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Study Guide for Final Exam: BIOL 1020/1027: Fall 2021

Unit 1

Chapter 1: Evolution, Themes of Biology, Scientific Inquiry

1.1 The study of life reveals common themes

-Review commonalities of all living organisms: evolution,

order/organization, reproduction, growth and development, energy

processing, internal regulation, response to the environment.

-Biosphere → molecule (and all levels in between)

-Domain → species (and all taxa in between)

1.2 Evolution accounts for the unity and diversity of life

-The central theory of biology is evolution by means of natural selection

-It explains why cilia are the same in lungs and paramecia, for example

-It explains the nested hierarchy of organismal groups (tigers are cats,

carnivores, mammals, vertebrates, animals, and eukaryotes)

1.3 Scientists make observations and form and test hypotheses

-Scientific method: observation, hypothesis, experiment, and analysis

Chapter 2: Chemical context of life

2.1 Matter consists of chemical elements in pure form and in combinations

called compounds

-Notation of elements (C, N, Na), the periodic table, elements most

important for life

2.2 An element’s properties depend on the structure of its atoms

-Subatomic particles (p+, n0,e-): their mass and charge

2.3 Chemical bonds

-interactions between electrons: covalent, polar covalent, ionic,

hydrogen bonds, van der Waals interactions

2.4 Chemical reactions

-making and breaking chemical bonds, dynamic equilibrium

Chapter 3: Water and life

3.1 Polar covalent bonds àhydrogen bonding

3.2 Four emergent properties of water contribute to Earth’s suitability for life

-ice floats, surface tension, specific heat, solvent

3.3 Acids and bases

-Water dissociates into H+ and OH-, pH scale: 0-14, pH=-log10[H+],

acids and bases, buffers, effects of acid precipitation

Chapter 4: Introduction to Organic Chemistry

4.1 Carbon compounds

-“organic” compounds because of role in living organisms, but not

restricted to living organisms (mechanism vs. vitalism)

4.2 Diversity of carbon compounds because of four bonds

-hydrocarbon chains (just carbon and hydrogen) can vary in length of

chain, branching, placement of double bonds, etc.

-types of isomers, structural, cis-trans, enantiomers

4.3 Functional groups

- molecules that change chemistry of organic molecules,

- frequently found in living organisms

-OH, COOH, C=O, -SH, -NH2, -PO4^2- ,CH3

Chapter 5: Structure and function of large biological molecules

5.1 Macromolecules are polymers, built from monomers

- Repeating units make life possible

- Formed by dehydration synthesis, broken down by hydrolysis

5.2 Carbohydrates are fuel and building material

-Monomers: simple sugars, mono- and disaccharides. (CH2O)n is basic

formula, all have carbonyl group (aldoses, ketoses) and carbon

backbone (triose, pentose, hexose)

-Polysaccharides: cellulose (most abundant, used for structure in plants),

glycogen (used for storage in animals) and starch (AKA amylose, used

for storage in plants), chitin (used for structure in fungi and arthropods)

-linkages between monomers may vary, alpha and beta forms

5.3 Lipids are diverse and hydrophobic

-fatty acids (FA) are primarily long hydrocarbon chains with COOH

group.

-FA may have double bonds in cis- or trans- (unsaturated)

-saturated FAs, longer chains, trans-unsaturated more likely to be solid at

room temperature

-Steroids are four-ring lipids, fats are triacylglycerol

-Functions: insulation, long-term energy storage, membranes

(phospholipids), steroids

-not true polymers

5.4 Proteins are diverse and have many functions

-subunits are amino acids (AAs), amine group (NH2) + alpha carbon +

carboxyl group (-COOH) + R-group (substitution on alpha carbon)

-AAs are grouped by chemistry of R-group (polar, nonpolar, charged)

-LOTS of functions! Enzymes, structure, hormones, storage of AAs, etc.

-peptide bonds between COOH and NH2 form primary structure

-hydrogen bonding between peptide bonds in different parts of chain

form secondary structure

-interactions between R-groups form tertiary structure

-interactions between polypeptide chains form quaternary structure

5.5 Nucleic acids store, transmit and express hereditary information

-two types àRNA and DNA

-Monomers are nucleotides= nitrogenous base + 5-C sugar + PO4^2-

-RNA has ribose (AUCG), DNA has deoxyribose (ATCG)

-purines = A,G; pyrimidines = C,T,U

-Sugar phosphate backbone, 5’à3’, antiparallel in DNA

UNIT 2

Chapter 6: Tour of the Cell

6.1 Microscopy and other biochemical tools to study cells

-Compound light microscopes, TEM and SEM

-Centrifugation

6.2 Eukaryotic cells have internal membranes to compartmentalize functions

-Prokaryotes: NO membrane bound organelles, smaller (1-room house)

-Eukaryotes: membrane-bound organelles including nucleus (many-room

house)

6.3 Nucleus and ribosomes

-Nuclear envelope = dbl membrane, contains DNA, nucleolus, pores,

nuclear lamina

-Ribosomes: small and large subunits, may be attached to RER. Different

sized subunits in proks and euks

6.4 Endomembrane system

-Rough endoplasmic reticulum and smooth endoplasmic reticulum (RER

and SER) different functions (what are they?)

-Golgi apparatus (=Golgi bodies), shipping and receiving, cis- and trans-faces.

Stack of pancakes

-Vesicles and vacuoles

6.5 Endosymbiont Theory of mitochondria and chloroplasts

- Both have inner and outer membranes, own DNA and ribosomes,

reproduce independently from other organelles/structures

-mitochondria: the powerhouse of the cell. Cristae, matrix,

intermembrane space, home of Krebs cycle and oxidative

phosphorylation in euks

-chloroplasts: the REAL powerhouse of the cell. Runs on solar energy

(photosynthesis), stacks of thylakoids=grana, made of membranes,

6.6 Cytoskeleton

-Three types of members, all made of structural proteins

-Microtubules: made of alpha and beta tubulin, aid in mitosis, power

flagella and cilia, move vesicles on “monorail”, resist compaction

-Microfilaments: made of actin, muscle contraction (with myosin),

contractile, cortical, cleavage furrow,

-Intermediate filaments: in between, may be made of different proteins

but keratin is typical. Make up nuclear lamina and ECM

6.7 Extracellular components

-junctions: desmosomes, tight junctions, gap junctions, plasmodesmata

-ECM=extra cellular matrix, helps with cell communication and cell

signaling

Chapter 7: Membrane structure and function

7.1 Fluid mosaic model of cell membrane structure

-Phospholipid bilayer studded with proteins

-Proteins function as transporters, cell-cell recognition, signal

transduction, anchoring enzymes together, cell-cell joining, and

anchorage to ECM

7.2 Selective permeability

-Small, non-polar molecules (like gasses) can pass through phospholipid

bilayer

- Polar, charged, and large molecules require transport via protein

channels

-Tonicity: hypotonic =lower solute concentration, isotonic = equal solute

concentration, hypertonic = higher solute concentration.

7.3 Passive transport

-Diffusion is movement from an area of high solute concentration to an

area of lower solute concentration

-Osmosis is diffusion of water across a semipermeable membrane with

its concentration gradient, from hypotonic to hypertonic

-Channel proteins and carrier proteins can allow solute molecules to

pass through without investment of energy as long as they flow with their

concentration gradient (hi to lo)

7.4 Active transport

-Solutes that flow against their concentration gradients require input of

energy, typically through ATP hydrolysis

-Active transport can generate concentration gradients than can do

cellular work (like in oxidative phosphorylation)

7.5 Bulk transport

-Large molecules/particles require energy to move into/out of cell even

with concentration gradient

-Exocytosis= moving out

-Phagocytosis, pinocytosis, receptor-mediated endocytosis = moving in.

Chapter 8: Intro to metabolism

8.1 Laws of thermodynamics

-Energy is limited, so cells must manage energy resources =bioenergetics

-Energy comes in many forms: e.g. kinetic, chemical, electromagnetic,

potential

-Metabolism = all cellular chemical reactions. Anabolism= building up,

catabolism = breaking down

-1st law of thermodynamics: conservation of energy. “Energy can be

transferred or transformed, but it cannot be created or destroyed”

-2nd law of thermodynamics: “Every transfer or transformation of energy

is <100% efficient, and increases the entropy of the universe”

8.2 Gibbs free energy and spontaneous/non-spontaneous reactions

-Gibbs free energy measures the embodied energy of molecules and can

be used to determine if a chemical reaction will happen

spontaneously/exothermically/releasing energy or nonspontaneously/

endothermically/required input of energy. The net

change in Gibbs free energy (ΔG) is negative for exothermic reactions

8.3 ATP powers cellular work

-ATP hydrolysis (breaking off the third PO4

2- group) is a strongly

exothermic reaction (-7.3 kcal/mole). This energy release can make a

net overall endothermic reaction exothermic by producing a

phosphorylated intermediate.

8.4 Enzymes are cellular catalysts

-Enzymes are able to speed up chemical reactions without being

changed in the reaction =catalyst.

-Enzymes function by lowering activation energy (EA), and cannot

change the ΔG for a reaction (because the G for reactants and products

are physical properties)

-Enzymes bind to substrates (reactant molecules) to form an enzyme substrate

complex. In the active site of an enzyme, conditions that speed

up the reaction occur, e.g. change in pH, straining substrate bonds,

aligning substrates.

-Enzymes can be inhibited by molecules in the active site (competitive

inhibition) or away from the active site (noncompetitive inhibition)

8.5 Enzyme regulation controls cell metabolism

-Multipartite enzymes can be regulated ALLOSTERICALLY, away from

the active site, by activation (all active sites function more efficiently) or

inhibition (all active sites function less efficiently), or by cooperativity

(one active sites makes other active sites more efficient)

-Enzymes can be inhibited by their products, or by products of other

enzymes in the metabolic pathway

-Enzymes can also be anchored together in membranes to make

metabolic pathways more efficient

Chapter 9: Cellular respiration and fermentation

9.1 Redox reactions are the essence of catabolism

-REDOX = oxidation-reduction reactions = moving of electrons.

-Oxidation is Loss of electrons, Reduction is Gain of electrons (OIL RIG)

-NAD⁺ is an electron shuttling molecule, NADH is the reduced form

9.2 Glycolysis converts glucose to pyruvate

-Glycolysis is universal, all known organisms perform glycolysis.

-Glycolysis is “sugar splitting”

-Glycolysis requires an investment of 2 ATP to yield 4 ATP.

-Glycolysis has two stages, energy investment and energy payoff

-Reactants are glucose, 2ATP, 2 NAD+

-Products are 2 pyruvate, 4 ATP, 2 NADH 2 H+

9.3 Citric acid cycle completes oxidation of pyruvate

-Pyruvate oxidation (PyrOx) also happens after glycolysis

-PyrOx converts pyruvate into acetyl CoA and moves it into

mitochondrion

-1 molecule of CO2 is released/pyruvate in PyrOx, and 1 molecule of

NADH is produced

-Acetyl CoA introduces the remains of glucose into the Citric Acid Cycle

-Citric Acid Cycle has eight steps, produces two more molecules of CO2,

and yields 1 ATP per turn of the cycle. Also, 2 NADH and 1 FADH2

9.4 Oxidative phosphorylation and chemiosmosis

-OxiPhos uses the electrons from NADH and FADH2 to pump H+ into the

mitochondrion’s intermembrane space using the electron transport chain

(ETC). The protons can only return to the mitochondrial matrix via ATP

synthase, which produces about 28 ATP/glucose. This produces the

most ATP

-Oxygen gas accepts the electrons now depleted in potential energy,

and forms water

9.5 Fermentation and anaerobic respiration

-Both of these occur in the absence of oxygen.

-Fermentation: keeps glycolysis running by putting electrons from NADH

onto pyruvate, producing either lactate, or ethanol and CO2, and

recycling NAD+ back to glycolysis (glycolysis stops, the organism dies)

-Anaerobic respiration includes glycolysis, PyrOx, Krebs cycle, and ETC.

The main difference is the final electron acceptor. It’s not oxygen, but

may be any of a number of different molecules that aren’t as efficient as

oxygen (like sulfate, for example)

Chapter 10: Photosynthesis

10.1 Photosynthesis converts light energy to chemical energy

-Plants, different types of eukaryotic algae (green, red, brown, golden),

cyanobacteria and other types of bacteria are capable of

photosynthesis

-Light energy is part of the spectrum of electromagnetic radiation, which

ranges from high energy, short wavelength (gamma rays) to low

energy, long wavelength (radio waves). Visible light ranges from about

700 nm (violet) to 400 nm (red)

-Photosynthetic pigments include chlorophyll a & b, and carotenoids and

absorb different wavelengths of light, rather than reflecting or

transmitting. Chlorophyll appears green because green light is reflected

and transmitted, not absorbed.

-Red and blue light are the most effective for photosynthesis in plants

10.2 Light reactions convert photons to ATP and NADPH

-Photosynthesis consists of light reactions and Calvin cycle.

-Light reactions occur in thylakoids

-Two photosystems: photosystem II (PSII) and photosystem I (PSI)

-Linear e- flow used both photosystems (II then I). Starts with hydrolysis

(water splitting) to harvest high energy electrons, produces O2 gas

(breathe deeply!) Electrons power ETC to produce proton gradient, to

drive ATP synthase (make ATP), shuttled to PS I, then to ferredoxin (Fd)

and then to NADP+ reductase to NADPH

-Cyclic e- flow only produces ATP, uses PSI. No O2, no NADPH

10.3 Calvin cycle reduces CO2 to sugar

-The Calvin cycle occurs in the stroma

-Rubisco =Ribulose bisphosphate carboxylase-oxygenase, most

abundant enzyme on Earth,

-1. CO2 fixation to ribulose bisphosphate (RuBP, 5 C molecule)

-2. Carbon is reduced by electrons from NADPH (consumes ATP)

-3. 1 molecule of G3P is released and RuBP is regenerated

10.4 Photorespiration happens and plants don’t like it.

-Rubisco evolved in a low O2, high CO2 environment. In high oxygen

concentration (like at present), oxygen competes with carbon dioxide

for the active site of rubisco. Oxygen fixation is a wasteful process:

photorespiration

-C3 plants (typical plants) grow better in cool and humid habitats, but in

hot dry climates, plants need to close stomata, which leads to high O2

concentration inside the leaf

-C4 plants have specialized anatomy that separates O2 and rubisco

spatially.

-CAM plants open stomata at night, fix CO2 into organic acids that

release the CO2 during the daytime: temporal separation of O2 and

rubisco.

UNIT 3: Genetics

Chapter 12: The Cell Cycle

Cell division: know the purposes (reproduction, growth and development,

repair)

Stages of mitosis: the order and what happens in each stage. Prophase,

prometaphase, metaphase, anaphase, telophase (and cytokinesis)

Three parts of interphase: G1, S, G2

Binary fission: cell division in prokaryotes NO MITOSIS IN PROKARYOTES.

Variants of mitosis exist in eukaryotes that aren’t plants or animals that are

somewhere between binary fission and the most derived forms (i.e. in plants

and animals)

Endogenous and exogenous (internal and external) factors in regulating the

cell cycle.

Cytoplasmic factor controls cell cycle, cyclins and cyclin-dependent kinases

(CDKs) form maturation-promoting factor (MPF).

Platelet derived growth factor (PDGF) can stimulate cell division exogenously.

Cells display anchorage dependence and density dependence

Cancer cells may lose anchorage dependence and density dependence. They

can produce their own growth factors or produce growth factors that trigger

other cells to divide (metastasis).

Definitions: Genome, chromosome, chromatin, sister chromatid, somatic cell,

gamete, zygote, centromere, mitosis, cytokinesis, cleavage furrow, cell plate,

kinetochore and nonkinetochore microtubules, CDK, cyclin, MPF, PDGF,

anchorage dependence, density dependence, cancer, transformation, benign,

malignant tumor, metastasis.

Chapter 13. Meiosis and Sexual life cycles

Understand the stages and purposes of meiosis

Understand the different life cycles of eukaryotes (gametic meiosis, zygotic

meiosis, alternation of generations)

Crossing over (synapsis), occurs only during prophase I, anaphase I:

separation of homologous chromosomes. Anaphase II: separation of sister

chromatids.

Understand similarities and differences between mitosis and meiosis.

Crossing over, independent assortment, random fertilization all contribute to

genetic variability

Definitions: Genetics, variation, heredity, meiosis, homologous chromosomes,

genes, gametes, locus (pl. loci), asexual reproduction, clone, sexual

reproduction, somatic cell, karyotype, autosomes, sex chromosomes, haploid,

diploid, zygote, recombinant chromosome

Chapter 14. Mendel and the gene idea.

Particulate vs. blending hypotheses for inheritance.

Gregor Mendel: monk who experimented with garden peas in the mid 1800s.

Why were peas a good model organism?

Law of segregation: two forms of a character (alleles) separate during gamete

formation and are distributed to the gametes. (purple and white flowers)

Law of independent assortment: genes for different traits are not always

inherited together. (round yellow peas and green wrinkled peas)

Know the difference between complete dominance, incomplete dominance,

and codominance. What are pleiotropy and epistasis?

Pedigree analysis can be used to track inheritance patterns in humans. Know

how to interpret a pedigree.

Definitions: trait, character, true-breeding, homozygous, heterozygous,

hybridization, P-generation, F1-generation, F2-generation, alleles, dominant,

recessive, Punnett square, phenotype, genotype, testcross, monohybrid,

dihybrid, complete dominance, incomplete dominance, codominance, multiple

alleles, pleiotropy, epistasis, quantitative characteristics, polygenic inheritance,

multifactorial, pedigree, carrier, sickle-cell allele.

Chapter 15: The chromosomal basis of inheritance.

Thomas Hunt Morgan: geneticist of the early 20th century. Worked with fruit

flies (Drosophila melanogaster) (Why were fruit flies a good model organism?)

Morgan produced many mutant forms of D. melanogaster. The “normal” fruit

flies he called “wild-type”. When he crossed white-eye mutants with red-eyed

wild type flies, he got all red eyed progeny in the F1 generation. The progeny

from the crosses in the F2 generation were 3 red:1 white, but only the males

had white eyes. This suggested that the white-eye gene was located on the X-chromosome.

Fruit flies, like humans, have and XY sex determination schema, but other

organisms do not (what are examples?)

For an X-linked, recessive characteristic, males will express the recessive

phenotype much, much more frequently than females. Examples in humans

include red-green colorblindness and hemophilia.

In females, one copy of the X chromosome is shut off, inactivated, and forms a

Barr body. During development, certain cell lineages in the same organism

will express different phenotypes if she is heterozygous for a locus on the X

chromosomes. This is how we get the calico phenotype in cats and lobsters.

Gene linkage: In a dihybrid cross, Morgan observed ratios of progeny that

differed from Mendel’s expectations.

When he crossed grey-bodied, normal winged flies with black-bodied, vestigial

winged flies, he obtained all grey-bodied, normal winged flies (as predicted by

Mendel for the F1 generation). When he crossed these progeny, he got a very

different ratio of offspring. He concluded that the genes for body color and

wing type were linked together, on the same chromosome.

Alfred Sturtevant (Morgan’s student) developed a linkage map by performing

crossed and calculating recombination frequencies. He discovered four linkage

groups, which provided further evidence for the chromosomal basis of

inheritance (b/c fruit flies have four sets of homologous chromosomes).

Many genetic disorders are the result of errors at the chromosomal level, either

due to entire chromosomes being misassigned to gametes (aneuploidy) or to

damage to parts of chromosomes.

Aneuploidy results when the homologs or sister chromatids are not properly

attached to the microtubules, and one cell receives all or none of the

corresponding chromosome (non-disjunction).

Plants are more tolerant of aneuploidy than animals, and are usually

polyploid.

Trisomy 21 (Down syndrome), Klinefelter syndrome (XXY), Triple X syndrome

(XXX), and Turner syndrome (XO) are all examples of human aneuploid

conditions.

Parts of chromosomes can be deleted, inverted, translocated, or duplicated.

This can lead to structures like Philadelphia chromosomes and conditions such

as cri du chat.

Definitions: chromosomal theory of inheritance, homozygous, heterozygous,

hemizygous, sex-linked gene, X-linked gene, Y-linked gene, Barr body,

recombinant, aneuploidy, nondisjunction, monosomy, trisomy, deletion,

inversion, duplication, translocation, reciprocal translocation.

Chapter 16: The molecular basis of inheritance

Watson and Crick (and Wilkins and Franklin) published on the structure of

DNA as a double helix with the nitrogenous bases hydrogen bonding to each

other in the central part and the sugars and phosphates forming a covalently

bonded backbone

Proof that DNA is the genetic material that can transfer cellular information

chemically.

Griffith: Infected mice with two strains of bacteria, one pathogenic (disease causing,

S strain) and the other harmless (R-strain). Live S strain alone killed

mice. Live R strain alone did not. Heat killed S strain alone did not. Heat

killed S strain + live R strain killed the mice, and Griffith reisolated live S strain.

Conclusion: something in the dead bacteria was being picked up by the live

bacteria and transforming them.

Hershey and Chase: Used radioactively-labeled protein (35S) and DNA (32P) to

infect E. coli bacteria with bacteriophage. Only the P-label was detected in the

bacteria. Conclusion: DNA must be getting into the bacteria and infecting

them, not protein.

Chargaff: discovered different organisms have different ratios of the four

nucleotides, but A=T and G=C. Conclusions: support for DNA as genetic

material and data about composition “Chargaff’s rules”

Watson and Crick: Used X-ray crystallography data from Rosalind Franklin.

They elucidated the structure of DNA as a double helix with a sugar-phosphate

backbone and nitrogenous bases hydrogen bonding in the center. Sugar

phosphate backbones on either side run antiparallel, 5’à3’ on one strand and

3’à5’ on the opposite strand. Purines base-pair with pyrimidines and vise

versa. A and T form two hydrogen bonds, and C and G form three hydrogen

bonds.

Meselson and Stahl: Demonstrated the semiconservative nature of DNA

replication (each strand has new nucleotides added so each replicated

molecule is half old and half new).

DNA replication begins at the origins of replication (ori sites) that are

recognized by the DNA replication machine. A replication bubble opens as

the two strands are pulled apart by helicase and the strands held apart by

single-strand binding proteins. Topoisomerase prevents overwinding of the

DNA, like the strands of a string.

In order to make new DNA, there must be a free 3’-OH group to add the new

nucleotides onto. To do this there must be a short (5-10 nucleotide) primer of

RNA added by the enzyme primase. This produces a free 3’-OH that DNA

polymerase III can build upon. The rate of elongation (adding of nucleotides)

is faster in prokaryotes than eukaryotes. The nucleotides that are added are

deoxyribonucleotide triphosphates (dNTPs), similar to the ATP produced in

cellular respiration only with deoxyribose for the 5 carbon sugar rather than

ribose in ATP. When dNTPs are added, the energy to catalyze the reaction

comes from cleaving off the two terminal phosphates as a molecule of

pyrophosphate.

Chapter 17: Gene expression

Beadle and Tatum’s experiments with Neurospora crassa (bread mold fungus)

demonstrate one geneàone polypeptide hypothesis.

Gene expression: the central dogma of molecular biology. DNA is transcribed

to produce RNA (mRNA), mRNA is translated to produce polypeptide.

The genetic code:

mRNA encodes amino acids (AA) via triplet codeà3 nucleotide words makes

a CODON.

64 combinations of 3 nucleotides (4X4X4), -3 stop codons (UAA, UAG, UGA)

and 1 start codon (AUG, also encodes AA methionine)

There is redundancy but no overlap in AA coding

The code is almost universal; any organism can express a gene from any other

organism.

Differences between prokaryotic and eukaryotic gene expression

Transcription and translation are spatially separated in euks

Transcription and translation are simultaneous in proks.

Transcription: DNAàmRNA

Initiationàelongationàtermination

Promoter region is bound by transcription factors that bind RNA polymerase II,

RNA pol II reads the template strand of the DNA in the 3’à5’ direction and

makes a complementary RNA strand in the 5’à3’ direction

Prokaryotes have a terminator sequence to terminate transcription

Eukaryotes have a polyadenylation signal (-AAAAAAAAAAAA)

Post-transcriptional processing in euks

Polyadenylation

G-capping at 5’ end

Splicing of introns by snRNPs and the spliceosome

Alternate splicing leads to different gene products (doesn’t happen in proks)

Translation

Occurs at ribosomes in cytoplasm

Also, Initiationàelongationàtermination

tRNA carries amino acids and has anticodons that complement codons in

mRNA

Ribosomes made up of protein and rRNA, have small and large subunits.

Three sites in large subunit, A-amino; P-peptide, and E-exit. mRNA is read in

5’à3’ direction

Mutations

Point mutations affect one or a few nucleotides

Single nucleotide changes may result in silent, missense, or nonsense mutation

INDELs may cause frameshift mutations (affecting every AA downstream from

the mutation)

Unit 4: Evolution -Study Guide

Chapter 22: A Darwinian View of Life

22.1 The Darwinian revolution challenged traditional views of a young Earth

inhabited by unchanging species

Darwin’s predecessors and contemporaries: Aristotle and the Old Testament claim that

species are fixed (unchanging). Linnaeus -taxonomy. Cuvier –paleontology and

catastrophism. Hutton and Lyell –geology and uniformitarianism. Lamarck –evolution

by means of acquired characteristics. Malthus –population growth in humans. A.R.

Wallace –biogeography and similar ideas to Darwin.

22.2 Descent with modification by natural selection explains the adaptations of

organisms and the unity and diversity of life

Darwin’s voyage on HMS Beagle influenced his ideas that would lead him to write

“Origin”. His focus was on adaptation, or “descent with modification”.

Darwin’s theory explains: the unity of life, the diversity of life, and the match between

organisms and their environment.

Darwin viewed the history of life as a tree with the branches indicating shared

common ancestry (“I think” figure, elephant phylogeny [family tree])

He also looked at artificial selection (human modification of plant and animal species)

Two observations lead Darwin to two inferences which are the crux of his theory.

O1. Members of a population vary in their inherited traits. O2. All species are

capable of producing more offspring than the environment can support, and most

offspring fail to survive and reproduce. Therefore, I1. Individuals whose inherited

traits give them a higher likelihood of surviving and reproducing will tend to leave

more offspring than individuals lacking those heritable traits, and I2. Differential

reproduction will lead to the accumulation of favorable traits over generations.

22.3 Evolution is supported by an overwhelming amount of scientific evidence

DIRECT OBSERVATION OF EVOLUTIONARY CHANGE: MRSA (methicillin resistant

Staphylococcus aureus)

HOMOLOGY: Similarity in structure (anatomical, physiological, molecular,

behavioral) resulting from shared common ancestry. E.g. forelimb structure in different

mammals (cat, bat, whale, human). Comparative embryology reveals anatomical

homologies and vestigial structures not seen in adults such as pharyngeal pouches and

a post-anal tail.

ANALOGY: Similarity in structure due to convergent evolution, NOT shared common

ancestry. Analogy occurs when similar environments enforce similar adaptive

constraints, e.g. flying squirrels and sugar gliders in the US and Australia, or cactuses

and euphorbs in deserts in N. America and Africa.

FOSSILS: An extensive fossil record shows the origin of new groups, extinctions, and

transitions within groups. E.g. the transition of cetaceans (whales and dolphins) from

land to sea.

BIOGEOGRAPHY: The geographic distribution of species provides evidence for

evolution. E.g., the genus of oaks (Quercus) has radiated into 100s of oak species

distributed throughout the northern hemisphere. Endemism occurs when a species is

found only a certain area. E.g. the watercress darter (Etheostoma nuchale) is a fish

that is endemic to the Black Warrior River of Alabama. Islands frequently have many

endemic species.

Chapter 23: Evolution of Populations

The population is the smallest unit of evolution. Microevolution is the change in allele

frequencies in a population over generations and it is driven by two random factors

(genetic drift and gene flow) and a non-random factor: natural selection.

23.1 Genetic variation makes evolution possible

Genetic variation occurs due to changes in the nucleotide sequences in DNA.

Variation can be discrete (all or none: purple/white) or quantitative (occurring along

a spectrum: height). There are many ways to measure genetic variation in a

population, such as average heterozygosity or nucleotide variability.

New alleles for genes form via mutation (silent, missense, nonsense) or gene

duplication.

23.2 The Hardy-Weinberg (HW) equation can be used to test whether a population is

evolving

The HW principle describes a situation where a population is NOT evolving and allele

and genotypic frequencies DO NOT change from one generation to another. It is a

NULL MODEL (meaning it is a useful way to describe a population that is NOT

evolving). For a gene to be maintained at HW equilibrium, five conditions must be

met:

1. No mutations

2. Random mating (no sexual selection)

3. No gene flow (no immigration or emigration)

4. No genetic drift (large population size)

5. No natural selection

23.3 Natural selection, genetic drift, and gene flow can alter allele frequencies in a

population

The three biggest contributors to shifts in allele frequencies (microevolution) are

natural selection, genetic drift, and gene flow.

NATURAL SELECTION increases the frequency of beneficial alleles, and diminishes the

frequency of harmful alleles (see Ch. 22).

GENETIC DRIFT (GD) is the result of a random decrease in population size, typically

through founder effect or genetic bottleneck. The smaller a sample from a parent

population, the greater the deviation in allele frequency. Alleles may be lost from a

population. The founder effect occurs when a new small number of individuals leave

a large population and start a new population in a new location, like an island. A

genetic bottleneck may occur when populations become fragmented or a catastrophic

event randomly destroys a large number of individuals in a population.

GD is most significant in small popualtions. GD causes random changes in allele

frequency. GD can lead to loss of genetic diversity and allele fixation (only one allele

for a gene present in the population)

GENE FLOW (GF) is the spread of alleles throughout a population and between

populations. It can increase or decrease the fitness of a population, but it is a random

process.

23.4 Natural selection is the only mechanism that consistently causes adaptive

evolution

Mutation, GD and GF are random processes that contribute to changes in allele

frequency in population. Natural selection is NOT RANDOM.

NOTE: DARWIN did NOT coin the phrase “survival of the fittest”. Survival and

reproduction together comprise fitness, so the term is circular, and implies a “high-bar”

for fitness. Survival of the fit-enough also applies.

Three modes of selection are typical when allele frequencies shift: directional,

disruptive, and stabilizing. Know the differences.

Sexual selection leads to mating success and can lead to sexual dimorphism (male

and female appear different).

Genetic variation can be preserved by diploidy or balancing selection.

Chapter 24: The Origin of Species

Speciation =origin of new species =divergence of old species

24.1 The biological species concept (BSC) emphasizes reproductive isolation

A biological species is “is a group of populations whose members have the potential

to interbreed in nature and produce viable, fertile offspring; they do not breed

successfully with other populations”. The key to species membership is GENE FLOW.

Species are kept distinct by REPRODUCTIVE ISOLATION, though HYBRIDS may

occur. Reproductive isolation is classified as PRE-ZYGOTIC or POST-ZYGOTIC.

PRE-ZYGOTIC: Habitat isolation, temporal isolation, behavioral isolation, mechanical

isolation, gametic isolation.

POST-ZYGOTIC: Reduced hybrid viability, reduced hybrid fertility, hybrid breakdown

BSC is limited in that it can’t resolve organisms that are asexual or extinct. Other

species concepts include morphological species concept, ecological species concept,

and phylogenetic species concept.

24.2 Speciation can take place with or without geographic separation

Allopatric (other country) vs. sympatric (same country) speciation

Allopatric speciation is much more common. Allopatric barriers not universal but

depend on species

Regions with more geographic barriers tend to be more biodiverse.

Sympatric speciation may result from polyploidy (autopolyploidy or allopolyploidy),

habitat differentiation, or sexual selection

Chapter 53. Intro to Ecology/Population Ecology

At the end of this chapter, you should be able to:

1. Define ecology

2. Describe the levels of specialization within ecology (global àorganismal)

3. Define density, dispersion, demographics,

4. Contrast the most common dispersion patterns and the underlying biological

principles that produce them