base - Thymine [T], Cytosine [C], Adenine [A], and Guanine

[G]. T and C are single ring structures, and A and G are larger double ring

structures.

RNA had Uracil [U] instead of Thymine [T], and a different sugar call ribose.

Watson and Cricks Discovery of the Double Helix

Cambridge University, x-ray crystallography

X-ray image taken by Rosalind Franklin

Watson concludes x-ray image reveals a double helix

Double helix - spiral shape made of two strands, in DNA the two strands are

polynucleotide strands

Specific base pairing - four kinds of nitrogenous bases pair in a specific way

Each base has chemical side groups that can best form hydrogen bonds wit

hone appropriate partner

Adenine [A] with Thymine [T]

Guanine [G] with Cytocine [C]

(At The Grocery Ctore, A-T G-C)

Double helix looks like a twisted rope ladder

No restriction on the sequence of nucleotides along the length of the DNA

Watson and Cricks discovery published in Nature scientific journal in 1953

Watson, Crick, and Wilkins received Noble Prize in 1962, (Franklin died of

cancer)

DNA Replication

Watson and Crick suggest that DNAs structure serves as a mold, or template, to

guide reproduction of another strand

If one knows the sequence of the nitrogenous bases on one strand of the double

helix, on can very easily determine the sequence of the nitrogenous bases in the

other strand by applying base pairing rules

Enzymes link the nucleotides to form the new DNA strands (2 from 1)

DNA replication is complex and requires the cooperation of more that a dozen

enzymes and other proteins


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DNA polymerase - enzymes that make the covalent bonds between the

nucleotides of a new DNA strand.

The process is both fast and amazingly accurate, DNA replication proceeds at 50

nucleotides per second, with fewer then one in a billion incorrectly paired

DNA polymerase and some of hte associated proteins are also involved in

repairing damaged DNA DNA can be harmed by toxic chemicals and by high-energy radiation

Origins of replication - specific sites on a double helix where DNA replication

begins

DNA replication

DNA replication proceeds in both directions, creating bubbles

Parental DNA opens up (bubbles get bigger) as daughter strands

elongate

Eukaryotic DNA has many origins where replication can start

simultaneously, shortening total time of process

Bubbles merge, yielding two completed double-stranded daughter DNA

molecules

DNA replication ensures that all the bodys cells in a multicellular organism can

carry the same genetic information

It is also the means by which genetic information is passed along to offspring

The Flow of Genetic Information from DNA to RNA to

Protein

How an Organisms Genotype Determines Its Phenotype

Genotype - an organisms genetic makeup; the sequence of nucleotide bases inits DNA.

Phenotype - an organisms physical traits that arise from the actions of a wide

variety of proteins.

Indirectly, DNA carries instructions to build proteins

central dogma [Francis Crick] - chain of command: DNA RNA Protein

Transcription - the transfer of genetic information from DNA to RNA molecules

Translation - the transfer of information from RNA into a protein

Relationship between genes and proteins first proposed by Archibad Garrod in

1909

George Beadle and Edward Tatum in the 1940s, from bread mold, make a

breakthrough and show individual genes dictate the production of specific

enzymes

The function of a gene is to dictate the production of a polypeptide

(polypeptide - amino acid polymer linked by peptide bonds)

From Nucleotides to Amino Acids: An Overview

When a segment of DNA is transcribed, the result is an RNA molecule


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transcription - is called so because the nucleic acid language of DNA has

simply been rewritten (transcribed) a sequence of bases of RNA; the language is

still that of nucleic acid.

RNA is synthesized using the DNA as a template

translation - is the conversion of the nucleic acid laguage to the polypeptide

language polypeptides are the polymers chains consisting of 20 different amino

acid monomers

the sequence of the nucleotides of the RNA molecule dictates the

sequence of amino acids of the polypeptide

triplets of bases are the smallest words (codons) of uniform length that

specify all the individual amino acids

64 possible code words (43); enough triplets to allow more that one

coding fro each of the 20 amino acids.

codons - the 3-base words of nucleic acid chains

1 DNA codon (3 nucleotides) 1 RNA codon (3 nucleotides) one amino acid

The Genetic Code

Genetic code - set of rules relating to nucleotide sequence to amino acid

sequence

AUG sequence of amino acids in RNA has dual function; amino acid methionine

(Met) and signal for the start of the polypeptide chain.

Three codons, UAA, UAG, and UGA, do not designate amino acids and function

as stop codons

The nucleotides making up the codons occur in a linear order in the DNA and

RNA, with no gaps separating the codons

Almost all the genetic code is shared by all organism, from the simplest of

bacteria to the most complex plants and animals.

Because diverse organisms share a common genetic code, it is possible to

program one species to produce a protein from another species by transplanting

DNA. (like transplanting the instructions for the production of GFP, green

florescent protein, from jelly fish to mice to make glowing mice)

Transcription: From DNA to RNA

RNA polymerase - transcription enzyme that lin RNA nucleotides

Three steps:

1. Intiation of Transcription - the attachment of RNA polymerase to promoter

and the start of RNA synthesis

promoter- a nucleotide sequence that provides the starttranscribing signal, a specific place where DNA polymerase

attaches

promoter dictates which of the two DNA strands is to betranscribed

2. RNA Elongation - RNA grows longer

RNA synthesis continues, RNA strand peels away from DNA


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template, allowing DNA strands to come back together within the

RNA polymerase

3. Termination of Transcription - sythesis stops

terminator- special sequence of bases in DNA template thatsignals the end of the gene

RNA polymerase molecule detaches from the RNA molecule andthe gene (section of DNA molecule), and DNA molecule strands

rejoin.

2 other types of RNA are also produced on top of the amino acid sequence that

are involved in building polypeptides

Processing of Eukaryotic RNA

Capping, tailing and splicing

Eukaryotic, unlike prokaryotic cells, modifies (or processes) RNA transcripts

before they move out to the cytoplasm

Cap and tail - additions that protect the RNA form attack by cellular enzymes

and help enzymes recognize RNA as mRNA (messenger RNA) Introns - non-coding sections of nucleotides randomly interspersed in RNA

between exons which are removed before mRNA enters cytoplasm.

Exons - parts of the genes that are expressed.

RNA splicing - the process of joining exons and clipping out introns.

RNA splicing is believed to play a significant role in human cells by allowing our

approximately 25,000 genes to produce many thousands more polypeptides by

varying the exons that are included in the final mRNA

Translation: The Process

Translation is the divided into the same three phases as transcription, Initiation,

Elongation, and Termination.

1. Initiation - bringing together mRNA, the first amino acid with its tRNA, and

the two subunits of a ribosome

i. An mRNA molecule attaches to a small ribosomal subunit. A

special tRNA initiator binds to the start codon (AUG or methionine)

with anticodon UAC

ii. A large ribosomal subunit binds to the small ribosomal subunit,

creating a functional ribosome. The initiator tRNA fits into the P

site on the ribosome

2. Elongation - amino acids are added one by one to the first amino acid in a

three-step process

i. Codon recognition - anticodon of an incoming tRNA molecule,carrying its amino acid, pairs with the mRNA codon in the A site of

the ribosome.

ii. Peptide bond formation - the polypeptide leaves the tRNA in the

P site and attaches tothe amino acid on the tRNA in the A site.

Ribosome catalyzes bond formation and the chain has one more

amino acid.


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iii. Translocation - the tRNA in the P site leaves the ribosome,

and the remaining tRNA in the A site, carrying the growing

polypeptide, moves to the P site and process is cycled back to

step (2.i), codon recognition.

3. Termination - elongation continues unit a stop codon is reached (UAA,

UAG, and UGA) in the ribosomes A site. The completed polypeptide,typically several hundred amino acids long, is freed, and the ribosome

splits into its subunits.

Review: DNA RNA Protein

In eukaryotic cells, transcription occurs in the nucleus, and RNA is processed

before it enters the cytoplasm

Translation is rapid; a single ribosome can make an average sized polypeptide in

less than a minute

As the polypeptide is being made it coils into its 3-dimentional tertiary structure.

Several polypeptides may come together forming a protein with a quaternary

structure. The overall significance of transcription and translation is that transcription are

processes whereby genes control the structure and the activities of cells - or

more broadly, the way a genotype produces the phenotype.

Genes in DNA dictates complementary sequence of nucleotides in the mRNA

(transcription) mRNA specifies the linear sequence of amino acids in a

polypeptide (translation) these polypeptides determine the appearance and

capabilities ofthe cell and organism

Mutations

Mutation - any change in the nucleotide sequence of DNA

Occasionally, a base substitution leads to an improved protien or one with

new capabilities that enhance the success of the mutant organism and itd

decendants

Types of Mutations: Base substitution, Deletions, and Insertions

1. Base substitution - replacement of one base, or nucleotide, by another.this can result in no change in the protein (base redundancy), and

insignificant change, or a change that might be crucial to the life of the

organism.

silent mutation - base substitution results in a base redundancyand no change in protein product.

missence mutation - when changes of a single nucleotide dochange the amino acid coding, but have little or no effect on theshape or function of the resulting protein.

nonsence mutation - base substitution that results in a changeof an amino acid codon into a stop codon, resulting protein is

incomplete

2. Nucleotide Deletion - when a nucleotide is deleted, all codons from thatpoint on (downstream) are misread. Resulting polypeptide is likely to be


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completely nonfuntional.

3. Nucleotide Insertions - When a nucleotide is inserted. Disrupts allcodons that follow (downstream), most likely producing a nonfuntional

polypeptide

Mutagens

Mutagens - physical and chemical agents that are sources of mutations

Most common mutagen is high-energy radiation such as x-rays and UV light

Chemical mutagens are various types, some are similar to normal DNA bases

which cause incorrect base pairing when incorperated into DNA.

Many mutagens act as carcinogens, agents that cause cancer.

Although mutations are often harmful, they can also be extremely useful in nature

and in the labratory

Mutations are one source of the rich diversity of genes in the living world, a

diversity that makes evolution by natural selection possible.

Mutations are responsible for the different alleles (an alternative version of a

gene) needed for genetic research.

Viruses and Other Noncellular Infectious Agents

Viruses are not considered alive because it is not cellular and cannot reproduce on its

own.

virus - nucleic acid molecule wrapped in a protein coat. genes in a box

viruses survive only by infecting a living cell with genetic material that direct the cells

molecular machinery to make more viruses.

Bacteriophages

Bacteriophages - viruses that attack bacteria. bacteria - eaters, phages forshort

T4 virus infects e. coli, head made of DNA enclosed in an elaborate protein

structure, tail, a hollow structure enclosed in a springlike sheath, and tail fibers

which are the legs that bend and touch the cell surface.

Lytic cycle - after many copies of the phage are produced, the bacterium lyses

releasing phages. Reproductive cycle for most bacteriophages

Lysogenic cycle - viral DNA replication occurs without phage production or

death of the host cell

1. Viral DNA, prophage (viral DNA in host DNA) is inserted into bacterial

chromosome

2. Host cell replicates, reproducing the prophage DNA with the cellular DNA.A single infected bacterium can quickly give rise to a large population of

bacteria that all carry prophages.

3. Something, like an environmental change, triggers the release of the

prophages from the bacterial chromosome, and switches to the lytic

cycle.

Diphtheria (upper respiratory tract illness), botulism, and scarlet fever


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would be harmless to humans if it were not for the prophage genes they

carry.

Plant Viruses

Most plant viruses have RNA rather than DNA as their genetic material.

Viruses must get past the outer protective of plants, which makes plants

damaged by wind, chilling, injury or insects more susceptible to infection that ahealthy plant

No cure for most viral plant diseases.

Animal Viruses

influenza virus is an example of an animal virus

Outer envelope made of phospholipid membrane that allow virus to enter and

leave a cell.

Projecting protein spikes

Many animal viruses have RNA as their genetic material (common cold, measels,

mumps, HIV, and polio are all RNA viruses)

RNA virus reproduction1. Protein spikes attach to receptor proteins on the cells plasma membrane

and the viral membrane fuses with the cells membrane allowing protein

coated RNA to enter the cytoplasm

2. Enzymes remove protein coat.

3. An enzyme that entered the cell as part of the virus, uses the viruss RNA

genome as a template for making complementary strands of RNA which

have two purposes (4 & 5)

4. mRNA for synthesis of proteins

5. Templates for new viral genome DNA

6. The new coat of proteins assemble around the new viral RNA

7. Virus leave the cell by cloaking themselves in the plasma membrane

DNA viruses include hepatitis, chicken pox, and herpes.

Herpesvirus (chickenpox, shingles, cold sores, and genital herpes) enveloped

DNA viruses that reproduce in the cells nucleus, rather than the cytoplasm.

Herpesvirus get envelopes from nuclear membrane, rather than plasma

membrane.

Copies of herpevirus DNA usually remain behind as mini-chromosomes in the

nuclei of certain nerve cells, and remain latent until they are triggered (by stress,

or sunburn, or catching a cold, etc.)

Over 75% of American adults are the thought to carry herpes simplex 1 (cold

sores), and over 20% carry herpes simplex 2 (genital herpes). Viruses that attack non replaceable tissue (like nerve cell poliovirus) are not easy

to recover fully from.

HIV, The AIDS Virus

AIDS - Acquired Immuno-Deficiency Syndrome

HIV - Human Immuno-deficiency Virus, a type of RNA virus which resembles the

influenza and mumps virus, but is a retrovirus


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Retrovirus - An RNA virus that reproduces by means of DNA molecule. Reverse

to the usual DNA RNA synthesis. Retroviruses use reverse transcriptase.

Reverse transcriptase - an enzyme carried by the virus and catalyzes reverse

transcription, the synthesis of DNA on a RNA template.

After the RNA of HIV is uncoated:

1. Reverse transcriptase uses the viral RNA as a template to make a DNAstrand

2. Adds a secondary DNA strand.

3. The double-stranded viral DNA enters the cell nucleus and inserts itself

into the cells chromosomal DNA, becoming a provirus.

4. Occasionally the provirus is transcribed into RNA

5. Occasionally this mRNA is translated into viral protiens

6. Transcribed viral RNA and translated viral proteins, both from inserted

provirus, combine and leave the cell and can then infect other cells.

HIV infects and eventually kills several kinds of white blood cells that are

important to bodies immune system.

Due to the damaged immune system, body is susceptible to other infections that

cause the syndrome (a collection of symptoms) tha eventually kills the AIDS

patients.

HIV was first recognized before 1981

Two types of HIV drugs, one that inhibits the action of the enzymes called

proteases, which help produce final versions of HIV proteins, and a second type

which inhibits reverse transcriptase enzyme of HIV (AZT)

Because AIDS has no cure yet, prevention is the only healthy option.

Viroids and Prions

Very small pathogens, smaller than viruses

Viroids - small circular RNA molecules that infect plants and duplicate

themselves without encoding proteins. Viroids seem to cause disease by

interfering with the regulatory systems that control plant growth.

Prions - infectious proteins, which somehow convert normal proteins which are

normally present in brain cells, into a misfolded prion version. Responsible for

mad-cow disease and Creutzfeldt-Jakab disease.

Emerging Viruses

Emerging Viruses - viruses that have appeared suddenly or have recently come

to the attention of medical scientists

Avian flu - if this virus evolves so that it can spread easily from person to person,

the potential for outbreak is significant RNA viruses tend to have unusually high rates of mutation because errors

in the replicating their RNA genomes are not subject to certain proof reading

mechanisms

Mutations enable viruses to evolve into new strains that can cause disease in

individuals who have developed resistance to ancestral virus (need for yearly flu

vaccines)


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Joshua Lederberg: We Live in evolutionary competition with microbes. There is

no guarantee that we will be the survivors.

Chapter 8 - Cellular Reproduction: Cells

from Cells (Part B)

Homologous Chromosomes

Individuals of the same sex and species have the same number and types of

chromosomes

Somatic cell - a typical body cell. (in humans, 46 chromosomes, diploid)

Karyotype - a display of the stained chromosomes during metaphase on mitosis, where

chromosomes are arranged in matching pairs.

Homologous chromosomes - two chromosomes of a matching pair; genes controlling

the same inherited characteristics. Nearly identical chromosomes, each of which

consists of two identical sister chromatids after chromosome duplication.

Females, the chromosomes of each pair are essentially identical

Males, the chromosome of one pair do not look alike (single pair of sex chromosomes).

Sex chromosomes - chromosomes that determine a persons sex. Males are XY;

females are XX.

Autosomes - All the chromosomes excluding the pair of sex chromosomes.

Gametes and the Life Cycle of a Sexual Organism

Life cycle - the sequence of stages leading from the adults (of a multicellular organism)of one generation, to the adults of the next generation.

Diploid - cells which contain pairs of homologous chromosomes. Diploid organismsinclude humans and many other animals and plants. Diploid number is represented by

2n.

Gametes - cells which only have a single set of chromosomes (n). Produced by testisor ovary by the process of meiosis. 22 autosomes plus an X or Y sex chromosome.

(haploid) Haploid - a cell with a single chromosome set; only has one member of eachhomologous pair. Haploid number = n. (Humans, n = 23)

Fertilization - In human life cycle, a haploid sperm cell from father fuses with a haploidegg cell from mother.

Zygote - the diploid resulting from the fertilized egg, with two sets of homologouschromosomes, one set from each parent.

Life cycle is completed as a sexually mature adult develops from the zygote.


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Mitotic cell division ensures that all somatic cells of the human body receive a copy ofthe zygotes 46 chromosomes.

All trillions of cells in the body can be traced back to the single zygote produced byfertilization.

All sexual life cycles involve alteration of diploid and haploid stages. Producing haploid gametes by meiosis keeps chromosome number from doubling every

generation

Overview of Meiosis:1. Each of the chromosomes is duplicated during interphase (before mitosis)

2. Meiosis I, the first division segregates two chromosomes from a homologous

pair, packaging them in separate haploid daughter cells. (Each chromosome is

still doubled)

3. Meiosis II, sister chromatids separate, producing 4 haploid daughter cells,

containing one single chromosome from a homologous pair.

The Process of Meiosis Meiosis - the process that produces haploid daughter cells in diploid organisms. Has

two special features. (Lecture: 3 special features)

1. Number of chromosomes is reduced to half.

2. Exchange of genetic material between homologous chromsomes, crossing over

crossing over occurs during the first Prophase (meiosis I)

3. Sister chromatid pairs move toward poles in Anaphase I

Two consecutive divisions, meiosis I and meiosis II, where duplication of chromosomes

is followed by two divisions, resulting in 4 haploid daughter cells

! - Keep in mind the difference between homologous chromosomes and sister

chromatids.

Interphase

chromosomes duplicate producing two identical sister chromatids.

Meiosis I: Homologous Chromosomes Seperate

1. Prophase I - As chromosomes coil up, special proteins cause the homologous

chromosomes to stick together in pairs. Homologous chromosomes cross over

or exchange corresponding segments. Spindle forms.

2. Metaphase I - Homologous pairs are aligned in the middle of the cell. The sister

chromatids of each chromosome are still attached at their centromeres, where

the spindle microtubles are anchored.

3. Anaphase I - The attachment between the homologous chromosomes of eachpair breaks and the chromosomes migrate toward the poles of the cell, separated

not from each other, but from their homologous partners (in mitosis, the sister

chromatids separate).

4. Telophase I & Cytokinesis - Chromosomes arrive at poles of the cell, each pole

now has haploid chromosome set (each chromosome is still in duplicate form).

Cytokinesis occurs and two daughter cells are formed.


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Meiosis II: Sister Chromatids Separate

Essentially the same as mitosis, except meiosis II starts with haploid cells that

has not undergone duplication.

1. Prophase II - Spindle forms and moves chromosomes to middle of cell

2. Metaphase II - chromosomes are aligned with microtubles attached to sister

chromatids of each chromosome.

3. Anaphase II - centromeres of sister chromatids separate, and sister chromatids

of each pair migrate to opposite pols of cell.

4. Telophase II & cytokinesis - nuclei form at cell poles, and cytokinesis occurs,

yielding 4 daughter cells, each with haploid number (n) of single chromosomes.

Review: Comparing Mitosis to Meiosis

Mitosis provides for growth, tissue repair, and asexual reproduction; produces daughter

dells that are genetically identical to parent cell

Meiosis is needed for sexual reproduction, yields genetically unique haploid daughtercells

2 special features (Lecture: 3 special features)

1. Chromosomes reduced by half

2. Exchange of genetic material crossing over

3. Sister chromatid pairs move toward poles in anaphase I

For both mitosis and meiosis, chromosomes duplicate only once in the preceding

Interphase.

Mitosis involves two nuclear and cytoplasmic divisions, yielding 4 haploid cells.

All the events unique to meiosis occur in meiosis I

Meiosis II virtually identical to mitosis, but meiosis II yields haploid daughter cells.

The Origins of Genetic Variation

Another look at meiosis

Independent Assortment of Chromosomes

The arrangement of homologous chromosomes varies. The side-by-side

orientation of each homologous pair of chromosomes (two sister chromatids) is

a matter of chance

Every chromosome pair randomly orients its homologous chromosomes

independently of all others at metaphase I.

Total number of chromosome combinations that can appear in gametes is 2n.

In humans n=23, resulting in about 8 million, or possible chromosome

combinations.

Random Fertilization

Fertilization requires two gamete (haploid) cells to fuse, resulting in

trillioncombinations of chromosomes between two


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parents without accounting for crossing over.

Crossing Over

Crossing over- the exchange of corresponding segments between chromatids

of homologous chromosome pairs during prophase I of meiosis.

Chiama - (plural: chiasmata) sites of crossing over.

Homologous chromatids remain attached to each other at the chiasma untilanaphase I.

The exchange of segments between nonsister chromatids - one maternal

(mother) chromatid and one paternal (father) chromatid of a homologous pair -

adds to the genetic variety resulting from sexual reproduction.

Genetic recombination - gametes that have chromosomes that are part

maternal and part paternal due to crossing over, called recombinant

chromosomes.

When Meiosis Goes Awry

Mistakes that occur during meiosis can result in genetic abnormalities that range from

mild to severe to fatal.

How Accidents During Meiosis Can Alter Chromosome Number

Nondisjunction - when the members of a chromosome pair fail to separate at

anaphase.

Nondisjuntions result in gametes with abnormal numbers of chromosomes.

Nondisjuctions can occur in meiosis I or meiosis II.

Meiosis I - pair of homologous chromosomes fail to separate in anaphase

I (nondisjuction), resulting in incorrect number of chromosomes in haploid

cells at the beginning of meiosis II that results in 4 abnormal gametes.

Meiosis II - nondisjunction of a pair of sister chromatids that occurs during

anaphase II that results in 2 abnormal gametes and 2 healthy gametes.

Down Syndrome: An Extra Chromosome 21

Trisomy 21 - three number 21 chromosomes, yeilding 47 chromsomes in total.

In most cases, a human embryo with an atypical number of chromosomes

develops so abnormally that it is spontaneously aborted (miscarried) long before

birth.

Some aberrations in chromosomes number results in individuals that do survive,

but individuals have a character set of symptoms call a syndrome.

Down syndrome - an individual with trisomy 21. Affects about 1 out of every 700

children.

Trisomy 21, or down syndrome, is the most common serious birth defect

in the U.S.

Characteristic facial features include fold at the inner corner of eye, a round face,

and flattened nose

Short stature, heart defects, susceptibility to leukemia and Alzheimers, short life

span, and mental retardation.


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Some live to middle age years and function well within society

Incidence of down syndrome has a positive correlation with the age of the

mother. (personal note: appears to be exponential increase after age 35).

Abnormal Numbers of Sex Chromosomes

Nondisjunctions affect autosomes (like chromosome 21) as well as sex

chromosomes (X and Y)

Unusual numbers of sex chromosomes seem to not upset the genetic balance as

much as autosomes.

Some possible reasons as to why sex chromosomes are more forgiving are

that Y chromosomes carry a small amount of information, and mammalian cells

normally operate with only one functioning X chromosome because other copies

become inactivated in each cell.

Klinefelters syndrome - XXY, have male sex organs and normal intelligence,

but the testes are abnormally small, the individual is sterile, and often has

breast enlargement and other feminine body contours. Can occur with multiple

nondisjunctions (more than 3 sex chromosomes XXYY, XXXY, and XXXXY) XYY, tend to be taller than average, no syndrome

XXX, cannot be distinguished from XX females

Turners Syndrome - XO, absence of second sex chromosome which results in

women with short stature, web skin between head and shoulders, sex organs do

not fully mature as adolescence, poor development of breasts and secondary

sex characteristics. Normal intelligence. Only known case where having 45

chromosomes is not fatal.

A single Y chromosome is enough to produce maleness, regardless to the

number of X chromosomes. Absence of Y results in femaleness

SexChromosome

Syndrome Origin Frequency

XXY Klinefelter (male) Meiosis egg or sperm 1/2000

XYY None (male) Meiosis in sperm 1/2000

XXX None (female) Meiosis in egg or sperm 1/1000

XO Turners (female) Meiosis in egg or sperm 1/5000

Advantages of Sex Sex must enhance evolutionary fitness

Varied genetic makeup, quickening adaptation to changing environment

Shuffling of genes might allow a population to rid itself of harmful genes more

rapidly.

Sex is awesome.


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Chapter 9 - Patterns of Inheritance Intro

Dog breeding

Explain inborn traits through genetics.

Generations of inbreeding can bring about serious genetic defects

Certain breeds have behavioral tendencies like herding in boarder collies and

sheep dogs

Heritable Variation and Patterns of Inheritance

Heredity - the transmission of traits from one generation to the next

Genetics - the scientific study of heredity Gregor Mandel, an Augustinian monk, deduced its fundamental principles by breeding

garden peas, and applying the scientific method and mathematics. He published his

findings in 1866, only seven years after Darwins The Origin of Species.

Mendel stressed that the heritable factors (today called genes) retain their individual

identities generation after generation, regardless to how they are mixed up or temporary

masked.

In an Abbey Garden

Mendels experimental model is a pea plant because reproduction can be highly

controlled. (Also easily observable traits, many offspring, short life cycle [gap

between generations is very short]) Charachter- a heritable feature that varies among individuals; flower color, seed

shape, etc.

Trait - a variant of a character; purple or white flower color, wrinkled or round

seed shape, etc.

Mendel manipulated the reproduction of pea plants by controlling pollination

patterns, with known pollen sources. Always sure of parentage.

True-breeding - purebred varieties produced through self-fertilization (in pea

plants) until no variation is observed.

Cross - the action of cross-fertilization.

P generation - parental plants

F1 Generation - hybrid offspring of P generation (F from filial, Latin for sonor daughter). 1 for first generation. F2, second generation.

Seven characteristics of pea plant studied: 1) Flower color, 2) Flower position, 3)

Seed color, 4) Seed shape, 5) Pod shape, 6) Pod color, 7) Stem length.

Mendels Law of Segregation

Monohybrid Crosses - hybrids between two true breeding varieties (true-

breeding purple flowers with true breeding white flowers)


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(like seed color and seed shape)

Mendel crossed homozygous plants having round-yellow seeds (RRYY) and

green-wrinkled seeds (rryy)

F1 generation is all RrYy; round-yellow

F2 generation phenotypic ratio: 9/16 round-yellow, 3/16 Round-green, 3/

16 Wrinkled-green, 1/16 Green-wrinkled (9:3:3:1) Punnet square (4 X 4) with 4 variations (RY, rY, Ry, ry) supports findings.

Law of Independent Assortment - Each pair of allele assorts independently of

the other pairs of alleles during gamete formation. (Inheritance of one factor has

no effect on the inheritance of another)

Using a Testcross to Determine an Unknown Genotype

Testcross - a mating between an individual of dominant phenotype but unknown

genotype, and a homozygous recessive individual.

Rules of Probability

Genetic crosses obey the law of probability

Rule of multiplication - the probability of a dual event is the product of theseperate probabilities of independent events. ( x x ; x = 1/16)

Family Pedigrees

Wild-type traits - phenotypes seen most often in nature; not nessisarily specified

by dominant alleles. (Absence of freckles ins more common than thier presence,

even though freckles are a dominant allele)

Pedigree - the collection of family history and the arrangement into a family tree.

Human Disorders Controlled by a Single Gene

Recessive Disorders

Most human genetic disorders are recessive

Most people who have recessive disorders are born to normal parentswho are both heterozygotes

Carrier- An individual who is heterozygous for a recessive allele for a

genetic disorder

Using Mendels laws, one can predict the fraction of affected offspring

that is likely to result from a marriage between two carriers

In single gene disorders, of the offspring form heterozygote parents will

be homozygous for recessive allele, and will be heterozygous carriers.

Cystic fibrosis - recessive genetic disease that is characterized by an

excessive secretion of very thick mucus form the lungs, pancreas, and

other organs. Affects 1 in 25 people of European ancestry. Inbreeding - mating between close blood relatives, which cause a higher

likelihood of producing offspring which are homozygous for a recessive

trait. (most lines of purebred dogs have known genetic defects.)

Dominant Disorders

Extra fingers of toes and toes which are webbed

Anchondroplasia - a form of dwarfism in which the head and torso

develop normally, but the arms and legs are short. (homozygous


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dominant genotype causes death of embryo; single copy disorder)

99.99% of population are homozygous for achodroplasia recessive trait.

Huntingtons disease - degeneration of the nervous system that usually

does not begin until middle age

A dominant allele is not necessarily better than the corresponding

recessive allele.Genetic Testing

Today there are many tests that can detect the presence of disease

causing allele in an individuals genome.

Amniocentesis; physician uses a needle to extract about 2 tablespoons of

amniotic fluid

Chronic villus sampling; physician inserts a narrow tub through the vagina

to the uterus and removes some placental fluid.

Testing fetal cells or DNA released into the mothers bloodstream

Variations on Mendels Laws Mendels laws stop short at explaining some patterns of genetic inheritance

Incomplete Dominance in Plants and People

Incomplete dominance - An appearance in between the phenotypes of two

parents

Hypercholesterolemia - a condition charachterized by dangerously high levels

of cholesterol in the blood, an example of incomplete dominance.

ABO Blood Groups: An Example of Multiple Alleles and

Codominance

Most gene in more than two forms, known as multiple alleles. ABO bloodgroups - and example of multiple alleles in humans. Red blood cells

may be coated with carbohydrate A, carbohydrate B, both (type AB), or neither

(type O)

Three different alleles: IA, IB, and i(neither A or B). Each person inherits one of

the alleles from each parent.

iiis type O, IAIB is type AB, IBIB or IBiis type B

IAIB exhibit codominance

Codominance - both alleles are expressed in heterozygous individuals.

Pleiotropy and Sickle-Cell Disease

Pleiotropy - the impact of one gene on more than one charachter Sickle-cell disease - a disorder that cuases red blood cells to produce abnormal

hemoglobin protein causing them to form a sickle shape which results in a

diverse set of symptoms.

One allele of sickle-cell results in a healthy individual, but at the molecular level

the two alleles are actually codominant.

Polygenic Inheritance


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Polygenic inheritance - the additive effects of two or more genes on a single

phenotype character.

Skin pigmentation in humans is controlled by 3 genes, AABBCC very dark,

AaBbCc intermediate, aabbcc very light

Role of the Environment

As geneticists learn more and more about out genes, its becoming clear thatmany human characters are influenced by both genes and environment.

Identical twins even have different traits because of effects of environment.

The Chromosomal Basis of Inheritance

The chromosome theory of inheritance is one of biologys most important concepts.

Chromosome theory of inhertance - theory that states that genes are located in

specific positions on chromosomes and that the behaviour of chromosomes during

meiosis and fertilization accounts for inheritance patterns

campbellessentialbiology4th ch.notes

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