Molecular Biology of the Gene Outline: Molecular … 101 Fall...5 Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings Figure 10.9B Transcription of a gene RNA

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Molecular Biology of the GeneOutline: Molecular Biology of the Gene

• Readings: Chapters 10-12 in Campbell et al• Historical Genetic Material Experiments• Chemical Nature of Nucleic Acids• Structure of DNA• DNA Replication• Gene Expression

– RNA and Protein Synthesis• Gene Technology

Griffith’s Bacterial Transformation Experiments

Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

Bacteriophage (Phage) Structure

Head

Tail

Tail fiber

DNA

300,

000 ×

Figure 10.1A


Phage/?Bacterial virus reproductive cycle – Hershey & Chase (1952)

Virus attaches to bacterial cell.

Virus injects DNA.

Virus DNA directs cell to

1. make more phage DNA

2. make protein parts.New phages assemble.

Cell lyses releasing new phages.

Figure 10.1C

Fig. 08.03

Hershey & Chase Phage Reproduction ExperimentsDNA is the Genetic material

2

DNA Structure

1. Nucleotides

2. Nitrogen Bases

3. Key Investigations1. X-Ray Crystallography2. Chargaff’s Rule3. Double Helix of Watson & Crick


A

C

T

G

T

Sugar-phosphate backbonePhosphate group

Nitrogenous base

Sugar

A

C

T

G

T

DNA polynucleotide

Phosphategroup

O

O–

OO P C N

N

Nitrogenous base

Sugar(deoxyribose)

DNA Nucleotide

Figure 10.2A DNA is a Nucleotide Polymer


C C

CC C

C

O

NC

H

HONH

H3C

H H

H

H

N

N

NH

OC

H HN

H CN

N N

NC

CCC

HH

N

NH

CC N

C HNC N

H C

O

HH

Thymine (T) Cytosine (C) Adenine (A) Guanine (G)

PurinesPyrimidines

Figure 10.2B Four Nitrogenous bases are in DNA

OH

O

PO4

Base

CH2O

Base

OPO

C

O–O

CH2

DNA = Nucleotide PolymerSugar-Phosphate Linkage

Sugar

Phosphate

Sugar

Nucleotide

Nucleotide

Chargaff’s Rule

Base Pair Ratio

A:T G:C1.1:1

1:11:11:11:1

1.1:1

1:11:1

1.1:11:11:11:1

Fig. 14.9ab

X-Ray Crystallography: Rosalind Franklin

DNA was helicalDNA had repetitive elements0.34 nm, 3.4 nm, 2.0nm

3

A

A

T

T

C

C

G

G

Phosphodiesterbond

Sugar-phosphate"backbone"

Watson & CrickDNA Model

Paired Nitrogen

Bases

Double Helix

G C

Major groove

3.4 nm

0.34 nm

2 nm

C GG C

G C

G C

C G

TA

TA

T A

T A

T A

T A

T A

G C

DNA StructureFranklin’s

Crystallography made sense!


Three representations of DNA

G CT A

A T

GG

CCA T

GC

T AT A

A TA T

G CA T

O

OOH

–O P

O O–O P

O

O OP– O

– O OP

O O

O

OH

H2C

H2C

H2C

H2C

O

O

O

O

O

O

O

O

P O–

O–

O–

O–

OH

HO

O

O

O

P

P

P

O

O

O

O

O

O

O

O

T A

G C

C G

A TCH2

CH2

CH2

CH2

Hydrogen bond

Ribbon model Chemical structure Computer model

Basepair

Figure 10.3D


Start Monday 11/3/06

DNA discovery (video)


Semiconservative DNA replication

A TC GG CA TT A

A TC GG CA TT A

A TC GG CA TT A

A TC GG CAT

A T

C G

ACTA

Parental moleculeof DNA

Both parental strands serve as templates

Two identical daughtermolecules of DNA

Nucleotides

1. Unwinding 2. Pairing 3. Joining

Figure 10.4A


DNA strands have an opposite orientation

P

P

P

P

P

P

P

P

HO

OH

A

C

G

T

T

C

G

A

2′1′3′

4′

1′ 4′3′

2′

5′ end 3′ end

3′ end 5′ end

Figure 10.5B

5′

5′

DNA replication – A Closer Look

4


DNA replication – A Closer LookFigure 10.4B

G C

A T

G C

A TC G

AGA

CG

CG

CG

TAG

C

TAT

AA

TT

A

CG

CG

CG

TA

G

C

T

A

TA

AT

TA

TCT

DNA must unwind


3′

5′3′

5′3′

5′

5′3′

Daughter strandsynthesizedcontinuously

Daughter strandsynthesizedin pieces

Parental DNA

DNA ligase

DNA polymerasemolecule

DNA replication – A Closer LookNew DNA strands are synthesized continuously & discontinuously

Figure 10.5C


10.5 DNA replication: A closer look• DNA replication

– Begins at specific sites on the double helix

Figure 10.5A

Origin of replication

Two daughter DNA molecules

Parental strand

Daughter strand

Bubble

DNA Synthesis Animation

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Normal Hemoglobin β chain (Sanger 1953)Valine Histidine Leucine Threonine Proline Glutamic

acid

Sickle cell anemia Hemoglobin β chain (Ingram 1956)

Valine Histidine Leucine Threonine Proline Glutamicacid

Glutamicacid

Valine

Genes Specify Sequences of Amino Acids

GENE = Unit of Heredity

GENE = Sequence of nucleotides that determines the amino acid sequence of a protein


DNA strand

Transcription

Translation

Polypeptide

RNA

A A A C C G G C A A A A

U U U G G C C G U U U U

Gene 1

Gene 2

Gene 3

DNA molecule

Gene Expression – The Central DogmaFigure 10.7

OneDNA strand

5


Figure 10.9B Transcription of a gene

RNA polymerase

DNA of genePromoter DNA

1 Initiation

2 Elongation

3 Termination GrowingRNA

Completed RNA


RNApolymerase

RNA nucleotides

Direction of transcription

Template Strand of DNANewly made RNA

TC

A T C C A A TT

GG

CC

AATTGGAT

G

U

C A U C C AA

U

Figure 10.9A Transcription of a gene – a closer look


Gene Expression – The Central Dogma

DNA

Transcription

RNA

Protein

Translation

Figure 10.6A

RNA leaves the nucleus and enters the cytoplasm


DNA strand

Transcription

Translation

Polypeptide

RNA

Amino acid

Codon

A A A C C G G C A A A A

U U U G G C C G U U U U

Gene 1

Gene 2

Gene 3

DNA molecule

Gene Expression – DNA is a triplet codeFigure 10.7

OneDNA strand

Codon Codon Codon


The genetic code (using RNA codons)

UUUUUC

UAUUACUAA Stop

UAG Stop

UGUUGC

UGA StopUGG Trp

CUUCUCCUACUG

CCUCCCCCACCG

CAUCACCAACAG

CGUCGCCGACGG

GUUGUCGUAGUG

GCUGCCGCAGCG

GAUGACGAAGAG

GGUGGCGGAGGG

ACUACCACAACG

AAUAACAAAAAG

AGUAGCAGAAGG

AUUAUCAUAAUG Met or

START

Phe

Leu

Leu

lle

Val Ala

Thr

Pro

Ser

UCUUCCUCAUCG

Asn

Lys

His

Gln

Asp

Glu

Ser

Arg

Arg

Gly

CysTyr

G

A

C

U

U C A GUCAG

UCAG

UCAG

UCAG

Third base

Second base

First base

UUAUUG

Figure 10.8A


An exercise in translating the genetic codeFigure 10.8B

T A C T T C A A A A T C

A T G A A G T T T T A G

A U G A A G U U U U A G

Transcription

Translation

RNA

DNA

Met Lys PhePolypeptide

Startcodon

Stopcodon

Strand to be transcribed

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Types of RNA

1. Ribosomal RNA rRNA

2. Transfer RNA tRNA

3. Messenger RNA mRNA


Anticodon

Anticodon

3’

3’

Transfer RNA Structure & Function

Amino acidattaches here

tRNA red&yellowATP (green)Enzyme (blue)


Ribosomes build polypeptides• A ribosome consists of two subunits

– Each made up of proteins and a kind of RNA called ribosomal RNA

tRNAmolecules

mRNA Small subunit

Growingpolypeptide

Largesubunit

Figure 10.12A Ribosome Structure


Subunits of a ribosomeHold tRNA and mRNA close together during translation

Largesubunit

mRNA-binding site

Smallsubunit

tRNA-binding sites

Growing polypeptide

Next amino acid to be added to polypeptide

mRNA

tRNA

CodonsFigure 10.12B, C

Ribosome Structure


Smallsubunit

Largesubunit

FunctionalRibosome

mRNABinding

site

E P A

Fig. 15.2(TE Art)

Ribosome StructureCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

fMet

E

P site

A 5'

3'

UUA C

A G

Protein Synthesis: Initiation

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Elongationfactor

Leu

tRNAfMet

P site

E A

mRNA

5'3'

U UA A AC

CA U UG G

G

AC

Fig. 15.16a(TE Art)

Protein Synthesis: Elongation


LeufMet

5'3'

U UA A A

ACC

CA U UG G

G

Fig. 15.16b(TE Art)

Protein Synthesis: Elongation

E


Leu

fMet

5'3'

U UA A A

ACC

CA U UG G

G

Fig. 15.16c(TE Art)

Protein Synthesis: Translocation

E


Leu

fMet

5' 3'U UA A AAC

CC

A U UG GG

Fig. 15.16d(TE Art)

Protein Synthesis: Translocation

A


Leu

Leu Leu LeutRNA

fMet fMetfMet fMet

P site

E site

A site

mRNA

5' 5' 5' 5'3' 3' 3' 3'U UA AAACC

CAU UG GGU UA AAACC

CAU UG GGU UA AAACC

CAU UG GGU UA AACCAU UG G

GAC

Fig. 15.16(TE Art)

Protein Synthesis

Initiation Elongation Translocation


Val Ser

Ala Trp

Polypeptide chainreleased

tRNA

AA A

C CU UG G5'

3'

Fig. 15.17b(TE Art)

Release Factor

Protein Synthesis: Termination

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Val ValSer Ser

AlaAla

TrpTrp

Releasefactor

P siteE

site Asite

mRNA

Polypeptide chainreleased

tRNA Largeribosomalsubunit

Smallribosomalsubunit

ACC

AAACC

U UGGA AACCU UGG5' 5'

3' 3'

tRNA

Fig. 15.17(TE Art)

Protein Synthesis: Termination

Protein Synthesis Animation


Eukaryotic mRNA is processed before leaving the nucleus

Exon Intron Exon Intron ExonDNA

Cap TranscriptionAddition of cap and tail

RNAtranscript with capand tail Introns removed Tail

Exons spliced togethermRNA

Coding sequenceNucleus

Cytoplasm

mRNA

Figure 10.10


• Alternative splicing may generate two or more types of mRNA from the same transcript

DNA

RNAtranscript

mRNA

Exons

or

Figure 11.7Eukaryotic RNA may be spliced in more than one way


Gene Expression in Prokaryotes

mRNA

Protein

Translation

Transcription

mRNA

IntronDNA

Primary RNA transcript

Protein

Processing5’ 3’

Cap Poly-A tail

Translation

Transcription

Gene Expression in Eukaryotes


DNA

mRNA

DNA

Protein

mRNA

Protein

Lactose

Promoter OperatorLactose-utilization genes

repressor

RNA polymerasecannot attach topromoter

RNA polymerasebound to promoter

Inactiverepressor

Enzymes for lactose utilization

Operon turned off(lactose absent)

Operon turned on(lactose inactivates repressor)

Regulatorygene

Figure 11.1B Protein Assemblies Control Gene Expression

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Transcription Factors assist in initiating eukaryotic transcriptionEnhancers Promoter

GeneDNA

Activator proteins

Other proteins

Transcriptionfactors

RNA polymerase

Bendingof DNA Transcription

Figure 11.6 Protein Assemblies Control Gene Expression

RNA polymerase

END

Gene Expression

Documents

Molecular Biology of the Gene Outline: Molecular … 101 Fall...5 Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings Figure 10.9B Transcription of a gene RNA