Overview: Life’s Operating Instructions - PowerPoint Presentation

Slide1

Overview: Life’s Operating Instructions

In 1953, James Watson and Francis Crick introduced an elegant double-helical model for the structure of deoxyribonucleic acid, or DNADNA, the substance of inheritance, is the most celebrated molecule of our timeHereditary information is encoded in DNA and reproduced in all cells of the bodyThis DNA program directs the development of biochemical, anatomical, physiological, and (to some extent) behavioral traits

Slide2

Figure 16.1

Slide3

1: DNA is the genetic material

Early in the 20th century, the identification of the molecules of inheritance loomed as a major challenge to biologists

Slide4

The Search for the Genetic Material:

Scientific InquiryWhen T. H. Morgan’s group showed that genes are located on chromosomes, the two components of chromosomes—DNA and protein—became candidates for the genetic materialThe key factor in determining the genetic material was choosing appropriate experimental organismsThe role of DNA in heredity was first discovered by studying bacteria and the viruses that infect them

Slide5

Evidence That DNA Can Transform Bacteria

The discovery of the genetic role of DNA began with research by Frederick Griffith in 1928Griffith worked with two strains of a bacterium, one pathogenic and one harmless

Slide6

In 1944, Oswald Avery, Maclyn McCarty, and Colin MacLeod announced that the transforming substance was DNA

Their conclusion was based on experimental evidence that only DNA worked in transforming harmless bacteria into pathogenic bacteriaMany biologists remained skeptical, mainly because little was known about DNA

Slide7

Evidence That Viral DNA Can Program Cells

More evidence for DNA as the genetic material came from studies of viruses that infect bacteriaSuch viruses, called bacteriophages (or phages), are widely used in molecular genetics research

Slide8

Figure 16.3

Phage

head

Tail

sheath

Tail fiber

DNA

Bacterial

cell

100 nm

Slide9

Additional Evidence That DNA Is the Genetic Material

It was known that DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group

In 1950, Erwin Chargaff reported that DNA composition varies from one species to the next

This evidence of diversity made DNA a more credible candidate for the genetic material

Slide10

Two

findings became known as Chargaff’s rulesThe base composition of DNA varies between speciesIn any species the number of A and T bases are equal and the number of G and C bases are equalThe basis for these rules was not understood until the discovery of the double helix

© 2011 Pearson Education, Inc.

Slide11

Figure 16.5

Sugar–phosphate

backbone

Nitrogenous bases

Thymine (T)

Adenine (A)

Cytosine (C)

Guanine (G)

Nitrogenous base

Phosphate

DNA

nucleotide

Sugar

(deoxyribose)

3



end

5



end

Slide12

Building a Structural Model of DNA:

Scientific InquiryAfter DNA was accepted as the genetic material, the challenge was to determine how its structure accounts for its role in heredityMaurice Wilkins and Rosalind Franklin were using a technique called X-ray crystallography to study molecular structureFranklin produced a picture of the DNA molecule using this technique

Slide13

Figure 16.6

(a) Rosalind Franklin

(b)

Franklin’s X-ray diffraction

photograph of DNA

Slide14

Franklin’s X-ray crystallographic images of DNA enabled Watson to deduce that DNA was helical

The X-ray images also enabled Watson to deduce the width of the helix and the spacing of the nitrogenous basesThe pattern in the photo suggested that the DNA molecule was made up of two strands, forming a double helix

Slide15

Figure 16.7

3.4 nm

1 nm

0.34 nm

Hydrogen bond

(a)

Key features of

DNA structure

Space-filling

model

(c)

(b) Partial chemical structure

3



end

5



end

3



end

5



end

T

T

A

A

G

G

C

C

C

C

C

C

C

C

C

C

C

G

G

G

G

G

G

G

G

G

T

T

T

T

T

T

A

A

A

A

A

A

Slide16

Figure 16.7b

(c) Space-filling model

Slide17

Figure 16.UN01

Purine



purine: too wide

Pyrimidine



pyrimidine: too narrow

Purine



pyrimidine: width

consistent with X-ray data

Slide18

Watson and Crick reasoned that the pairing was more specific, dictated by the base structures

They determined that adenine (A) paired only with thymine (T), and guanine (G) paired only with cytosine (C)The Watson-Crick model explains Chargaff’s rules: in any organism the amount of A = T, and the amount of G = C

Slide19

Figure 16.8

Sugar

Sugar

Sugar

Sugar

Adenine (A)

Thymine (T)

Guanine (G)

Cytosine (C)

Slide20

2: Many proteins work together in DNA replication and repair

The relationship between structure and function is manifest in the double helixWatson and Crick noted that the specific base pairing suggested a possible copying mechanism for genetic material

Slide21

The Basic Principle: Base Pairing to a Template Strand

Since the two strands of DNA are complementary, each strand acts as a template for building a new strand in replicationIn DNA replication, the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules

Slide22

Figure 16.9-3

(a) Parent molecule

(b)

Separation of

strands

(c)

“Daughter” DNA molecules,

each consisting of one

parental strand and one

new strand

A

A

A

A

A

A

A

A

A

A

A

A

T

T

T

T

T

T

T

T

T

T

T

T

C

C

C

C

C

C

C

C

G

G

G

G

G

G

G

G

Slide23

DNA Replication:

A Closer LookThe copying of DNA is remarkable in its speed and accuracyMore than a dozen enzymes and other proteins participate in DNA replication

Slide24

Getting Started

Replication begins at particular sites called origins of replication, where the two DNA strands are separated, opening up a replication “bubble”A eukaryotic chromosome may have hundreds or even thousands of origins of replicationReplication proceeds in both directions from each origin, until the entire molecule is copied

Slide25

Figure 16.12

(a) Origin of replication in an

E. coli

cell

(b) Origins of replication in a eukaryotic cell

Origin of

replication

Parental (template) strand

Double-

stranded

DNA molecule

Daughter (new)

strand

Replication

fork

Replication

bubble

Two daughter

DNA molecules

Origin of replication

Double-stranded

DNA molecule

Parental (template)

strand

Daughter (new)

strand

Bubble

Replication fork

Two daughter DNA molecules

0.5



m

0.25



m

Slide26

At the end of each replication bubble is a

replication fork, a Y-shaped region where new DNA strands are elongatingHelicases are enzymes that untwist the double helix at the replication forksSingle-strand binding proteins bind to and stabilize single-stranded DNA

Topoisomerase

corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands

Slide27

Figure 16.13

Topoisomerase

Primase

RNA

primer

Helicase

Single-strand binding

proteins

5



3



5



5



3



3



Slide28

DNA polymerases cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the 3

 endThe initial nucleotide strand is a short RNA primer

Slide29

An enzyme called

primase can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a templateThe primer is short (5–10 nucleotides long), and the 3 end serves as the starting point for the new DNA strand

Slide30

Synthesizing a New DNA Strand

Enzymes called DNA polymerases catalyze the elongation of new DNA at a replication forkMost DNA polymerases require a primer and a DNA template strandThe rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells

Slide31

Figure 16.14

New strand

Template strand

Sugar

Phosphate

Base

Nucleoside

triphosphate

DNA

polymerase

Pyrophosphate

5



5



5



5



3



3



3



3



OH

OH

OH

P

P

i

2

P

i

P

P

P

A

A

A

A

T

T

T

T

C

C

C

C

C

C

G

G

G

G

Slide32

Figure 16.15

Leading

strand

Lagging

strand

Overview

Origin of replication

Lagging

strand

Leading

strand

Primer

Overall directions

of replication

Origin of

replication

RNA primer

Sliding clamp

DNA pol

III

Parental DNA

3



5



5



3



3



5



3



5



3



5



3



5



Slide33

To elongate the other new strand, called the

lagging strand, DNA polymerase must work in the direction away from the replication forkThe lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase

Slide34

Origin of replication

Overview

Leading

strand

Leading

strand

Lagging

strand

Lagging strand

Overall directions

of replication

Template

strand

RNA primer

for fragment 1

Okazaki

fragment 1

RNA primer

for fragment 2

Okazaki

fragment 2

Overall direction of replication

3



3



3



3



3



3



3



3



3



3



3



3



5



5



5



5



5



5



5



5



5



5



5



5



2

2

2

1

1

1

1

1

2

1

Figure 16.16

Slide35

Figure 16.17

Overview

Leading

strand

Origin of

replication

Lagging

strand

Leading

strand

Lagging

strand

Overall directions

of replication

Leading strand

DNA pol

III

DNA pol

III

Lagging strand

DNA pol

I

DNA ligase

Primer

Primase

Parental

DNA

5



5



5



5



5



3



3



3



3



3



3

2

1

4

Slide36

Figure 16.17a

Overview

Leading

strand

Origin of

replication

Lagging

strand

Leading

strand

Lagging

strand

Overall directions

of replication

Leading strand

DNA pol

III

Primer

Primase

Parental

DNA

5



5



3



3



3



Slide37

Overview

Leading

strand

Origin of

replication

Lagging

strand

Leading

strand

Lagging

strand

Overall directions

of replication

Leading strand

Primer

DNA pol

III

DNA pol

I

Lagging strand

DNA ligase

5



5



5



3



3



3



3

4

2

1

Figure 16.17b

Slide38

The DNA Replication Complex

The proteins that participate in DNA replication form a large complex, a “DNA replication machine”

The DNA replication machine may be stationary during the replication process

Recent studies support a model in which DNA polymerase molecules “reel in” parental DNA and “extrude” newly made daughter DNA molecules

Slide39

Figure 16.18

Parental DNA

DNA pol

III

Leading strand

Connecting

protein

Helicase

Lagging strand

DNA

pol

III

Lagging

strand

template

5



5



5



5



5



5



3



3



3



3



3



3



Slide40

Proofreading and Repairing DNA

DNA polymerases proofread newly made DNA, replacing any incorrect nucleotidesIn mismatch repair of DNA, repair enzymes correct errors in base pairingDNA can be damaged by exposure to harmful chemical or physical agents such as cigarette smoke and X-rays; it can also undergo spontaneous changesIn nucleotide excision repair

, a

nuclease

cuts out and replaces damaged stretches of DNA

Slide41

Figure 16.19

Nuclease

DNA

polymerase

DNA

ligase

5



5



5



5



5



5



5



5



3



3



3



3



3



3



3



3



Slide42

Replicating the Ends of DNA Molecules

Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomesThe usual replication machinery provides no way to complete the 5 ends, so repeated rounds of replication produce shorter DNA molecules with uneven endsThis is not a problem for prokaryotes, most of which have circular chromosomes

Slide43

Figure 16.20a

Ends of parental

DNA strands

Leading strand

Lagging strand

Last fragment

Next-to-last fragment

Lagging strand

RNA primer

Parental strand

Removal of primers and

replacement with DNA

where a 3



end is available

3



3



3



5



5



5



Slide44

Figure 16.20b

Second round

of replication

Further rounds

of replication

New leading strand

New lagging strand

Shorter and shorter daughter molecules

3



3



3



5



5



5



Slide45

Eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends called

telomeresTelomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA moleculesIt has been proposed that the shortening of telomeres is connected to aging

Slide46

Figure 16.21

1



m

Slide47

If chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce

An enzyme called telomerase catalyzes the lengthening of telomeres in germ cells

Slide48

The shortening of telomeres might protect cells from cancerous growth by limiting the number of cell divisions

There is evidence of telomerase activity in cancer cells, which may allow cancer cells to persist

Slide49

3. A chromosome consists of a DNA molecule packed together with proteins

The bacterial chromosome is a double-stranded, circular DNA molecule associated with a small amount of proteinEukaryotic chromosomes have linear DNA molecules associated with a large amount of proteinIn a bacterium, the DNA is “supercoiled” and found in a region of the cell called the nucleoid

Slide50

Chromatin

, a complex of DNA and protein, is found in the nucleus of eukaryotic cellsChromosomes fit into the nucleus through an elaborate, multilevel system of packing

Slide51

Figure 16.22a

DNA double helix

(2 nm in diameter)

DNA, the double helix

Nucleosome

(10 nm in diameter)

Histones

Histones

Histone

tail

H1

Nucleosomes, or “beads on

a string” (10-nm fiber)

Slide52

Figure 16.22b

30-nm fiber

30-nm fiber

Loops

Scaffold

300-nm fiber

Chromatid

(700 nm)

Replicated

chromosome

(1,400 nm)

Looped domains

(300-nm fiber)

Metaphase

chromosome

Slide53

Chromatin undergoes changes in packing during the cell cycle

At interphase, some chromatin is organized into a 10-nm fiber, but much is compacted into a 30-nm fiber, through folding and loopingThough interphase chromosomes are not highly condensed, they still occupy specific restricted regions in the nucleus

Slide54

Figure 16.23

5



m

Slide55

Overview: The Flow of Genetic Information

Gene expression, the process by which DNA directs protein synthesis, includes two stages: transcription and translation

Slide56

Concept 1: Genes specify proteins via transcription and translation

How was the fundamental relationship between genes and proteins discovered?

Slide57

Evidence from the Study of Metabolic Defects

In 1902, British physician Archibald Garrod first suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactionsHe thought symptoms of an inherited disease reflect an inability to synthesize a certain enzymeLinking genes to enzymes required understanding that cells synthesize and degrade molecules in a series of steps, a metabolic pathway

Slide58

Nutritional Mutants in

Neurospora: Scientific InquiryGeorge Beadle and Edward Tatum exposed bread mold to X-rays, creating mutants that were unable to survive on minimal mediaUsing crosses, they and their coworkers identified three classes of arginine-deficient mutants, each lacking a different enzyme necessary for synthesizing arginine

They developed a one gene–one enzyme hypothesis, which states that each gene dictates production of a specific enzyme

© 2011 Pearson Education, Inc.

Slide59

Basic Principles of Transcription and Translation

RNA is the bridge between genes and the proteins for which they codeTranscription is the synthesis of RNA under the direction of DNATranscription produces messenger RNA (mRNA)Translation

is the synthesis of a polypeptide, using information in the mRNA

Ribosomes

are the sites of translation

Slide60

Figure 17.UN01

DNA

RNA

Protein

Slide61

Figure 17.3

DNA

mRNA

Ribosome

Polypeptide

TRANSCRIPTION

TRANSLATION

TRANSCRIPTION

TRANSLATION

Polypeptide

Ribosome

DNA

mRNA

Pre-mRNA

RNA PROCESSING

(a) Bacterial cell

(b) Eukaryotic cell

Nuclear

envelope

Slide62

The Genetic Code

How are the instructions for assembling amino acids into proteins encoded into DNA? There are 20 amino acids, but there are only four nucleotide bases in DNAHow many nucleotides correspond to an amino acid?

Slide63

Codons: Triplets of Nucleotides

The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, three-nucleotide wordsThe words of a gene are transcribed into complementary nonoverlaping three-nucleotide words of mRNAThese words are then translated into a chain of amino acids, forming a polypeptide

Slide64

Figure 17.4

DNA

template

strand

TRANSCRIPTION

mRNA

TRANSLATION

Protein

Amino acid

Codon

Trp

Phe

Gly

5



5



Ser

U

U

U

U

U

3



3



5



3



G

G

G

G

C

C

T

C

A

A

A

A

A

A

A

T

T

T

T

T

G

G

G

G

C

C

C

G

G

DNA

molecule

Gene 1

Gene 2

Gene 3

C

C

Slide65

During transcription, one of the two DNA strands, called the

template strand, provides a template for ordering the sequence of complementary nucleotides in an RNA transcriptThe template strand is always the same strand for a given geneDuring translation, the mRNA base triplets, called codons, are read in the 5 to 3



direction

Slide66

Cracking the Code

All 64 codons were deciphered by the mid-1960sOf the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to end translationThe genetic code is redundant (more than one codon may specify a particular amino acid) but not ambiguous; no codon specifies more than one amino acidCodons must be read in the correct

reading frame

(correct groupings) in order for the specified polypeptide to be produced

Slide67

Figure 17.5

Second mRNA base

First mRNA base (5

 end of codon)

Third mRNA base (3

 end of codon)

UUU

UUC

UUA

CUU

CUC

CUA

CUG

Phe

Leu

Leu

I

le

UCU

UCC

UCA

UCG

Ser

CCU

CCC

CCA

CCG

UAU

UAC

Tyr

Pro

Thr

UAA Stop

UAG Stop

UGA Stop

UGU

UGC

Cys

UGG

Trp

G

C

U

U

C

A

U

U

C

C

C

A

U

A

A

A

G

G

His

Gln

Asn

Lys

Asp

CAU

CGU

CAC

CAA

CAG

CGC

CGA

CGG

G

AUU

AUC

AUA

ACU

ACC

ACA

AAU

AAC

AAA

AGU

AGC

AGA

Arg

Ser

Arg

Gly

ACG

AUG

AAG

AGG

GUU

GUC

GUA

GUG

GCU

GCC

GCA

GCG

GAU

GAC

GAA

GAG

Val

Ala

GGU

GGC

GGA

GGG

Glu

Gly

G

U

C

A

Met or

start

UUG

G

Slide68

Figure 17.6

(a) Tobacco plant expressing

a firefly gene

gene

(b) Pig expressing a jellyfish

Slide69

Concept 2: Transcription is the DNA-directed synthesis of RNA:

a closer lookTranscription is the first stage of gene expression

Slide70

Molecular Components of Transcription

RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotidesThe RNA is complementary to the DNA template strandRNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine

Slide71

The DNA sequence where RNA polymerase attaches is called the

promoter; in bacteria, the sequence signaling the end of transcription is called the terminatorThe stretch of DNA that is transcribed is called a transcription unit

Slide72

Figure 17.7-4

Promoter

RNA polymerase

Start point

DNA

5



3



Transcription unit

3



5



Elongation

5



3



3



5



Nontemplate strand of DNA

Template strand of DNA

RNA

transcript

Unwound

DNA

2

3



5



3



5



3



Rewound

DNA

RNA

transcript

5



Termination

3

3



5



5



Completed RNA transcript

Direction of transcription (“downstream”)

5



3



3



Initiation

1

Slide73

Synthesis of an RNA Transcript

The three stages of transcriptionInitiationElongationTermination

Slide74

RNA Polymerase Binding and Initiation of Transcription

Promoters signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start pointTranscription factors mediate the binding of RNA polymerase and the initiation of transcription

The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a

transcription initiation complex

A promoter called a

TATA box

is crucial in forming the initiation complex in eukaryotes

Slide75

Figure 17.8

Transcription initiation

complex forms

3

DNA

Promoter

Nontemplate strand

5



3



5



3



5



3



Transcription

factors

RNA polymerase

II

Transcription factors

5



3



5



3



5



3



RNA transcript

Transcription initiation complex

5



3



TATA box

T

T

T

T

T

T

A

A

A

A

A

A

A

T

Several transcription

factors bind to DNA

2

A eukaryotic promoter

1

Start point

Template strand

Slide76

Elongation of the RNA Strand

As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a timeTranscription progresses at a rate of 40 nucleotides per second in eukaryotesA gene can be transcribed simultaneously by several RNA polymerasesNucleotides are added to the 3



end of the growing RNA molecule

Slide77

Nontemplate

strand of DNA

RNA nucleotides

RNA

polymerase

Template

strand of DNA

3



3



5



5



5



3



Newly made

RNA

Direction of transcription

A

A

A

A

A

A

A

T

T

T

T

T

T

T

G

G

G

C

C

C

C

C

G

C

C

C

A

A

A

U

U

U

end

Figure 17.9

Slide78

Termination of Transcription

The mechanisms of termination are different in bacteria and eukaryotesIn bacteria, the polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modificationIn eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10–35 nucleotides past this polyadenylation sequence

Slide79

Concept 3: Eukaryotic cells modify RNA after transcription

Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasmDuring RNA processing, both ends of the primary transcript are usually alteredAlso, usually some interior parts of the molecule are cut out, and the other parts spliced together

Slide80

Alteration of mRNA Ends

Each end of a pre-mRNA molecule is modified in a particular wayThe 5 end receives a modified nucleotide 5



cap

The 3



end gets a

poly-A tail

These modifications share several functions

They seem to facilitate the export of mRNA

They protect mRNA from hydrolytic enzymes

They help ribosomes attach to the 5



end

Slide81

Figure 17.10

Protein-coding

segment

Polyadenylation

signal

5



3



3



5



5



Cap

UTR

Start

codon

G

P

P

P

Stop

codon

UTR

AAUAAA

Poly-A tail

AAA

AAA

…

Slide82

Split Genes and RNA Splicing

Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regionsThese noncoding regions are called intervening sequences, or intronsThe other regions are called exons because they are eventually expressed, usually translated into amino acid sequences

RNA splicing

removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence

Slide83

Figure 17.11

5



Exon Intron

Exon

5



Cap

Pre-mRNA

Codon

numbers

1

30

31

104

mRNA

5



Cap

5



Intron

Exon

3



UTR

Introns cut out and

exons spliced together

3



105



146

Poly-A tail

Coding

segment

Poly-A tail

UTR

1

146

Slide84

In some cases, RNA splicing is carried out by spliceosomes

Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites

Slide85

Figure 17.12-3

RNA transcript (pre-mRNA)

5



Exon 1

Protein

snRNA

snRNPs

Intron

Exon 2

Other

proteins

Spliceosome

5



Spliceosome

components

Cut-out

intron

mRNA

5



Exon 1

Exon 2

Slide86

Ribozymes

Ribozymes are catalytic RNA molecules that function as enzymes and can splice RNAThe discovery of ribozymes rendered obsolete the belief that all biological catalysts were proteins

Slide87

Three properties of RNA enable it to function as an enzyme

It can form a three-dimensional structure because of its ability to base-pair with itselfSome bases in RNA contain functional groups that may participate in catalysisRNA may hydrogen-bond with other nucleic acid molecules

Slide88

The Functional and Evolutionary Importance of Introns

Some introns contain sequences that may regulate gene expressionSome genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicingThis is called alternative RNA splicingConsequently, the number of different proteins an organism can produce is much greater than its number of genes

Slide89

Proteins often have a modular architecture consisting of discrete regions called

domainsIn many cases, different exons code for the different domains in a proteinExon shuffling may result in the evolution of new proteins

Slide90

Gene

DNA

Exon 1

Exon 2

Exon 3

Intron

Intron

Transcription

RNA processing

Translation

Domain 3

Domain 2

Domain 1

Polypeptide

Figure 17.13

Slide91

Concept 4: Translation is the RNA-directed synthesis of a polypeptide:

a closer lookGenetic information flows from mRNA to protein through the process of translation

Slide92

Molecular Components of Translation

A cell translates an mRNA message into protein with the help of transfer RNA (tRNA)tRNA transfer amino acids to the growing polypeptide in a ribosomeTranslation is a complex process in terms of its biochemistry and mechanics

Slide93

Figure 17.14

Polypeptide

Ribosome

Trp

Phe

Gly

tRNA with

amino acid

attached

Amino

acids

tRNA

Anticodon

Codons

U

U

U

U

G

G

G

G

C

A

C

C

C

C

G

A

A

A

C

G

C

G

5



3



mRNA

Slide94

The Structure and Function of Transfer RNA

Molecules of tRNA are not identicalEach carries a specific amino acid on one endEach has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA

Slide95

A tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long

Flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf

Slide96

Figure 17.15

Amino acid

attachment

site

3



5



Hydrogen

bonds

Anticodon

(a) Two-dimensional structure

(b) Three-dimensional structure

(c) Symbol used

in this book

Anticodon

Anticodon

3



5



Hydrogen

bonds

Amino acid

attachment

site

5



3



A

A

G

Slide97

Because of hydrogen bonds, tRNA actually twists and folds into a three-dimensional molecule

tRNA is roughly L-shaped

Slide98

Accurate translation requires two steps

First: a correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetaseSecond: a correct match between the tRNA anticodon and an mRNA codonFlexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to more than one codon

Slide99

Aminoacyl-tRNA

synthetase (enzyme)

Amino acid

P

P

P

Adenosine

ATP

P

P

P

P

P

i

i

i

Adenosine

tRNA

Adenosine

P

tRNA

AMP

Computer model

Amino

acid

Aminoacyl-tRNA

synthetase

Aminoacyl tRNA

(“charged tRNA”)

Figure 17.16-4

Slide100

tRNA

molecules

Growing

polypeptide

Exit tunnel

E

P

A

Large

subunit

Small

subunit

mRNA

5



3



(a) Computer model of functioning ribosome

Exit tunnel

Amino end

A site (Aminoacyl-

tRNA binding site)

Small

subunit

Large

subunit

E

P

A

mRNA

E

P site (Peptidyl-tRNA

binding site)

mRNA

binding site

(b) Schematic model showing binding sites

E site

(Exit site)

(c) Schematic model with mRNA and tRNA

5



Codons

3



tRNA

Growing polypeptide

Next amino

acid to be

added to

polypeptide

chain

Figure 17.17

Slide101

A ribosome has three binding sites for tRNA

The P site holds the tRNA that carries the growing polypeptide chainThe A site holds the tRNA that carries the next amino acid to be added to the chainThe E site is the exit site, where discharged tRNAs leave the ribosome

Slide102

Building a Polypeptide

The three stages of translationInitiationElongationTerminationAll three stages require protein “factors” that aid in the translation process

Slide103

Ribosome Association and Initiation of Translation

The initiation stage of translation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunitsFirst, a small ribosomal subunit binds with mRNA and a special initiator tRNAThen the small subunit moves along the mRNA until it reaches the start codon (AUG)

Proteins called initiation factors bring in the large subunit that completes the translation initiation complex

Slide104

Figure 17.18

Initiator

tRNA

mRNA

5



5



3



Start codon

Small

ribosomal

subunit

mRNA binding site

3



Translation initiation complex

5



3



3



U

U

A

A

G

C

P

P site

i



GTP

GDP

Met

Met

Large

ribosomal

subunit

E

A

5



Slide105

Elongation of the Polypeptide Chain

During the elongation stage, amino acids are added one by one to the preceding amino acid at the C-terminus of the growing chainEach addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocationTranslation proceeds along the mRNA in a 5′ to 3′ direction

Slide106

Amino end of

polypeptide

mRNA

5



E

A

site

3



E

GTP

GDP



P

i

P

A

E

P

A

GTP

GDP



P

i

P

A

E

Ribosome ready for

next aminoacyl tRNA

P

site

Figure 17.19-4

Slide107

Termination of Translation

Termination occurs when a stop codon in the mRNA reaches the A site of the ribosomeThe A site accepts a protein called a release factorThe release factor causes the addition of a water molecule instead of an amino acidThis reaction releases the polypeptide, and the translation assembly then comes apart

Slide108

Figure 17.20-3

Release

factor

Stop codon

(UAG, UAA, or UGA)

3



5



3



5



Free

polypeptide

2

GTP

5



3



2

GDP



2

i

P

Slide109

Polyribosomes

A number of ribosomes can translate a single mRNA simultaneously, forming a polyribosome (or polysome)Polyribosomes enable a cell to make many copies of a polypeptide very quickly

Slide110

Figure 17.21

Completed

polypeptide

Incoming

ribosomal

subunits

Start of

mRNA

(5

 end)

End of

mRNA

(3

 end)

(a)

Polyribosome

Ribosomes

mRNA

(b)

0.1

m

Growing

polypeptides

Slide111

Protein Folding and Post-Translational Modifications

During and after synthesis, a polypeptide chain spontaneously coils and folds into its three-dimensional shapeProteins may also require post-translational modifications before doing their jobSome polypeptides are activated by enzymes that cleave themOther polypeptides come together to form the subunits of a protein

Slide112

Targeting Polypeptides to Specific Locations

Two populations of ribosomes are evident in cells: free ribsomes (in the cytosol) and bound ribosomes (attached to the ER)Free ribosomes mostly synthesize proteins that function in the cytosol Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell

Ribosomes are identical and can switch from free to bound

Slide113

Polypeptide synthesis always begins in the cytosol

Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ERPolypeptides destined for the ER or for secretion are marked by a signal peptide

Slide114

Figure 17.22

Ribosome

mRNA

Signal

peptide

SRP

1

SRP

receptor

protein

Translocation

complex

ER

LUMEN

2

3

4

5

6

Signal

peptide

removed

CYTOSOL

Protein

ER

membrane

Slide115

Concept 5: Mutations of one or a few nucleotides can affect protein structure

and functionMutations are changes in the genetic material of a cell or virusPoint mutations are chemical changes in just one base pair of a gene

The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein

Slide116

Figure 17.23

Wild-type hemoglobin

Wild-type hemoglobin DNA

3



3



3



5



5



3



3



5



5



5



5



3



mRNA

A

A

G

C

T

T

A

A

G

mRNA

Normal hemoglobin

Glu

Sickle-cell hemoglobin

Val

A

A

A

U

G

G

T

T

Sickle-cell hemoglobin

Mutant hemoglobin DNA

C

Slide117

Types of Small-Scale Mutations

Point mutations within a gene can be divided into two general categoriesNucleotide-pair substitutionsOne or more nucleotide-pair insertions or deletions

Slide118

Substitutions

A nucleotide-pair substitution replaces one nucleotide and its partner with another pair of nucleotidesSilent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code

Missense mutations

still code for an amino acid, but not the correct amino acid

Nonsense mutations

change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein

Slide119

Wild type

DNA template strand

mRNA

5



5



3



Protein

Amino end

A instead of G

(a) Nucleotide-pair substitution

3



3



5



Met

Lys

Phe

Gly

Stop

Carboxyl end

T

T

T

T

T

T

T

T

T

T

A

A

A

A

A

A

A

A

A

C

C

C

C

A

A

A

A

A

A

G

G

G

G

G

C

C

G

G

G

U

U

U

U

U

G

(b) Nucleotide-pair insertion or deletion

Extra A

3



5



5



3



Extra U

5



3



T

T

T

T

T

T

T

T

A

A

A

A

A

A

T

G

G

G

G

G

A

A

A

A

C

C

C

C

C

A

T

3



5



5



3



5



T

T

T

T

T

A

A

A

A

C

C

A

A

C

C

T

T

T

T

T

A

A

A

A

A

T

G

G

G

G

U instead of C

Stop

U

A

A

A

A

A

G

G

G

U

U

U

U

U

G

Met

Lys

Phe

Gly

Silent (no effect on amino acid sequence)

T instead of C

T

T

T

T

T

A

A

A

A

C

C

A

G

T

C

T

A

T

T

T

A

A

A

A

C

C

A

G

C

C

A instead of G

C

A

A

A

A

A

G

A

G

U

U

U

U

U

G

U

A

A

A

A

G

G

G

U

U

U

G

A

C

A

A

U

U

A

A

U

U

G

U

G

G

C

U

A

G

A

U

A

U

A

A

U

G

U

G

U

U

C

G

Met

Lys

Phe

Ser

Stop

Stop

Met

Lys

missing

missing

Frameshift causing immediate nonsense

(1 nucleotide-pair insertion)

Frameshift causing extensive missense

(1 nucleotide-pair deletion)

missing

T

T

T

T

T

T

C

A

A

C

C

A

A

C

G

A

G

T

T

T

A

A

A

A

A

T

G

G

G

C

Leu

Ala

Missense

A instead of T

T

T

T

T

T

A

A

A

A

A

C

G

G

A

G

A

C

A

U

A

A

A

G

G

G

U

U

U

U

U

G

T

T

T

T

T

A

T

A

A

A

C

G

G

G

G

Met

Nonsense

Stop

U instead of A

3



5



3



5



5



3



3



5



5



3



3



5



3



Met

Phe

Gly

No frameshift, but one amino acid missing

(3 nucleotide-pair deletion)

missing

3



5



5



3



5



3



U

T

C

A

A

A

C

A

T

T

A

C

G

T

A

G

T

T

T

G

G

A

A

T

C

T

T

C

A

A

G

Met

3



T

A

Stop

3



5



5



3



5



3



Figure 17.24

Slide120

Insertions and Deletions

Insertions and deletions are additions or losses of nucleotide pairs in a geneThese mutations have a disastrous effect on the resulting protein more often than substitutions do Insertion or deletion of nucleotides may alter the reading frame, producing a

frameshift mutation

Slide121

Figure 17.24d

Wild type

DNA template strand

mRNA

5



5



Protein

Amino end

Stop

Carboxyl end

3



3



3



5



Met

Lys

Phe

Gly

A

A

A

A

A

A

A

A

A

A

T

T

T

T

T

T

T

T

T

T

C

C

C

C

C

C

G

G

G

G

G

G

A

A

A

A

A

G

G

G

U

U

U

U

U

(b) Nucleotide-pair insertion or deletion: frameshift causing

immediate nonsense

Extra A

Extra U

5



3



5



3



3



5



Met

1 nucleotide-pair insertion

Stop

A

C

A

A

G

T

T

A

T

C

T

A

C

G

T

A

T

A

T

G

T

C

T

G

G

A

T

G

A

A

G

U

A

U

A

U

G

A

U

G

U

U

C

A

T

A

A

G

Slide122

Mutagens

Spontaneous mutations can occur during DNA replication, recombination, or repairMutagens are physical or chemical agents that can cause mutations

Slide123

Concept 6: While gene expression differs among the domains of life, the concept of a gene is universal

Archaea are prokaryotes, but share many features of gene expression with eukaryotes

Slide124

Comparing Gene Expression in Bacteria, Archaea, and Eukarya

Bacteria and eukarya differ in their RNA polymerases, termination of transcription, and ribosomes; archaea tend to resemble eukarya in these respectsBacteria can simultaneously transcribe and translate the same geneIn eukarya, transcription and translation are separated by the nuclear envelope

In archaea, transcription and translation are likely coupled

Slide125

Figure 17.25

RNA polymerase

DNA

mRNA

Polyribosome

RNA

polymerase

DNA

Polyribosome

Polypeptide

(amino end)

mRNA

(5

 end)

Ribosome

0.25

m

Direction of

transcription

Slide126

What Is a Gene?

Revisiting the QuestionThe idea of the gene has evolved through the history of geneticsWe have considered a gene asA discrete unit of inheritance A region of specific nucleotide sequence in a chromosome

A DNA sequence that codes for a specific polypeptide chain

Slide127

Figure 17.26

TRANSCRIPTION

DNA

RNA

polymerase

Exon

RNA

transcript

RNA

PROCESSING

NUCLEUS

Intron

RNA transcript

(pre-mRNA)

Poly-A

Poly-A

Aminoacyl-

tRNA synthetase

AMINO ACID

ACTIVATION

Amino

acid

tRNA

5

 Cap

Poly-A

3



Growing

polypeptide

mRNA

Aminoacyl

(charged)

tRNA

Anticodon

Ribosomal

subunits

A

A

E

TRANSLATION

5

 Cap

CYTOPLASM

P

E

Codon

Ribosome

5



3

