chapter 16- end review. fig. 16-7 (c) space-filling model hydrogen bond 3 end 5 end 3.4 nm 0.34 nm 3...

Chapter 16- endREVIEW

Fig. 16-7

(c) Space-filling model

Hydrogen bond 3 end

3.4 nm

0.34 nm

(b) Partial chemical structure

(a) Key features of DNA structure

Fig. 16-9-3

(a) Parent molecule

(c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand

(b) Separation of strands

Fig. 16-12Origin of replication

Parental (template) strand Daughter (new) strand

Replication forkReplication bubble

Two daughter DNA molecules(a) Origins of replication in E. coliOrigin of replicationDouble-stranded DNA

moleculeParental (template) strandDaughter (new) strand

Bubble Replication fork

Two daughter DNA molecules(b) Origins of replication

in eukaryotes

0.5 µm

0.25 µm

Double-strandedDNA molecule

Fig. 16-17

OverviewOrigin of replicationLeading strand

Leading strand

Lagging strand

Lagging strandOverall

directions of

replicationLeading strand

Lagging strand

Helicase

Parental DNA

DNA pol III

PrimerPrimase

DNA ligase

DNA pol IIIDNA pol I

Single-strand

binding protein

Fig. 16-19Ends of parental DNA strands

Leading strand

Lagging strand

Last fragment Previous fragment

Parental strand

RNA primer

Removal of primers and replacement with DNA where a 3 end is available

Second round of replication

New leading strand

New lagging strand

Further rounds of replication

Shorter and shorter daughter molecules

Fig. 17-3

TRANSCRIPTION

TRANSLATION

mRNARibosome

Polypeptide

(a) Bacterial cell

Nuclearenvelope

TRANSCRIPTION

RNA PROCESSINGPre-mRNA

TRANSLATION Ribosome

Polypeptide

(b) Eukaryotic cell

Fig. 17-4

DNAmolecule

Gene 1

Gene 2

Gene 3

DNAtemplatestrand

TRANSCRIPTION

TRANSLATION

Protein

Amino acid

Fig. 17-7

Promoter Transcription unit

Start pointDNA

RNA polymerase

Initiation1

UnwoundDNA

RNAtranscript

Template strandof DNA

Elongation

RewoundDNA

RNAtranscript

Termination

35Completed RNA transcript

Newly madeRNA

Templatestrand of DNA

Direction oftranscription(“downstream”)

RNApolymerase

RNA nucleotides

Nontemplatestrand of DNA

Elongation

Fig. 17-8A eukaryotic promoterincludes a TATA box

Promoter

TATA box Start point

Template

TemplateDNA strand

Transcriptionfactors

Several transcription factors mustbind to the DNA before RNApolymerase II can do so.

Additional transcription factors bind tothe DNA along with RNA polymerase II,forming the transcription initiation complex.

RNA polymerase IITranscription factors

RNA transcript

Transcription initiation complex

Fig. 17-10

Pre-mRNA

Codingsegment

Introns cut out andexons spliced together

Exon Intron5

1 30 31 104

Exon Intron

3Poly-A tail

Poly-A tail5 Cap

5 UTR 3 UTR1 146

Fig. 17-17

ACGMet

GTP GDPInitiator

mRNA5 3

Start codon

mRNA binding siteSmallribosomalsubunit

P site

Translation initiation complex

Largeribosomalsubunit

Fig. 17-18-4

Amino endof polypeptide

GDPGTP

Ribosome ready fornext aminoacyl tRNA

Fig. 17-19-3

Releasefactor

5Stop codon(UAG, UAA, or UGA)

Freepolypeptide

Fig. 17-21

Ribosome

Signalpeptide

Signal-recognitionparticle (SRP)

CYTOSOL Translocationcomplex

SRPreceptorprotein

ER LUMEN

Signalpeptideremoved

ERmembrane

Protein

Fig. 17-23Wild-type

3DNA template strand5

Carboxyl endAmino end

Protein

A instead of G

U instead of C

Silent (no effect on amino acid sequence)

T instead of C

A instead of G

Missense

A instead of T

U instead of A

Nonsense No frameshift, but one amino acid missing (3 base-pair deletion)

Frameshift causing extensive missense (1 base-pair deletion)

Frameshift causing immediate nonsense (1 base-pair insertion)

missing

Extra U

Extra A

(a) Base-pair substitution (b) Base-pair insertion or deletion

Fig. 17-24RNA polymerase

Polyribosome

0.25 µmDirection oftranscription

RNApolymerase

Polyribosome

Polypeptide(amino end)

Ribosome

mRNA (5 end)

Fig. 17-25

TRANSCRIPTION

RNA PROCESSING

RNAtranscript

5RNApolymerase

Poly-A

RNA transcript(pre-mRNA)

Intron

NUCLEUS

Aminoacyl-tRNAsynthetase

AMINO ACID ACTIVATIONAminoacid

tRNACYTOPLASM

Poly-A

Growingpolypeptide

Activatedamino acid

TRANSLATION

Ribosomalsubunits

AAnticodon

Ribosome

Fig. 18-3

Polypeptide subunits that make upenzymes for tryptophan synthesis

(b) Tryptophan present, repressor active, operon off

Tryptophan(corepressor)

(a) Tryptophan absent, repressor inactive, operon on

No RNA made

Activerepressor

Protein

mRNA 5

Protein Inactiverepressor

RNApolymerase

Regulatorygene

Promoter Promoter

trp operon

Genes of operon

OperatorStop codonStart codon

trpR trpE trpD trpC trpB

Fig. 18-3a

Polypeptide subunits that make upenzymes for tryptophan synthesis

(a) Tryptophan absent, repressor inactive, operon on

mRNA 5

Protein Inactiverepressor

RNApolymerase

Regulatorygene

Promoter Promoter

trp operon

Genes of operon

OperatorStop codonStart codon

trpR trpE trpD trpC trpB

Fig. 18-3b-1

No RNA made

Activerepressor

Protein

Fig. 18-3b-2

No RNA made

Activerepressor

Protein

Fig. 18-4

(b) Lactose present, repressor inactive, operon on

(a) Lactose absent, repressor active, operon off

Protein

mRNA 5

Protein Activerepressor

RNApolymerase

Regulatorygene

Promoter

Operator

Inactiverepressor

Allolactose(inducer)

NoRNAmade

RNApolymerase

Permease Transacetylase

lac operon

-Galactosidase

lacYlacZ lacAlacI

lacI lacZ

Fig. 18-4a

(a) Lactose absent, repressor active, operon off

ProteinActiverepressor

RNApolymerase

Regulatorygene

Promoter

Operator

NoRNAmade

lacI lacZ

Fig. 18-4b

(b) Lactose present, repressor inactive, operon on

Protein

mRNA 5

Inactiverepressor

Allolactose(inducer)

RNApolymerase

Permease Transacetylase

lac operon

-Galactosidase

lacYlacZ lacAlacI

Repressible and Inducible Operons: Two Types of Negative Gene Regulation

• A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription

• The trp operon is a repressible operon• An inducible operon is one that is usually off; a

molecule called an inducer inactivates the repressor and turns on transcription

• The lac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose

• By itself, the lac repressor is active and switches the lac operon off

• A molecule called an inducer inactivates the repressor to turn the lac operon on

• Inducible enzymes usually function in catabolic pathways; their synthesis is induced by a chemical signal

• Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high levels of the end product

• Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor

Positive Gene Regulation

• Some operons are also subject to positive control through a stimulatory protein, such as catabolite activator protein (CAP), an activator of transcription

• When glucose (a preferred food source of E. coli) is scarce, CAP is activated by binding with cyclic AMP

• Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription

• When glucose levels increase, CAP detaches from the lac operon, and transcription returns to a normal rate

• CAP helps regulate other operons that encode enzymes used in catabolic pathways

Fig. 18-5

(b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized

Inactive lacrepressor

Allolactose

InactiveCAP

CAP-binding site

Promoter

ActiveCAP

Operator

lacZRNApolymerasebinds andtranscribes

Inactive lacrepressor

OperatorPromoter

CAP-binding site

RNApolymerase lesslikely to bind

InactiveCAP

(a) Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized

Fig. 18-6

Signal

NUCLEUS

Chromatin modification

Chromatin

Gene availablefor transcription

Intron

RNA processing

Primary transcript

mRNA in nucleus

Transport to cytoplasm

mRNA in cytoplasm

Translation

CYTOPLASM

Degradationof mRNA

Protein processing

Polypeptide

Active protein

Cellular function

Transport to cellulardestination

Degradationof protein

Transcription

Fig. 18-6a

Signal

NUCLEUS

Chromatin

Intron

RNA processing

Primary transcript

mRNA in nucleus

CYTOPLASM

Transcription

Fig. 18-6b

mRNA in cytoplasm

Translation

CYTOPLASM

Degradationof mRNA

Protein processing

Polypeptide

Active protein

Cellular function

Fig. 18-6

Signal

NUCLEUS

Chromatin

Intron

RNA processing

Primary transcript

mRNA in nucleus

mRNA in cytoplasm

Translation

CYTOPLASM

Degradationof mRNA

Protein processing

Polypeptide

Active protein

Cellular function

Transcription

Fig. 18-6a

Signal

NUCLEUS

Chromatin

Intron

RNA processing

Primary transcript

mRNA in nucleus

CYTOPLASM

Transcription

Fig. 18-6b

mRNA in cytoplasm

Translation

CYTOPLASM

Degradationof mRNA

Protein processing

Polypeptide

Active protein

Cellular function

• Proximal control elements are located close to the promoter

• Distal control elements, groups of which are called enhancers, may be far away from a gene or even located in an intron

Enhancers and Specific Transcription Factors

• An activator is a protein that binds to an enhancer and stimulates transcription of a gene

• Bound activators cause mediator proteins to interact with proteins at the promoter

Animation: Initiation of Transcription

Fig. 18-9-1

Enhancer TATAbox

PromoterActivators

DNAGene

Distal controlelement

Fig. 18-9-2

Enhancer TATAbox

PromoterActivators

DNAGene

Group ofmediator proteins

DNA-bendingprotein

Generaltranscriptionfactors

Fig. 18-9-3

Enhancer TATAbox

PromoterActivators

DNAGene

Group ofmediator proteins

DNA-bendingprotein

Generaltranscriptionfactors

RNApolymerase II

Transcriptioninitiation complex RNA synthesis

Fig. 18-10

Controlelements

Enhancer

Availableactivators

Albumin gene

(b) Lens cell

Crystallin geneexpressed

Availableactivators

LENS CELLNUCLEUS

LIVER CELLNUCLEUS

Crystallin gene

Promoter

(a) Liver cell

Crystallin genenot expressed

Albumin geneexpressed

Albumin genenot expressed

Fig. 18-11

RNA splicing

PrimaryRNAtranscript

Troponin T gene

Protein Processing and Degradation

• After translation, various types of protein processing, including cleavage and the addition of chemical groups, are subject to control

• Proteasomes are giant protein complexes that bind protein molecules and degrade them

Animation: Protein Degradation

Animation: Protein Processing

Fig. 18-12

Proteasomeand ubiquitinto be recycledProteasome

Proteinfragments(peptides)Protein entering a

proteasome

Ubiquitinatedprotein

Protein tobe degraded

Ubiquitin

Structure of Viruses

• Viruses are not cells• Viruses are very small infectious particles consisting

of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope

Fig. 19-3

Capsomere

Capsomereof capsid

Glycoprotein18 250 nm 70–90 nm (diameter)

Glycoproteins

80–200 nm (diameter) 80 225 nm

Membranousenvelope RNA

Capsid

HeadDNA

Tailsheath

Tailfiber

50 nm50 nm50 nm20 nm(a) Tobacco mosaic virus

(b) Adenoviruses (c) Influenza viruses (d) Bacteriophage T4

Concept 19.2: Viruses reproduce only in host cells

• Viruses are obligate intracellular parasites, which means they can reproduce only within a host cell

• Each virus has a host range, a limited number of host cells that it can infect

Transcriptionand manufactureof capsid proteins

Self-assembly of new virus particles and their exit from the cell

Entry anduncoating

Fig. 19-4VIRUS1

Capsid

Replication

HOST CELL

Viral DNA

Capsidproteins

Viral DNA

Fig. 19-6

PhageDNA

The phage injects its DNA.

Bacterialchromosome

Phage DNAcircularizes.

Daughter cellwith prophage

Occasionally, a prophageexits the bacterialchromosome,initiating a lytic cycle.

Cell divisionsproducepopulation ofbacteria infectedwith the prophage.

The cell lyses, releasing phages.

Lytic cycle

Lytic cycleis induced or Lysogenic cycle

is entered

Lysogenic cycle

Prophage

The bacterium reproduces,copying the prophage andtransmitting it to daughter cells.

Phage DNA integrates intothe bacterial chromosome,becoming a prophage.

New phage DNA and proteinsare synthesized andassembled into phages.

Fig. 19-7

Capsid

Envelope (withglycoproteins)

Capsid and viral genomeenter the cell

HOST CELL

Viral genome (RNA)

Template

Glyco-proteins

Capsidproteins Copy of

genome (RNA)

New virus

Fig. 19-8aGlycoprotein

Reversetranscriptase HIV

RNA (twoidenticalstrands)

Capsid

Viral envelope

HOST CELL

Reversetranscriptase

Viral RNA

RNA-DNAhybrid

NUCLEUS

Provirus

ChromosomalDNA

RNA genomefor thenext viralgeneration

New virus

Evolution of Viruses

• Viruses do not fit our definition of living organisms• Since viruses can reproduce only within cells, they

probably evolved as bits of cellular nucleic acid• Candidates for the source of viral genomes are

plasmids, circular DNA in bacteria and yeasts, and transposons, small mobile DNA segments

• Plasmids, transposons, and viruses are all mobile genetic elements

Overview: The DNA Toolbox• Sequencing of the human genome was completed

by 2007• DNA sequencing has depended on advances in

technology, starting with making recombinant DNA• In recombinant DNA, nucleotide sequences from

two different sources, often two species, are combined in vitro into the same DNA molecule

• Methods for making recombinant DNA are central to genetic engineering, the direct manipulation of genes for practical purposes

• DNA technology has revolutionized biotechnology, the manipulation of organisms or their genetic components to make useful products

• An example of DNA technology is the microarray, a measurement of gene expression of thousands of different genes

• Gene cloning involves using bacteria to make multiple copies of a gene

• Foreign DNA is inserted into a plasmid, and the recombinant plasmid is inserted into a bacterial cell

• Reproduction in the bacterial cell results in cloning of the plasmid including the foreign DNA

• This results in the production of multiple copies of a single gene

Fig. 20-2

DNA of chromosome

Cell containing geneof interest

Gene inserted intoplasmid

Plasmid put intobacterial cell

RecombinantDNA (plasmid)

Recombinantbacterium

Bacterialchromosome

Bacterium

Gene ofinterest

Host cell grown in cultureto form a clone of cellscontaining the “cloned”gene of interest

Plasmid

Gene ofInterest

Protein expressedby gene of interest

Basic research andvarious applications

Copies of gene Protein harvested

Basicresearchon gene

Basicresearchon protein

Gene for pest resistance inserted into plants

Gene used to alter bacteria for cleaning up toxic waste

Protein dissolvesblood clots in heartattack therapy

Human growth hor-mone treats stuntedgrowth

Using Restriction Enzymes to Make Recombinant DNA

• Bacterial restriction enzymes cut DNA molecules at specific DNA sequences called restriction sites

• A restriction enzyme usually makes many cuts, yielding restriction fragments

• The most useful restriction enzymes cut DNA in a staggered way, producing fragments with “sticky ends” that bond with complementary sticky ends of other fragments

Animation: Restriction Enzymes

Fig. 20-3-3Restriction site

Sticky end

Restriction enzymecuts sugar-phosphatebackbones.

One possible combination

Recombinant DNA molecule

DNA ligaseseals strands.

DNA fragment addedfrom another moleculecut by same enzyme.Base pairing occurs.

Fig. 20-5

Bacterial clones

Recombinantplasmids

Recombinantphage DNA

Foreign genomecut up withrestrictionenzyme

(a) Plasmid library (b) Phage library (c) A library of bacterial artificial chromosome (BAC) clones

Phageclones

Large plasmidLarge insertwith many genes

BACclone

Fig. 20-6-5

DNA innucleus

mRNAs in cytoplasm

Reversetranscriptase Poly-A tail

DNAstrand

Primer

DegradedmRNA

DNA polymerase

• A probe can be synthesized that is complementary to the gene of interest

• For example, if the desired gene is

– Then we would synthesize this probe G5 3… …G GC C CT T TA A A

C3 5C CG G GA A AT T T

Fig. 20-85

Genomic DNA

TECHNIQUE

Cycle 1yields

2molecules

Denaturation

Annealing

Extension

Cycle 2yields

4molecules

Cycle 3yields 8

molecules;2 molecules

(in whiteboxes)

match targetsequence

Targetsequence

Primers

Newnucleo-tides

Fig. 20-9a

Mixture ofDNA mol-ecules ofdifferentsizes

Powersource

Longermolecules

Shortermolecules

AnodeCathode

TECHNIQUE

Powersource

Fig. 20-10

Normalallele

Sickle-cellallele

Largefragment

(b) Electrophoresis of restriction fragments from normal and sickle-cell alleles

201 bp175 bp

376 bp

(a) DdeI restriction sites in normal and sickle-cell alleles of -globin gene

Normal -globin allele

Sickle-cell mutant -globin allele

Large fragment

376 bp

201 bp175 bp

DdeIDdeI

DdeI DdeI DdeI DdeI

Fig. 20-11TECHNIQUE

Nitrocellulosemembrane (blot)

Restrictionfragments

Alkalinesolution

DNA transfer (blotting)

Sponge

Heavyweight

Papertowels

Preparation of restriction fragments Gel electrophoresis

I II III

I II IIII II III

Radioactively labeledprobe for -globin gene

DNA + restriction enzyme

III HeterozygoteII Sickle-cellallele

I Normal-globinallele

Film overblot

Probe detectionHybridization with radioactive probe

Fragment fromsickle-cell-globin allele

Fragment fromnormal -globin allele

Probe base-pairswith fragments

Nitrocellulose blot

DNA Sequencing• Relatively short DNA fragments can be sequenced

by the dideoxy chain termination method

• Modified nucleotides called dideoxyribonucleotides (ddNTP) attach to synthesized DNA strands of different lengths

• Each type of ddNTP is tagged with a distinct fluorescent label that identifies the nucleotide at the end of each DNA fragment

• The DNA sequence can be read from the resulting spectrogram

Fig. 20-12

DNA(template strand)

TECHNIQUE

RESULTS

DNA (template strand)

DNA polymerase

Primer Deoxyribonucleotides

Shortest

Dideoxyribonucleotides(fluorescently tagged)

Labeled strands

Longest

Shortest labeled strand

Longest labeled strand

Directionof movementof strands

Detector

Last baseof longest

labeledstrand

Last baseof shortest

labeledstrand

Fig. 20-12a

DNA(template strand)

TECHNIQUE

DNA polymerase

Primer Deoxyribonucleotides Dideoxyribonucleotides(fluorescently tagged)

Fig. 20-12bTECHNIQUE

RESULTS

DNA (template strand)

Shortest

Labeled strands

Longest

Shortest labeled strand

Longest labeled strand

Directionof movementof strands

Detector

Last baseof longest

labeledstrand

Last baseof shortest

labeledstrand

Studying the Expression of Single Genes

• Changes in the expression of a gene during embryonic development can be tested using– Northern blotting– Reverse transcriptase-polymerase chain reaction

• Both methods are used to compare mRNA from different developmental stages

• Northern blotting combines gel electrophoresis of mRNA followed by hybridization with a probe on a membrane

• Identification of mRNA at a particular developmental stage suggests protein function at that stage

• Reverse transcriptase-polymerase chain reaction (RT-PCR) is quicker and more sensitive

• Reverse transcriptase is added to mRNA to make cDNA, which serves as a template for PCR amplification of the gene of interest

• The products are run on a gel and the mRNA of interest identified

Fig. 20-13

TECHNIQUE

RESULTS

Gel electrophoresis

-globingene

PCR amplification

Embryonic stages

Primers

1 2 3 4 5 6

mRNAscDNA synthesis 1

Identifying Protein-Coding Genes Within DNA Sequences

• Computer analysis of genome sequences helps identify sequences likely to encode proteins

• Comparison of sequences of “new” genes with those of known genes in other species may help identify new genes

Understanding Genes and Their Products at the Systems Level

• Proteomics is the systematic study of all proteins encoded by a genome

• Proteins, not genes, carry out most of the activities of the cell

Concept 21.5: Duplication, rearrangement, and mutation of DNA contribute to genome evolution

• The basis of change at the genomic level is mutation, which underlies much of genome evolution

• The earliest forms of life likely had a minimal number of genes, including only those necessary for survival and reproduction

• The size of genomes has increased over evolutionary time, with the extra genetic material providing raw material for gene diversification

Alterations of Chromosome Structure

• Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs

• Following the divergence of humans and chimpanzees from a common ancestor, two ancestral chromosomes fused in the human line

• Duplications and inversions result from mistakes during meiotic recombination

• Comparative analysis between chromosomes of humans and 7 mammalian species paints a hypothetical chromosomal evolutionary history

Rearrangements of Parts of Genes: Exon Duplication and Exon Shuffling

• The duplication or repositioning of exons has contributed to genome evolution

• Errors in meiosis can result in an exon being duplicated on one chromosome and deleted from the homologous chromosome

• In exon shuffling, errors in meiotic recombination lead to some mixing and matching of exons, either within a gene or between two nonallelic genes

Darwin’s Focus on Adaptation

• In reassessing his observations, Darwin perceived adaptation to the environment and the origin of new species as closely related processes

• From studies made years after Darwin’s voyage, biologists have concluded that this is indeed what happened to the Galápagos finches

Fig. 22-6

(a) Cactus-eater (c) Seed-eater

(b) Insect-eater

Descent with Modification

• Darwin never used the word evolution in the first edition of The Origin of Species

• The phrase descent with modification summarized Darwin’s perception of the unity of life

• The phrase refers to the view that all organisms are related through descent from an ancestor that lived in the remote past

• In the Darwinian view, the history of life is like a tree with branches representing life’s diversity

• Darwin’s theory meshed well with the hierarchy of Linnaeus

Fig. 22-8a

Elephas maximus(Asia)

Stegodon

Mammuthus

Loxodontaafricana(Africa)

Loxodonta cyclotis(Africa)

010425.52434

Millions of years ago Years ago

Platybelodon

Artificial Selection, Natural Selection, and Adaptation

• Darwin noted that humans have modified other species by selecting and breeding individuals with desired traits, a process called artificial selection

• Darwin then described four observations of nature and from these drew two inferences

Fig. 22-9

Kohlrabi

Brussels sprouts

Leaves

Wild mustard

Flowersand stems

Broccoli

Cauliflower

Flowerclusters

Cabbage

Terminalbud

Lateralbuds

• Observation #1: Members of a population often vary greatly in their traits

• Observation #2: Traits are inherited from parents to offspring

• Observation #3: All species are capable of producing more offspring than the environment can support

• Observation #4: Owing to lack of food or other resources, many of these offspring do not survive

• Inference #1: Individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more offspring than other individuals

• Inference #2: This unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations

Natural Selection: A Summary

• Individuals with certain heritable characteristics survive and reproduce at a higher rate than other individuals

• Natural selection increases the adaptation of organisms to their environment over time

• If an environment changes over time, natural selection may result in adaptation to these new conditions and may give rise to new species

Video: Seahorse Camouflage

• Note that individuals do not evolve; populations evolve over time

• Natural selection can only increase or decrease heritable traits in a population

• Adaptations vary with different environments

The Fossil Record

• The fossil record provides evidence of the extinction of species, the origin of new groups, and changes within groups over time

Fig. 22-15

Bristolia insolens

Bristolia bristolensis

Bristolia harringtoni

Bristolia mohavensis

Latham Shale dig site, SanBernardino County, California

Fig. 22-17

Humerus

Radius

Carpals

Metacarpals

Phalanges

Human WhaleCat Bat

Fig. 22-18

Human embryoChick embryo (LM)

Pharyngealpouches

Post-analtail

Fig. 22-19

Hawks andother birds

Ostriches

Crocodiles

Lizardsand snakes

Amphibians

Mammals

Lungfishes

Tetrapod limbs

Amnion

Feathers

Homologouscharacteristic

Branch point(common ancestor)

Tetrapo

Convergent Evolution

• Convergent evolution is the evolution of similar, or analogous, features in distantly related groups

• Analogous traits arise when groups independently adapt to similar environments in similar ways

• Convergent evolution does not provide information about ancestry

Fig. 22-20

Sugarglider

Flyingsquirrel

AUSTRALIA

NORTHAMERICA

Overview: The Smallest Unit of Evolution

• One misconception is that organisms evolve, in the Darwinian sense, during their lifetimes

• Natural selection acts on individuals, but only populations evolve

• Genetic variations in populations contribute to evolution

• Microevolution is a change in allele frequencies in a population over generations

• Two processes, mutation and sexual reproduction, produce the variation in gene pools that contributes to differences among individuals

Concept 23.1: Mutation and sexual reproduction produce the genetic variation that makes evolution possible

• Population geneticists measure polymorphisms in a population by determining the amount of heterozygosity at the gene and molecular levels

• Average heterozygosity measures the average percent of loci that are heterozygous in a population

• Nucleotide variability is measured by comparing the DNA sequences of pairs of individuals

Mutation

• Mutations are changes in the nucleotide sequence of DNA

• Mutations cause new genes and alleles to arise• Only mutations in cells that produce gametes can

be passed to offspring

Animation: Genetic Variation from Sexual Recombination

Gene Pools and Allele Frequencies

• A population is a localized group of individuals capable of interbreeding and producing fertile offspring

• A gene pool consists of all the alleles for all loci in a population

• A locus is fixed if all individuals in a population are homozygous for the same allele

Hardy-Weinberg Equilibrium

• The Hardy-Weinberg principle states that frequencies of alleles and genotypes in a population remain constant from generation to generation

• In a given population where gametes contribute to the next generation randomly, allele frequencies will not change

• Mendelian inheritance preserves genetic variation in a population

• Hardy-Weinberg equilibrium describes the constant frequency of alleles in such a gene pool

• If p and q represent the relative frequencies of the only two possible alleles in a population at a particular locus, then– p2 + 2pq + q2 = 1– where p2 and q2 represent the frequencies of the

homozygous genotypes and 2pq represents the frequency of the heterozygous genotype

• The five conditions for nonevolving populations are rarely met in nature:– No mutations – Random mating – No natural selection – Extremely large population size– No gene flow

• Three major factors alter allele frequencies and bring about most evolutionary change:– Natural selection– Genetic drift– Gene flow

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

The Founder Effect

• The founder effect occurs when a few individuals become isolated from a larger population

• Allele frequencies in the small founder population can be different from those in the larger parent population

The Bottleneck Effect

• The bottleneck effect is a sudden reduction in population size due to a change in the environment

• The resulting gene pool may no longer be reflective of the original population’s gene pool

• If the population remains small, it may be further affected by genetic drift

Gene Flow

• Gene flow consists of the movement of alleles among populations

• Alleles can be transferred through the movement of fertile individuals or gametes (for example, pollen)

• Gene flow tends to reduce differences between populations over time

• Gene flow is more likely than mutation to alter allele frequencies directly

• Relative fitness is the contribution an individual makes to the gene pool of the next generation, relative to the contributions of other individuals

• Selection favors certain genotypes by acting on the phenotypes of certain organisms

Fig. 23-13

Original population

(c) Stabilizing selection(b) Disruptive selection(a) Directional selection

Phenotypes (fur color)Fr

sOriginalpopulation

Evolvedpopulation

• Because the environment can change, adaptive evolution is a continuous process

• Genetic drift and gene flow do not consistently lead to adaptive evolution as they can increase or decrease the match between an organism and its environment

Sexual Selection

• Sexual selection is natural selection for mating success

• It can result in sexual dimorphism, marked differences between the sexes in secondary sexual characteristics

Fig. 23-15

• Intrasexual selection is competition among individuals of one sex (often males) for mates of the opposite sex

• Intersexual selection, often called mate choice, occurs when individuals of one sex (usually females) are choosy in selecting their mates

• Male showiness due to mate choice can increase a male’s chances of attracting a female, while decreasing his chances of survival

• Heterozygote advantage occurs when heterozygotes have a higher fitness than do both homozygotes

• Natural selection will tend to maintain two or more alleles at that locus

• The sickle-cell allele causes mutations in hemoglobin but also confers malaria resistance

Heterozygote Advantage

• In frequency-dependent selection, the fitness of a phenotype declines if it becomes too common in the population

• Selection can favor whichever phenotype is less common in a population

Frequency-Dependent Selection

Fig. 23-18

“Right-mouthed”

“Left-mouthed”

“left

” in

Sample year

0’82 ’83 ’84 ’85 ’86 ’87 ’88 ’89 ’90

Why Natural Selection Cannot Fashion Perfect Organisms

1. Selection can act only on existing variations2. Evolution is limited by historical constraints3. Adaptations are often compromises4. Chance, natural selection, and the environment

interact

• CH 24

• Speciation, the origin of new species, is at the focal point of evolutionary theory

• Evolutionary theory must explain how new species originate and how populations evolve

• Microevolution consists of adaptations that evolve within a population, confined to one gene pool

• Macroevolution refers to evolutionary change above the species level

Animation: Macroevolution

• Prezygotic barriers block fertilization from occurring by:– Impeding different species from attempting to mate– Preventing the successful completion of mating– Hindering fertilization if mating is successful

• Postzygotic barriers prevent the hybrid zygote from developing into a viable, fertile adult:– Reduced hybrid viability– Reduced hybrid fertility– Hybrid breakdown

Fig. 24-4a

Habitat Isolation Temporal Isolation

Prezygotic barriers

Behavioral Isolation

Matingattempt

Mechanical Isolation

(f)(e)(c)(a)

Individualsof

differentspecies

Fig. 24-4i

Prezygotic barriers

Gametic Isolation

Fertilization

Reduced Hybrid Viability

Postzygotic barriers

Reduced Hybrid Fertility Hybrid Breakdown

Viable,fertile

offspring

(g) (h) (i)

Concept 24.2: Speciation can take place with or without geographic separation

• Speciation can occur in two ways:– Allopatric speciation– Sympatric speciation

Fig. 24-5

(a) Allopatric speciation (b) Sympatric speciation

Polyploidy• Polyploidy is the presence of extra sets of

chromosomes due to accidents during cell division• An autopolyploid is an individual with more than

two chromosome sets, derived from one species

Fig. 24-10-1

2n = 6 4n = 12

Failure of celldivision afterchromosomeduplication givesrise to tetraploidtissue.

Fig. 24-10-2

2n = 6 4n = 12

Gametesproducedare diploid..

Fig. 24-10-3

2n = 6 4n = 12

Gametesproducedare diploid..

Offspring withtetraploidkaryotypes maybe viable andfertile.

• An allopolyploid is a species with multiple sets of chromosomes derived from different species

Fig. 24-11-1

Species A2n = 6

Normalgameten = 3

Meioticerror

Species B2n = 4

Unreducedgametewith 4chromosomes

Fig. 24-11-2

Species A2n = 6

Normalgameten = 3

Meioticerror

Species B2n = 4

Hybridwith 7chromosomes

Fig. 24-11-3

Species A2n = 6

Normalgameten = 3

Meioticerror

Species B2n = 4

Normalgameten = 3

Fig. 24-11-4

Species A2n = 6

Normalgameten = 3

Meioticerror

Species B2n = 4

Normalgameten = 3

Viable fertilehybrid(allopolyploid)2n = 10

Patterns in the Fossil Record

• The fossil record includes examples of species that appear suddenly, persist essentially unchanged for some time, and then apparently disappear

• Niles Eldredge and Stephen Jay Gould coined the term punctuated equilibrium to describe periods of apparent stasis punctuated by sudden change

• The punctuated equilibrium model contrasts with a model of gradual change in a species’ existence

Fig. 24-17

(a) Punctuated pattern

(b) Gradual pattern

CH 25 ORIGIN OF LIFE

Protobionts

• Replication and metabolism are key properties of life

• Protobionts are aggregates of abiotically produced molecules surrounded by a membrane or membrane-like structure

• Protobionts exhibit simple reproduction and metabolism and maintain an internal chemical environment

Self-Replicating RNA and the Dawn of Natural Selection

• The first genetic material was probably RNA, not DNA

• RNA molecules called ribozymes have been found to catalyze many different reactions– For example, ribozymes can make complementary

copies of short stretches of their own sequence or other short pieces of RNA

The Fossil Record

• Sedimentary rocks are deposited into layers called strata and are the richest source of fossils

Video: Grand Canyon

Fig. 25-4Present

Dimetrodon

Coccosteus cuspidatus

Fossilizedstromatolite

Stromatolites Tappania, aunicellulareukaryote

Dickinsoniacostata

Hallucigenia

Casts ofammonites

Rhomaleosaurus victor, a plesiosaur

2.5 cm4.5 cm

How Rocks and Fossils Are Dated

• Sedimentary strata reveal the relative ages of fossils• The absolute ages of fossils can be determined by

radiometric dating• A “parent” isotope decays to a “daughter” isotope

at a constant rate• Each isotope has a known half-life, the time

required for half the parent isotope to decay

Fig. 25-5

Time (half-lives)

Accumulating “daughter” isotope

Remaining “parent” isotopeFr

a in i

1 2 3 4

1/41/8 1/16

• Radiocarbon dating can be used to date fossils up to 75,000 years old

• For older fossils, some isotopes can be used to date sedimentary rock layers above and below the fossil

• The magnetism of rocks can provide dating information

• Reversals of the magnetic poles leave their record on rocks throughout the world

Photosynthesis and the Oxygen Revolution

• Most atmospheric oxygen (O2) is of biological origin

• O2 produced by oxygenic photosynthesis reacted with dissolved iron and precipitated out to form banded iron formations

• The source of O2 was likely bacteria similar to modern cyanobacteria

The First Eukaryotes

• The oldest fossils of eukaryotic cells date back 2.1 billion years

• The hypothesis of endosymbiosis proposes that mitochondria and plastids (chloroplasts and related organelles) were formerly small prokaryotes living within larger host cells

• An endosymbiont is a cell that lives within a host cell

Fig. 25-9-4

Ancestral photosyntheticeukaryote

Photosyntheticprokaryote

Mitochondrion

Plastid

Nucleus

Cytoplasm

DNAPlasma membrane

Endoplasmic reticulum

Nuclear envelope

Ancestralprokaryote

Aerobicheterotrophicprokaryote

Mitochondrion

Ancestralheterotrophiceukaryote

• Key evidence supporting an endosymbiotic origin of mitochondria and plastids:– Similarities in inner membrane structures and

functions

– Division is similar in these organelles and some prokaryotes

– These organelles transcribe and translate their own DNA

– Their ribosomes are more similar to prokaryotic than eukaryotic ribosomes

The Origin of Multicellularity

• The evolution of eukaryotic cells allowed for a greater range of unicellular forms

• A second wave of diversification occurred when multicellularity evolved and gave rise to algae, plants, fungi, and animals

The Cambrian Explosion

• The Cambrian explosion refers to the sudden appearance of fossils resembling modern phyla in the Cambrian period (535 to 525 million years ago)

• The Cambrian explosion provides the first evidence of predator-prey interactions

The Colonization of Land

• Fungi, plants, and animals began to colonize land about 500 million years ago

• Plants and fungi likely colonized land together by 420 million years ago

• Arthropods and tetrapods are the most widespread and diverse land animals

• Tetrapods evolved from lobe-finned fishes around 365 million years ago

Continental Drift

• At three points in time, the land masses of Earth have formed a supercontinent: 1.1 billion, 600 million, and 250 million years ago

• Earth’s continents move slowly over the underlying hot mantle through the process of continental drift

• Oceanic and continental plates can collide, separate, or slide past each other

• Interactions between plates cause the formation of mountains and islands, and earthquakes

Fig. 25-13

SouthAmerica

Pangaea

Gondwana

Laurasia

Eurasia

IndiaAfrica

AntarcticaAustralia

North America

Madagascar

Present

The “Big Five” Mass Extinction Events

• In each of the five mass extinction events, more than 50% of Earth’s species became extinct

Fig. 25-14

l exti

Time (millions of years ago)

CenozoicMesozoicPaleozoicE O S D C P Tr J

488 444 416 359 299 251 200 145

EraPeriod

• The Permian extinction defines the boundary between the Paleozoic and Mesozoic eras

• This mass extinction occurred in less than 5 million years and caused the extinction of about 96% of marine animal species

• This event might have been caused by volcanism, which lead to global warming, and a decrease in oceanic oxygen

• The Cretaceous mass extinction 65.5 million years ago separates the Mesozoic from the Cenozoic

• Organisms that went extinct include about half of all marine species and many terrestrial plants and animals, including most dinosaurs

Fig. 25-15

NORTHAMERICA

ChicxulubcraterYucatán

Peninsula

• The presence of iridium in sedimentary rocks suggests a meteorite impact about 65 million years ago

• The Chicxulub crater off the coast of Mexico is evidence of a meteorite that dates to the same time

Consequences of Mass Extinctions

• Mass extinction can alter ecological communities and the niches available to organisms

• It can take from 5 to 100 million years for diversity to recover following a mass extinction

• Mass extinction can pave the way for adaptive radiations

Adaptive Radiations

• Adaptive radiation is the evolution of diversely adapted species from a common ancestor upon introduction to new environmental opportunities

Fig. 25-18

Close North American relative,the tarweed Carlquistia muirii

Argyroxiphium sandwicense

Dubautia linearisDubautia scabra

Dubautia waialealae

Dubautia laxa

HAWAII0.4

millionyears

OAHU3.7

millionyears

KAUAI5.1

millionyears

1.3millionyears

MOLOKAIMAUI

Changes in Rate and Timing

• Heterochrony is an evolutionary change in the rate or timing of developmental events

• It can have a significant impact on body shape• The contrasting shapes of human and chimpanzee

skulls are the result of small changes in relative growth rates

Animation: Allometric Growth

Fig. 25-19

(a) Differential growth rates in a human

(b) Comparison of chimpanzee and human skull growth

NewbornAge (years)

Adult1552

Chimpanzee fetus Chimpanzee adult

Human fetus Human adult

• Heterochrony can alter the timing of reproductive development relative to the development of nonreproductive organs

• In paedomorphosis, the rate of reproductive development accelerates compared with somatic development

• The sexually mature species may retain body features that were juvenile structures in an ancestral species

Changes in Spatial Pattern

• Substantial evolutionary change can also result from alterations in genes that control the placement and organization of body parts

• Homeotic genes determine such basic features as where wings and legs will develop on a bird or how a flower’s parts are arranged

• Hox genes are a class of homeotic genes that provide positional information during development

• If Hox genes are expressed in the wrong location, body parts can be produced in the wrong location

• For example, in crustaceans, a swimming appendage can be produced instead of a feeding appendage

• Evolution of vertebrates from invertebrate animals was associated with alterations in Hox genes

• Two duplications of Hox genes have occurred in the vertebrate lineage

• These duplications may have been important in the evolution of new vertebrate characteristics

Chapter 27Cell-Surface Structures

• An important feature of nearly all prokaryotic cells is their cell wall, which maintains cell shape, provides physical protection, and prevents the cell from bursting in a hypotonic environment

• Eukaryote cell walls are made of cellulose or chitin

• Bacterial cell walls contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides

Fig. 27-3

Cellwall

Peptidoglycanlayer

Plasma membrane

Protein

Gram-positivebacteria

(a) Gram-positive: peptidoglycan traps crystal violet.

Gram-negativebacteria

(b) Gram-negative: crystal violet is easily rinsed away, revealing red dye.

20 µm

Cellwall

Plasma membrane

Protein

Carbohydrate portionof lipopolysaccharide

Outermembrane

Peptidoglycanlayer

Fig. 27-9

Endospore

0.3 µm

• Prokaryotes have considerable genetic variation• Three factors contribute to this genetic

diversity:– Rapid reproduction– Mutation– Genetic recombination

Concept 27.2: Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes

Transformation and Transduction

• A prokaryotic cell can take up and incorporate foreign DNA from the surrounding environment in a process called transformation

• Transduction is the movement of genes between bacteria by bacteriophages (viruses that infect bacteria)

Fig. 27-11-1

Donorcell

Phage DNA

Fig. 27-11-2

Donorcell

Phage DNA

Fig. 27-11-3

Recipientcell

Recombination

Donorcell

Phage DNA

Fig. 27-11-4

Recombinant cell

Recipientcell

A+ B–

Recombination

Donorcell

Phage DNA

Conjugation and Plasmids

• Conjugation is the process where genetic material is transferred between bacterial cells

• Sex pili allow cells to connect and pull together for DNA transfer

• A piece of DNA called the F factor is required for the production of sex pili

• The F factor can exist as a separate plasmid or as DNA within the bacterial chromosome

The F Factor as a Plasmid

• Cells containing the F plasmid function as DNA donors during conjugation

• Cells without the F factor function as DNA recipients during conjugation

• The F factor is transferable during conjugation

Fig. 27-13

F plasmid

F+ cell

F– cell

Matingbridge

Bacterial chromosome

Bacterialchromosome

(a) Conjugation and transfer of an F plasmid

F+ cell

F– cell

(b) Conjugation and transfer of part of an Hfr bacterial chromosome

F factor

Hfr cell A+A+

A+A– A– A–

A– A+

RecombinantF– bacterium

Chapter 39R Plasmids and Antibiotic Resistance

• R plasmids carry genes for antibiotic resistance• Antibiotics select for bacteria with genes that

are resistant to the antibiotics• Antibiotic resistant strains of bacteria are

becoming more common

R Plasmids and Antibiotic Resistance

• R plasmids carry genes for antibiotic resistance• Antibiotics select for bacteria with genes that

are resistant to the antibiotics• Antibiotic resistant strains of bacteria are

becoming more common

Fig. 38-3(a)

Development of a malegametophyte (in pollen grain)

Microsporangium(pollen sac)

Microsporocyte (2n)

4 microspores (n)

Each of 4microspores (n)

Malegametophyte

Generative cell (n)

(b) Development of a femalegametophyte (embryo sac)

Megasporangium (2n)

Megasporocyte (2n)

Integuments (2n)

Micropyle

MEIOSIS

Survivingmegaspore (n)

3 antipodal cells (n)

2 polar nuclei (n)

1 egg (n)

2 synergids (n)

ale gam

ryo sa

Embryosac

Integuments (2n)

Ragweedpollengrain

Nucleus oftube cell (n)

MITOSIS

20 µm

75 µm

Double Fertilization

• After landing on a receptive stigma, a pollen grain produces a pollen tube that extends between the cells of the style toward the ovary

• Double fertilization results from the discharge of two sperm from the pollen tube into the embryo sac

• One sperm fertilizes the egg, and the other combines with the polar nuclei, giving rise to the triploid (3n) food-storing endosperm

Animation: Plant Fertilization

Fig. 38-5Stigma

Pollen tube

2 sperm

Micropyle

Polar nuclei

Synergid

2 sperm

Endospermnucleus (3n)(2 polar nucleiplus sperm)

Zygote (2n)(egg plus sperm)

Pollen grain

Polar nuclei

• Fruits are also classified by their development: – Simple, a single or several fused carpels– Aggregate, a single flower with multiple separate

carpels– Multiple, a group of flowers called an inflorescence

Fig. 38-10

FlowerStamenCarpels

Stigma

Pea flowerOvule

Carpel(fruitlet)

Raspberry flower

Stigma

Stamen

Pineapple inflorescence Apple flower

Stigma

Stamen

Each segmentdevelopsfrom thecarpelof oneflower

Pea fruit Raspberry fruit Pineapple fruit Apple fruit

(a) Simple fruit (b) Aggregate fruit (c) Multiple fruit (d) Accessory fruit

Petal Style

Ovary(in receptacle)

Sepals

Receptacle

Remains ofstamens and styles

• Fruits are also classified by their development: – Simple, a single or several fused carpels– Aggregate, a single flower with multiple separate

carpels– Multiple, a group of flowers called an inflorescence

• In the late 1800s, Charles Darwin and his son Francis conducted experiments on phototropism, a plant’s response to light

• They observed that a grass seedling could bend toward light only if the tip of the coleoptile was present

• They postulated that a signal was transmitted from the tip to the elongating region

Video: Phototropism

Fig. 39-5RESULTS

Control

Darwin and Darwin: phototropic responseonly when tip is illuminated

Illuminatedside ofcoleoptile

Shadedside of coleoptile

Tipremoved

Tip coveredby opaquecap

Tip coveredby trans-parent cap

Site of curvature covered by opaque shield

Boysen-Jensen: phototropic response when tip separatedby permeable barrier, but not with impermeable barrier

Tip separatedby gelatin(permeable)

Tip separatedby mica(impermeable)

Table 39-1

Concept 39.3: Responses to light are critical for plant success

• Light cues many key events in plant growth and development

• Effects of light on plant morphology are called photomorphogenesis

• Plants detect not only presence of light but also its direction, intensity, and wavelength (color)

• A graph called an action spectrum depicts relative response of a process to different wavelengths

• Action spectra are useful in studying any process that depends on light

Fig. 39-17

Dark (control)

RESULTS

DarkRed

Red Far-red Red Dark Red Far-red Red Far-red

Red Far-red Dark

Fig. 39-19

Synthesis

Far-redlight

Slow conversionin darkness(some plants)

Enzymaticdestruction

Responses:seed germination,control offlowering, etc.

Red light

• Circadian rhythms are cycles that are about 24 hours long and are governed by an internal “clock”

• Circadian rhythms can be entrained to exactly 24 hours by the day/night cycle

• The clock may depend on synthesis of a protein regulated through feedback control and may be common to all eukaryotes

Photoperiodism and Control of Flowering

• Some processes, including flowering in many species, require a certain photoperiod

• Plants that flower when a light period is shorter than a critical length are called short-day plants

• Plants that flower when a light period is longer than a certain number of hours are called long-day plants

• Flowering in day-neutral plants is controlled by plant maturity, not photoperiod

Fig. 39-2124 hours

Criticaldark period

Flashof light

Darkness

(a) Short-day (long-night) plant

Flashof light

(b) Long-day (short-night) plant

Fig. 39-22

24 hours

RFRRFR

Critical dark period

Short-day(long-night)

Long-day(short-night)

Defenses Against Herbivores

• Herbivory, animals eating plants, is a stress that plants face in any ecosystem

• Plants counter excessive herbivory with physical defenses such as thorns and chemical defenses such as distasteful or toxic compounds

• Some plants even “recruit” predatory animals that help defend against specific herbivores

Fig. 39-28

Recruitment of parasitoid wasps that lay their eggs within caterpillars

Synthesis and release of volatile attractants

Chemical in saliva

Wounding

Signal transduction pathway

The Hypersensitive Response

• The hypersensitive response– Causes cell and tissue death near the infection site– Induces production of phytoalexins and PR proteins,

which attack the pathogen– Stimulates changes in the cell wall that confine the

pathogen

Fig. 39-29

Signal

Hypersensitiveresponse

Signal transduction pathway

Avirulent pathogen

Signal transduction

pathway

Acquired resistance

R-Avr recognition andhypersensitive response

Systemic acquiredresistance

Systemic Acquired Resistance

• Systemic acquired resistance causes systemic expression of defense genes and is a long-lasting response

• Salicylic acid is synthesized around the infection site and is likely the signal that triggers systemic acquired resistance

Fig. 39-UN2

Plasma membrane

Reception Response

CELLWALL

CYTOPLASM

Transduction

Receptor

Hormone or environmental stimulus

Relay proteins and

second messengers

Activation of cellular responses

chapter 16- end review. fig. 16-7 (c) space-filling model hydrogen bond 3 end 5 end 3.4 nm 0.34 nm 3...

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