introductory topics handout

1

Welcome to Biology 101

Foundations of Biology I

Fardad Firooznia, PhD

535 Marshak

Ext 6580

[email protected]

Syllabus and Course Policies

Lectures, Labs,

and Readings

Foundations of Modern BIOLOGY

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Cells are the structural and functional units of life

The Cell Theory

– 1665 Robert Hooke: cellulae

– Late 1600s Antoni van Leeuwenhoek: cells move

– 1830s botanist Matthias Jakob Schleiden and the zoologist Theodor Schwann put forth the cell theory


The Cell Theory

– 1858 Rudolf Virchow

– 1862 Louis Pasteur’s experiment

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Pasteur’s Experiment

Question being asked?

Hypothesis?

Experimental prediction?

Image source: Sadava,Hillis, Heller, and Berenbaum

(2011). Life: The science of Biology, 9th ed. Sinauer Associates, Inc., Sunderland, MA


Image source: Sadava,Hillis, Heller, and Berenbaum (2011). Life: The science of Biology, 9th ed. Sinauer

Associates, Inc., Sunderland, MA


The Cell Theory


– All living cells arise from preexisting cells

– No spontaneous creation


– Early earth and origin of life?

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Two distinct groups of cells exist

– Prokaryotic cells

– Simple and small

– Bacteria are prokaryotic

– Eukaryotic cells

– Possess organelles separated by membranes

– Plants, animals, protists, and fungi are eukaryotic

Copyright © 2009 Pearson Education, Inc.

DNA (no nucleus)

Prokaryotic cell

Membrane

Eukaryotic cell

Nucleus (contains DNA)

Organelles

Evolution: the unifying theme

Nothing in biology makes sense except in the light of evolution - Theodosious Dobzhansky

Darwin’s contribution

– Evolution is not his idea

– How it occurs: natural selection

– Descent with modification:

– Unity and diversity

– Heredity?

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Modern genetics

Mendel’s contribution

– 1866, but ignored till 1900’s

– Discrete heritable factors

– Retain individuality generation after generation

Modern biochemistry and molecular biology

Modern biochemistry

– 1953, Watson, Crick, and Wilkins

– Rosalind Franklin

– Structure of DNA

– Redefined genes and chromosomes and reproduction

and inheritance!

Nucleus DNA

Cell

Nucleotide

(a) DNA double helix (b) Single strand of DNA

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Darwin’s Insight

What did he know and what did he infer?

– By mid 1800s, new knowledge due to

– Global exploration: diversity and similarity of life

– Comparative anatomy

– Fossils and geology

Darwin’s Insight


Emu Ostrich Rhea

Image sources:

http://gallery.hd.org/_exhibits/natural-science/_more2003/_more09/ostrich-in-Addo-Park-Eastern-Cape-South-Africa-WL.jpg

http://agcj.tamu.edu/307/2003c/Parker/images/emu4.jpg


Darwin’s Insight


Image source:

http://www.galapagoscruises.be/darwins-finches.jp






















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Darwin’s Insight

– Comparative anatomy (Ernst Haeckel’s drawings from 1874)

– Forelimbs of vertebrates: start developmentally the same way http://www.talkorigins.org/faqs/anatomy.html

Image Source: http://home.honolulu.hawaii.edu/~pine/book1qts/embryo-compare.jpg

Note:

segmentation, tail,

gill pouch,

notochord

Darwin’s Insight


• Giant Irish Elk and Cuvier’s anatomical works

• Neither moose, nor reindeer, … it was extinct

Image source: Freeman and Herron, 2007, Evolutionary Analysis, 4th edition, Pearson Education, Inc.

Darwin’s Insight


• General pattern of correspondence between Fossils and living forms from the same locale

• Giant ground sloth in Argentina

Image source:

http://library.thinkquest.org/5393/cindy_sloth.JPG

http://www.talkorigins.org/faqs/anatomy.html

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Darwin’s Insight


• General pattern of correspondence between Fossils and living forms from the same locale

• Glyptodonts and armadillos in Argentina

Darwin’s Insight


– By mid 1800s, new knowledge due to


– Comparative anatomy


– Georges-Louis Leclerc de Buffon and origin of species

– Charles Lyell: theory of uniformity

Darwin’s Insight


1. Malthus’ writings: human individuals produce more offspring than the environment can support

Inferred?

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Darwin’s Insight



2. Variation in populations

Inferred?

Darwin’s Insight




3. Some variation is heritable

Inferred?

Darwin’s Insight




3. Some variation is heritable

4. Artificial selection by animal breeders

Inferred?

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Evolution explains the unity and diversity of life

In 1859, Charles Darwin published On the Origin of Species by Means of Natural Selection

– The book accomplished two things

– Presented evidence to support the idea of evolution

– Proposed a mechanism for evolution called natural

selection


Population with varied inherited traits 1

Elimination of individuals with certain traits 2

Reproduction of survivors 3

Evolution explains the unity and diversity of life

Darwin’s four tenets

– Organisms produce more offspring than the environment can support; this leads to competition

– There is variation in a population

– Some variation is heritable

– There will be differential survival AND reproduction: natural selection of adaptive traits


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The Scientific Method

Steps

1. Observation

2. State the problem

3. Form a Hypothesis

4. Test/ Experiment

5. Collect and analyze the data

6. Draw conclusions

7. Repeat

Observations

What do you see?

Why is it interesting?

Can it be tested?

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Hypothesis

The statement of the problem.

Is the statement testable?

Is the statement falsifiable?

State the hypothesis as a null hypothesis.

Can’t prove something true but can prove

something false.

Methods and Procedures

Variables

Independent = what is altered

Dependent = what is studied

Standardized (controlled)

Intra and inter subject variability

Methods and Procedures

Control treatments

Repetition

Reproducibility

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Result and Analysis

Data collection

Data organization and analysis

Using tables

Using graphs

Conclusion

Reexamine the hypothesis in light of the evidence collected

Did the data disprove the null hypothesis?

Restate the hypothesis in light of the evidence

Future Directions

What new questions are raised?

What should be the next step?

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The Good, The Bad, And The Ugly

I grow two tomato plants from seed in separate pots next to each other on my porch. I use the

same potting soil in each pot and water both at the same time each day. To one pot I add a small

amount of Miracle-Gro, while I add no extra fertilizer to the other. At the end of 6 weeks, the Miracle-Gro plant has increased in weight by

210%, while the other plant has increased by only 65%. Does Miracle-Gro aid in plant growth?


150 patients with Crohn’s disease are given an experimental treatment in which they all drink

―cocktails‖ containing thousands of pinworm eggs. Within one week, 72% of the patients report a

reduction in their abdominal pain. Is ingesting pinworm eggs an effective treatment for the

symptoms of Crohn’s disease?


A study at a Southern university reported that the average final exam grade of students who chose to

enroll in an online version of a class was equal to that of students who took the class on-campus

from the same professor. Is on-line learning as effective as traditional in-class learning?

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In 1972, half of a group of 111 low-income children from Chapel Hill, NC were randomly chosen for

enrollment in an intensive pre-school program, while the other half were not enrolled in any

preschool program. 30 years later the preschool group had a higher % attending college, higher

average GPA for those who did attend college, and higher average wages than the non-preschool

group. Does preschool have some lasting effects on career outcomes?


The following is from a study published in 1946 by a Scottish physician who claimed there was a

relationship between morning sickness and ―excessive mother attachment‖:

―A study of the emotional state of these patients … revealed a common feature—i.e., sexual

relationship with the husband gave rise to disgust … I have confirmed the findings in many hundreds

of women. In doing so I noted that a high proportion of them at marriage were unduly

attached to their mothers.‖


An article in the nursing literature reported on successful coping strategies in women with severe

pregnancy sickness: ―Most women reduced their social commitments during the early months of

pregnancy, becoming much more dependent on their mothers and close friends for help in meal

preparation and child care.‖

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Dependent variable?

Indepdendent

variable?

Standardized

variables?

Control(s)?

Image source: Sadava,Hillis, Heller, and Berenbaum

(2011). Life: The science of Biology, 9th ed. Sinauer Associates, Inc., Sunderland, MA


The Cell Theory


– All living cells arise from preexisting cells

– No spontaneous creation


– Early earth and origin of life?

Origin of Life

When and How did life begin?

When:

earth formed about 4.5 BYA

radiometric dating of the oldest known rocks: 3.9 BYA

Chemical indicator of organic synthesis:

C12 : C13 Ratio

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Electron cloud

Protons

2e– Nucleus

Electrons

Mass number = 4 Neutrons

2

2

2

Atoms consist of protons, neutrons, and electrons

Although all atoms of an element have the same atomic number, some differ in mass number

– The variations are isotopes, which have the same numbers of protons and electrons but different numbers

of neutrons

– One isotope of carbon has 8 neutrons instead of 6 (written 14C)

– Unlike 12C, 14C is an unstable (radioactive) isotope that gives

off energy

– 13C has 7 neutrons in stead of 6 and is stable and non-radioactive


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Origin of Life


When:

earth formed about 4.5 BYA

radiometric dating of the oldest known rocks: 3.9 BYA

Chemical indicator of organic synthesis:

C12 : C13 Ratio

Origin of Life


When:

oldest bacteria impressions ~ 3.5 BYA

South Africa and Australia microfossils: 3.1-3.4 BYA

eukaryotic cells about 2 BYA

Origin of Life


How?

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Origin of Life


How do we know the conditions of the early earth’s atmosphere?

Origin of Life

atmosphere:

CO, CO2, H2, N2, NH3, CH4, H2S, H2O vapor

no ozone, lots of reactive H2

energy:

cooling earth:

inorganic metals in rocks and clay:

Origin of Life

What does it mean to be living?

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Origin of Life

Need:

1 basic blocks of life

2 cellular organization

3 reproduction/heredity and self-replication

Origin of Life

Need:

1 basic blocks of life

organic compounds: monomers and polymers

Time to review some basic chemistry

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Ionic bonds are attractions between ions of opposite charge

An ion is an atom or molecule with an electrical charge resulting from gain or loss of electrons

– Loss:

– Gain:

Two ions with opposite charges attract each other

– When the attraction holds the ions together, it is called an ionic bond


Na Sodium atom

Transfer of electron

Cl Chlorine atom

Na+ Sodium ion

Cl– Chloride ion

Sodium chloride (NaCl)

+ –

Na+

Cl–

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Covalent bonds join atoms into molecules through electron sharing

A covalent bond results when atoms share outer-shell electrons

– A molecule is formed when atoms are held together by covalent bonds


Unequal electron sharing creates polar molecules

In water:

– Oxygen attracts electrons more strongly than hydrogen

– Electrons spend more time near oxygen

– Polar covalent bond


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(–) (–)

O

H H

(+) (+)

Hydrogen bonds are weak bonds important in the chemistry of life

Water molecules are electrically attracted to oppositely charged regions on neighboring molecules

– Because the positively charged region is always a hydrogen atom, the bond is called a hydrogen bond


Hydrogen bond

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Ion in solution

Salt crystal

2.15 The chemistry of life is sensitive to acidic and basic conditions

A few water molecules can break apart into ions

– Some are hydrogen ions (H+)

– Some are hydroxide ions (OH–)

– Both are extremely reactive

– A balance between the two is critical for chemical processes to occur in a living organism


2.15 The chemistry of life is sensitive to acidic and basic conditions

Chemicals other than water can contribute H+ to a solution

– They are called acids

– An example is hydrochloric acid (HCl)

An acidic solution has a higher concentration of H+ than OH–


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The chemistry of life is sensitive to acidic and basic conditions

Some chemicals accept hydrogen ions and remove them from solution

– These chemicals are called bases

– For example, sodium hydroxide (NaOH) provides OH– that combines with H+ to produce H2O (water)

– This reduces the H+ concentration


The chemistry of life is sensitive to acidic and basic conditions

A pH scale (pH = potential of hydrogen) is used to describe whether a solution is acidic or basic

– pH ranges from 0 (most acidic) to 14 (most basic)

– A solution that is neither acidic or basic is neutral (pH = 7)


Acidic solution

pH scale

Battery acid

0

1

2

3

4

5

Lemon juice, gastric juice

Grapefruit juice, soft drink, vinegar, beer

Tomato juice

Rain water

Human urine

Saliva

Pure water

6

7

Human blood, tears

Seawater

8

9

10

11

12

13

Milk of magnesia

Household ammonia

Household bleach

Oven cleaner

Neutral solution

Basic solution

NEUTRAL [H+]=OH–]

Incre

asi

ng

ly A

CID

IC

(Hig

he

r co

nce

ntr

ati

on

of

H+)

14

Incre

asi

ng

ly B

AS

IC

(Lo

we

r co

nce

ntr

ati

on

of

H+)

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EVOLUTION CONNECTION: The search for extraterrestrial life centers on the search for water

An important question is, has life evolved elsewhere?

– Water is necessary for life as we know it

The National Aeronautics and Space Administration

(NASA) has evidence that water was once abundant on Mars

– Scientists have proposed that reservoirs of water beneath the surface of Mars could harbor microbial life


INTRODUCTION TO ORGANIC COMPOUNDS


3.2 Characteristic chemical groups help determine the properties of organic compounds

An organic compound has unique properties that depend upon

– The size and shape of the molecule and

– The groups of atoms (functional groups) attached to it

A functional group affects a biological molecule’s function in a characteristic way


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Estradiol

Male lion Testosterone

Female lion

CARBOHYDRATES

Sugars: (CH2O)n


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Glucose

(an aldose)

Fructose

(a ketose)

Disaccharide (condensation / dehydration reaction)

Starch granules in potato tuber cells

Glycogen granules in muscle tissue

Cellulose fibrils in a plant cell wall

Cellulose molecules

Glucose monomer

GLYCOGEN

CELLULOSE

Hydrogen bonds

STARCH

Polysaccharide

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LIPIDS

Glycerol + Fatty Acids

May have other modifications, such as phosphate groups


Water

Hydrophobic tails

Hydrophilic heads (phosphate groups)

Water

Lipids in Typical Biological Membranes

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PROTEINS

Polymers of Amino Acids = Polypeptides

May have several polypeptides together as one protein


Carboxyl group

Amino group

Different Amino Acids have Different Properties

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Peptide Bonds

Groove

Collagen

Polypeptide

chain

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NUCLEIC ACIDS

Polymers of nucleotides

Nucleotide: sugar, phosphate, and nitrogenous base


Phosphate group

Nitrogenous base

(adenine)

Sugar

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Figure 5.27

Components of nucleic acids

Base pair

Origin of Life

Theory of Abiogenesis: Alexander Oparin

Needed:

synthesis of macromolecules, esp. proteins

separation from their environment

heredity and replication machinery

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Origin of Life

Miller-Urey experiments 1950’s

atmosphere: CH4, NH3, H2O, H2 gases

no O2

liquid water

temperature less than 100 C

bombarded with electrical energy

Origin of Life

Miller-Urey experiments

1950’s

Results:

formaldehyde (CH2O)

hydrogen cyanide (important for amino and nucleic acids)

formic acid (HCOOH)

some amino acids

urea (N H2CON H2)

Origin of Life

Later experiments:

other amino acids

adenine (need for nucleic acids) from

HCN and NH3

fatty acids

sugars from formaldehyde

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Origin of Life

Polymerization:

Sidney Fox's work near hydrothermal vents

The importance of clay particles

Origin of Life

Cellular Organization

membrane-bound bag

derived primarily through production of fatty acids and some polypeptides

beginning of plasma membrane

Water

Hydrophobic tails

Hydrophilic heads (phosphate groups)

Water

Lipids in Typical Biological Membranes

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Origin of Life

Replication

need RNA for protein synthesis in cells

need enzymes to replicate RNA

the chicken or egg question!

Thom Cech (and Sidney Altman) discovered ribozymes

in 1986

1989 Nobel Prize!

Origin of Life

The First Prokaryotes!

Origin of Life

The First Eukaryotes?

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DNA (no nucleus)

Prokaryotic cell

Membrane

Eukaryotic cell

Nucleus (contains DNA)

Organelles

Human height

Length of some nerve and muscle cells

10 m

Frog egg

Chicken egg

Un

aid

ed

ey

e

1 m

100 mm (10 cm)

10 mm (1 cm)

1 mm

Lig

ht

mic

ros

co

pe

Ele

ctr

on

mic

ros

co

pe

100 nm

100 µm

10 µm

1 µm

Most plant and animal cells

Viruses

Nucleus

Most bacteria

Mitochondrion

10 nm

Lipids

Ribosome

Proteins

Mycoplasmas (smallest bacteria)

1 nm Small molecules

0.1 nm Atoms

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Figure 6.7

The plasma membrane and the membranes of organelles

Nucleoid

Ribosomes

Plasma membrane

Cell wall

Capsule

Flagella

Bacterial chromosome

A typical rod-shaped bacterium

Pili

A thin section through the bacterium Bacillus coagulans (TEM)

Eukaryotic cells are partitioned into functional compartments

Manufacturing involves the nucleus, ribosomes, endoplasmic reticulum, and Golgi apparatus

– Manufacture of a protein, perhaps an enzyme, involves all of these


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Breakdown of molecules involves lysosomes, vacuoles, and peroxisomes

– Breakdown of an internalized bacterium by a phagocytic cell would involve all of these



Energy processing involves mitochondria in animal cells and both mitochondria and chloroplasts in

plant cells

– Generation of energy-containing molecules, such as adenosine triphosphate, occurs in mitochondria and chloroplasts



Structural support, movement, and communication involve the cytoskeleton, plasma

membrane, and cell wall

– An example of the importance of these is the response and movement of phagocytic cells to an infected area


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Membranes within a eukaryotic cell partition the cell into compartments, areas where cellular

metabolism occurs

– Each compartment is fluid-filled and maintains conditions that favor particular metabolic processes and activities


Smooth endoplasmic reticulum

Rough endoplasmic reticulum

CYTOSKELETON:

NUCLEUS:

Nuclear envelope

Chromosomes

Nucleolus

Ribosomes

Golgi apparatus

Plasma membrane

Mitochondrion

Peroxisome

Centriole

Lysosome

Microtubule

Intermediate filament

Microfilament

Smooth endoplasmic reticulum

Rough endoplasmic reticulum

CYTOSKELETON:

NUCLEUS:

Nuclear envelope

Chromosome

Nucleolus Ribosomes

Golgi apparatus

Plasma membrane

Mitochondrion

Peroxisome

Cell wall

Central vacuole Microtubule

Intermediate filament

Microfilament

Cell wall of adjacent cell

Chloroplast

Plasmodesmata

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Mitochondrion

Intermembrane space

Inner membrane

Cristae

Matrix

Outer membrane

Chloroplast

Stroma

Inner and outer membranes

Granum

Intermembrane space

Flagellum

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Central microtubules

Outer microtubule doublet

Radial spoke

Dynein arms

Plasma membrane

Triplet

Cross sections:

Flagellum

Basal body

Basal body

Bacterial flagellum

Salmonella Figure 16.4 D Image sources: http://media-2.web.britannica.com/eb-media/02/58702-004-429BF178.jpg http://morayeel.louisiana.edu/SeaweedsLab/Gavio/bacterial%20cell%20copy

Origin of Life


Lynn Margulis and the Serial Endosymbiotic Theory (SET)

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Origin of Life

1. Trace the history of prokaryotic and eukaryotic life on earth as

outlined in the article.

2. What was Wallin’s theory of mitochondrial evolution and why was it rejected at the time?

3. Why does Lynn Margulis believe that endosymbiosis was the result of adaptation to an aerobic environment?

4. What are the basic tenets of the theory of Autogeny? What are

some problems associated with this theory?

5. What evidence is presented in support of the SET?

6. If the assumption that endosymbiosis was the result of adaptation to an aerobic environment turns out to be incorrect, how might it

affect the scientific acceptance of the theory of serial endosymbiosis?

Origin of Life


Evolution of nucleus: role of viruses?!

Virus injecting its gene into a proto-nucleus in a bacterium?

The mimivirus evidence?

See article

introductory topics handout

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