Honors Biology Ch. 12 Molecular Genetics. CH. 12Molecular Genetics I.DNA: The Genetic Material -...

HonorsBiologyCh. 12

HonorsBiologyCh. 12

Molecular

Genetics Molecular

Genetics

CH. 12 Molecular Genetics

CH. 12 Molecular Genetics

I.I. DNA: The Genetic DNA: The Genetic MaterialMaterial

- DNA: The Chemical - DNA: The Chemical Basis of Heredity that Basis of Heredity that forms the universal forms the universal genetic code of cellsgenetic code of cells

A. Discovery of the Genetic Material

A. Discovery of the Genetic Material - In the early 1900’s scientists

were debating what was the genetic material: DNA vs. Protein.

1.Griffith 1.Griffith - In 1928 Griffith showed that a

heat killed, but lethal strain of pneumonia bacteria could ‘transform’ a harmless strain of pneumonia.

Can the Genetic Trait of Pathogenicity Be Transferred between Bacteria?

Can the Genetic Trait of Pathogenicity Be Transferred between Bacteria?

Bacteria of the “S” (smooth) strain of Streptococcus pneumoniae are pathogenic because they have a capsule that protects them from an animal’s defense system. Bacteria of the “R” (rough) strain lack a capsule and are nonpathogenic. Frederick Griffith injected mice with the two strains as shown below:

Griffith concluded that the living R bacteria had been transformed into pathogenic S bacteria by an unknown, heritable substance from the dead S cells.

EXPERIMENT

RESULTS

CONCLUSION

Living S(control) cells

Living R(control) cells

Heat-killed(control) S cells

Mixture of heat-killed S cellsand living R cells

Mouse dies Mouse healthy Mouse healthy Mouse dies

Living S cellsare found inblood sample.

2.Avery 2.Avery - In 1944 Avery isolated DNA,

proteins, and lipids from the heat-killed, lethal bacteria, and concluded that DNA was the transforming

agent.

3.Hershey and Chase 3.Hershey and Chase - In 1952 Hershey and Chase used

bacteria-infecting viruses containing either radioactively label S or P to show that DNA was the genetic material.

PhageheadPhagehead

Tail Tail Tail fiber

Tail fiber

DNA DNA

BacterialcellBacterialcell

100

nm

Viruses Infecting a Bacterial Cell

Viruses Infecting a Bacterial Cell

Is DNA or Protein the Genetic Material of Phage T2?Is DNA or Protein the Genetic Material of Phage T2?

In their famous 1952 experiment, Alfred Hershey and Martha Chase used radioactive sulfur and phosphorus to trace the fates of the protein and DNA, respectively, of T2 phages that infected bacterial cells.

EXPERIMENT

Radioactivity(phage protein)in liquid

Phage

Bacterial cell

Radioactiveprotein

Emptyprotein shell

PhageDNA

DNA

Centrifuge

Pellet (bacterialcells and contents)

RadioactiveDNA

Centrifuge

Pellet

Radioactivity(phage DNA)in pellet

Batch 1: Phages weregrown with radioactivesulfur (35S), which wasincorporated into phageprotein (pink).

Batch 2: Phages weregrown with radioactivephosphorus (32P), which was incorporated into phage DNA (blue).

1 2 3 4Agitated in a blender toseparate phages outsidethe bacteria from thebacterial cells.

Mixed radioactivelylabeled phages withbacteria. The phagesinfected the bacterial cells.

Centrifuged the mixtureso that bacteria formeda pellet at the bottom ofthe test tube.

Measured theradioactivity inthe pellet and the liquid

Phage proteins remained outside the bacterial cells during infection, while phage DNA entered the cells. When cultured, bacterial cells with radioactive phage DNA released new phages with some radioactive phosphorus.

Hershey and Chase concluded that DNA, not protein, functions as the T2 phage’s genetic material.

RESULTS

CONCLUSION

B. DNA Structure B. DNA Structure - The structure of DNA was discovered

by James Watson and Francis Crick in 1953.

Watson and Crick with Their DNA Model

Watson and Crick with Their DNA Model

- Rosalind Franklin used X-Ray diffraction to discover the shape and dimensions of DNA.

Rosalind Franklin Franklin’s X-ray diffractionPhotograph of DNA

1.Components of DNA (3 Main Parts)

c. Bases

a. Sugar(Deoxyribose)

b.Phosphate

c.c. BasesBases(1)Adenine(A)

Guanine (G)(2)Cytosine(C)

Thymine (T)

2.Nucleotide:- a subunit of a

nucleic acid containing a sugar, a phosphate, and a base

3.3.DNA Shape:DNA Shape:- double helixa. backbone - sugars

and phosphatesb. paired bases form

on the insidec. Base Pairing Rule: A : T , C : G

The Watson-Crick Model The Watson-Crick Model of DNA Structureof DNA Structure

Link to an interview with James Watson

(1:42)

II. Replication of DNAII. Replication of DNA ::- process by which DNA makes an

exact copy of itself

- occurs before mitosis during interphase

A.A.Semiconservative Semiconservative ReplicationReplication

- DNA strands separate and serve as templates for rebuilding the other half.

A

C

T

A

G

A

C

T

A

G

A

C

T

A

G

A

C

T

A

G

T

G

A

T

C

T

G

A

T

C

A

C

T

A

G

A

C

T

A

G

T

G

A

T

C

T

G

A

T

C

T

G

A

T

C

T

G

A

T

C

Parental DNA double helix

New double helix with 1 old &1 new strand

DNA DNA ReplicatioReplicatio

nn

FreeNucleotid

es

1.Unwinding - DNA helicase unwinds and

unzips DNA molecule.

- RNA primase adds a short segment (RNA primer)

on each DNA strand.

Overall direction of replication

Helicase unwinds theparental double helix.

Molecules of single-strand binding proteinstabilize the unwoundtemplate strands.

The leading strand issynthesized continuously in the5 3 direction by DNA pol III.

Leadingstrand Origin of replication

Laggingstrand

Laggingstrand

LeadingstrandOVERVIEW

Leadingstrand

Replication fork

DNA pol III

Primase

PrimerDNA pol III Lagging

strand

DNA pol I DNA ligase

1

2 3

Primase begins synthesisof RNA primer for fifthOkazaki fragment.

4

DNA pol III is completing synthesis ofthe fourth fragment, when it reaches theRNA primer on the third fragment, it willdissociate, move to the replication fork,and add DNA nucleotides to the 3 endof the fifth fragment primer.

5 DNA pol I removes the primer from the 5 endof the second fragment, replacing it with DNAnucleotides that it adds one by one to the 3’ endof the third fragment. The replacement of thelast RNA nucleotide with DNA leaves the sugar-phosphate backbone with a free 3 end.

6 DNA ligase bondsthe 3 end of thesecond fragment tothe 5 end of the firstfragment.

7

Parental DNA

5

3

43

21

5

3

DNA Replication

DNA Replication

2.Base Pairing - DNA polymerase adds nucleotides

with the complementary base on the 3’ end of each strand.

- The leading strand is synthesized continuously by adding nucleotides to 3’ end.

- The lagging strand is synthesized from Okazaki fragments which are later connected by DNA ligase.

3. Joining - RNA primers are replaced by

DNA nucleotides

- DNA ligase connects the fragments together.

Link to DNA

Replication Video Clip

(2:19)

Overall direction of replication

Helicase unwinds theparental double helix.

Molecules of single-strand binding proteinstabilize the unwoundtemplate strands.

The leading strand issynthesized continuously in the5 3 direction by DNA pol III.

Leadingstrand Origin of replication

Laggingstrand

Laggingstrand

LeadingstrandOVERVIEW

Leadingstrand

Replication fork

DNA pol III

Primase

PrimerDNA pol III Lagging

strand

DNA pol I DNA ligase

1

2 3

Primase begins synthesisof RNA primer for fifthOkazaki fragment.

4

DNA pol III is completing synthesis ofthe fourth fragment, when it reaches theRNA primer on the third fragment, it willdissociate, move to the replication fork,and add DNA nucleotides to the 3 endof the fifth fragment primer.

5 DNA pol I removes the primer from the 5 endof the second fragment, replacing it with DNAnucleotides that it adds one by one to the 3’ endof the third fragment. The replacement of thelast RNA nucleotide with DNA leaves the sugar-phosphate backbone with a free 3 end.

6 DNA ligase bondsthe 3 end of thesecond fragment tothe 5 end of the firstfragment.

7

Parental DNA

53

43

21

5

3

A Summary of DNA Replication

A Summary of DNA Replication

TelomeresTelomeres

1 µm

B.DNA Replication in Prokaryotes

- Prokaryotic chromosomes made of one circular DNA strand without proteins.

- DNA replication begins at a single origin of replication and occurs very quickly.

Origins of Replication in

Eukaryotes

Origins of Replication in

Eukaryotes

Replication begins at specific siteswhere the two parental strandsseparate and form replicationbubbles.

The bubbles expand laterally, asDNA replication proceeds in bothdirections.

Eventually, the replicationbubbles fuse, and synthesis ofthe daughter strands iscomplete.

1

2

3

Origin of replication

Bubble

Parental (template) strand

Daughter (new) strand

Replication fork

Two daughter DNA molecules

In eukaryotes, DNA replication begins at many sites along the giantDNA molecule of each chromosome.

In this micrograph, three replicationbubbles are visible along the DNA ofa cultured Chinese hamster cell (TEM).

(b)(a)

0.25 µm

C.Chromosome Structure C.Chromosome Structure - Chromosomes of eukaryotes are made of

DNA and proteins forming bead-shaped nucleosomes which are coiled and folded to form chromatin.

Structure of a Eukaryotic

Chromosome

Structure of a Eukaryotic

Chromosome

C.Chromosome Structure C.Chromosome Structure - Chromosomes of eukaryotes are made of

DNA and proteins forming bead-shaped nucleosomes which are coiled and folded to form chromatin.

Link to DNA Packaging

Video Clip (1:43)

III. DNA, RNA, and Protein

III. DNA, RNA, and Protein

A. ‘Central Dogma’- DNA codes for RNA which guides protein synthesis

1.Gene1.Gene- a specific sequence of bases

in DNA that determines the sequence of amino acids in a protein

- composed of 50-20,000amino acids- 4 Levels of Structure:a) Primary:

- sequence of amino acidsb) Secondary:

- either -helical or “β-pleated sheet”c) Tertiary:

- globular (3-dimensional)d) Quaternary:

- 2+ polypeptides combined

2.Proteins2.Proteins

Illustration of Protein Structure

Primary(Amino Acid Sequence)

Primary(Amino Acid Sequence)

Secondary(Helix)

Secondary(Helix)

Tertiary(Bending)Tertiary

(Bending)

Quaternary(Layering)Quaternary(Layering)

Structural Proteins

Structural Proteins

HairHair

HornHorn

SpiderwebSpiderweb

||SS||SS||

||SS||SS||

HairStructure

HairStructure

Single hair Hair Cell

MicrofibrilProtofibril

Hydrogen bonds

disulfide bridges

Curling of HairCurling of Hair|| SS || SS ||

|| SS || SS ||

|| SS || SS ||

StraightHair

||SS ||

SS ||

|| SS || SS ||

|| SS || SS ||

||SS||SS||

||SS||

SS||

NaturallyCurlyHair

|| SS || SS ||

|| SS || SS |||| SS || SS ||

|| SS || SS || ||SS||

SS||

||SS

||

SS||

PermanentWave

B.RNA Structure:

- Nucleic acid that makes protein

DNA RNA Shape double helix single helixSugar deoxyribose riboseBase thymine uracilSize very large smallerLocation nucleus cytoplasmFunction - stores genetic - makes

info protein- replication- makes RNA

B. RNA Structure:

C.Transcription:

- the copying of a genetic message from DNA to RNA

Original DNA

DNA base pairs

separate

C.Transcription:

- the copying of a genetic message from DNA to RNA

DNA half ‘transcribes’

RNA

C.Transcription:

- the copying of a genetic message from DNA to RNA

RNA released to make protein

C.Transcription:

- the copying of a genetic message from DNA to RNALink to

Transcription Video Clip

(1:54)

Transcription: First Two Steps

Transcription: Last Step

11 22tRNA

docking sitesAmino

acidtRNA

Smallsubunit

Ribosomecontains rRNA

Largesubunit

CC

AA

GG

AA

UU

GG

GG

AA

GG

UU

UU

AA

UU

GG

GG

mRNAmRNA

AA GG UU

Met

anticodon

Three Types of RNA

codons

D.D. Messenger RNA (mRNA):Messenger RNA (mRNA):D.D. Messenger RNA (mRNA):Messenger RNA (mRNA):- carries the information for

making a protein from DNAto the ribosomes

- acts as a template (pattern)- contains codonscodons:

triplets of bases that code for a particular amino acid

- Start Codon:(AUG) - marks the start of a polypeptide

- Stop Codon:(UAA, UAG, UGA) - marks the end

E. Transfer RNA (tRNA):E. Transfer RNA (tRNA):- carries amino acid to specific

place on mRNA- contains Anticodon:

triplet of bases complimentary to mRNA codon

F. Ribosomal RNA (rRNA):F. Ribosomal RNA (rRNA):- transcribed in nucleus and

combined with protein into ribosomes (site of protein synthesis)

IV.IV. Translation:Translation:IV.IV. Translation:Translation:- protein synthesis- decoding the "message" of

mRNA into a protein

Link to Translation Video Clip

(2:05)

Information Flow:Information Flow:Information Flow:Information Flow:DNA RNA ProteinDNA RNA Protein

Translation: Translation: InitiationInitiation

Translation: Elongation Translation: Elongation 11

Translation: Elongation Translation: Elongation 22

Translation: Elongation Translation: Elongation 33

Translation: Elongation Translation: Elongation 44

Translation: Elongation Translation: Elongation 55

Translation: Translation: TerminationTermination

V. Genetic Regulation and Mutations

V. Genetic Regulation and Mutations

A. Prokaryotic Gene Expression

A. Prokaryotic Gene Expression- Prokaryotic cells regulated gene

expression with a set of genes called an operon.

- An operon consists of1. Operator2. Promoter3. Regulatory gene4. Protein coding genes

Trp Operon: Inducible Operon

Trp Operon: Inducible Operon

Regulation of a Metabolic Pathway

(a) Regulation of enzyme activity

Enzyme 1

Enzyme 2

Enzyme 3

Enzyme 4

Enzyme 5

Regulationof geneexpression

Feedbackinhibition

Tryptophan

Precursor

(b) Regulation of enzyme production

trpD Gene

trpE Gene

trpC Gene

trpB Gene

trpA Gene

–

–

The trp operon: regulated synthesis of repressible

enzymes

Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes.Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes.

Genes of operon

Inactiverepressor

Protein

Operator

Polypeptides that make upenzymes for tryptophan synthesis

Promoter

Regulatorygene

RNA polymerase

Start codon Stop codon

Promoter

trp operon

5

3mRNA 5

trpDtrpE trpC trpB trpAtrpRDNA

mRNA

E D C B A

DNA

mRNA

Protein

Tryptophan(corepressor)

Active repressor

No RNA made

Tryptophan present, repressor active, operon off. As tryptophanaccumulates, it inhibits its own production by activating the repressor protein.Tryptophan present, repressor active, operon off. As tryptophanaccumulates, it inhibits its own production by activating the repressor protein.

Lac Operon: Repressible Operon

Lac Operon: Repressible Operon

Video Clip about the Lac operon (2:31).

The lac Operon: Regulated Synthesis of Inducible

Enzymes

DNA

mRNA

ProteinActiverepressor

RNApolymerase

NoRNAmade

lacZlacl

Regulatorygene Operator

Promoter

Lactose absent, repressor active, operon off. The lac repressor is innately active, and inthe absence of lactose it switches off the operon by binding to the operator.Lactose absent, repressor active, operon off. The lac repressor is innately active, and inthe absence of lactose it switches off the operon by binding to the operator.

5

3

mRNA 5'

DNA

mRNA

Protein

Allolactose(inducer)

Inactiverepressor

lacl lacz lacY lacA

RNApolymerase

Permease Transacetylase-Galactosidase

5

3

Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced.Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced.

mRNA 5

lac operon

LUX Operon Controls Light Production

LUX Operon Controls Light Production

Video Clip about how a single transcription factor controls the LUX operon, which contains five genes necessary to produce bioluminescence in bacteria (2:26).

Light Emitted by

Bacterial Luciferase

Light Emitted by

Bacterial Luciferase

B. Eukaryotic Gene Expression

B. Eukaryotic Gene Expression- Eukaryotic cells regulate gene

expression using various transcription factors and other processes.

Distal controlelement

Activators

Enhancer

PromoterGene

TATAbox

Generaltranscriptionfactors

DNA-bendingprotein

Group ofMediator proteins

RNAPolymerase II

RNAPolymerase II

RNA synthesisTranscriptionInitiation complex

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation

Protein processingand degradation

A DNA-bending proteinbrings the bound activators

closer to the promoter.Other transcription factors,

mediator proteins, and RNApolymerase are nearby.

2

Activator proteins bindto distal control elementsgrouped as an enhancer in the DNA. This enhancer hasthree binding sites.

1

The activators bind tocertain general transcription

factors and mediatorproteins, helping them form

an active transcriptioninitiation complex on the promoter.

3

Eukaryotic Gene Expression

Eukaryotic Gene Expression

C. MutationsC. Mutations- any change in the nucleotide sequence of DNA- can occur in any cell* Somatic (body cell) Mutations:

- may be harmful but not inherited* Gamete (germ cell) Mutations:

- can be inherited

C.MutationsC.Mutations- usually recessive- many are harmful- some are neutral- some beneficial

(leads to evolution)- Mutagens: cause mutations1) Radiation- UV, X-rays, etc.2) Chemicals (asbestos, etc.)

D.Types of Mutations:D.Types of Mutations:1. Point Mutation

- change of a single base- ex: sickle-cell anemia

AUG GGG CUU CUU AAU

AUG GGG CAU CUU AAU

Normal Red Blood Cells

Sickled Cells

Link to a Video Clip about Sickle

Cell Disease(0:59)

2.Frameshift Mutation2.Frameshift Mutation- addition or deletion of a single base

AUG GGG CUU CUU AAU

AUG GGG CAU UCU UAA U

3.Chromosomal Mutation3.Chromosomal Mutation- change in an entire chromosome or in

chromosome number within a cell

a) Translocation:a) Translocation:- transfer of a chromosome

segment to a nonhomologous chromosome

Normal

Translocation

b) Inversion:b) Inversion:- rotation of a chromosome segment

Normal

Inversion

c) Insertion:c) Insertion:- breaking off of a chromosome

segment and attaching to its homologue

Normal

Insertion

d) Deletion :d) Deletion :- chromosome segment left out

Normal

Deletion

The The EndEnd

AminoAcids

ActiveProtein

Overview ofInformation

Flow

Overview ofInformation

Flow

InactiveProtein

(Cytoplasm)

DNA(Nucleus)

rRNA tRNA

1 Transcription

+ Proteins

RibosomestRNA

tRNA-AA

mRNA

mRNA

2 Translation

3 Modification

ProductSubstrate

4 Degradation

GG GG GG AA GG CC GG AA UU UU UU

CC AA AA CC AA UU CC CC UU

Methionine Glycine Valine

templateDNA strand

(a) complementaryDNA strand

(b) mRNA

(c) tRNA

(d) protein

amino acids

anticodons

codons

gene

GG GG GG AA GG TT TT CC TT GG AA

GG TT CC CC CC CC AA AA AA TT CC

Complementary Base Pairing

Complementary Base Pairing

Incorporation of a Nucleotide into a DNA

Strand

Incorporation of a Nucleotide into a DNA

StrandNew strand Template strand

5’ end 3’ end

Sugar A TBase

C

G

G

C

A

C

T

PP

P

OH

P P

5’ end 3’ end

5’ end 5’ end

A T

C

G

G

C

A

C

T

3’ end

Nucleosidetriphosphate

Pyrophosphate

2 P

OH

Phosphate