fill in ap paper and then make a chart enzyme role in what process? helicase dna polymerase...

Fill in AP paper and thenmake a chart

Enzyme Role In what process?

HelicaseDNA polymeraseTopoisomerasePrimaseLigaseNucleaseTelomeraseRNA polymerasesnRNA

DNA Replication: A Closer Look

• The copying of DNA is remarkable in its speed and accuracy

• More than a dozen enzymes and other proteins participate in DNA replication

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Origins of ReplicationVideo

• At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating

• Helicases are enzymes that untwist the double helix at the replication forks

• Single-strand binding protein binds to and stabilizes single-stranded DNA until it can be used as a template

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

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Fig. 16-13

Topoisomerase

Helicase

PrimaseSingle-strand binding proteins

RNA primer

55

5 3

3

3

DNA Polymerase

3’ 5’

3’5’ Pol

Pol

Leading and Lagging Strands

5’

5’

3’

3’

Leading Strand

Lagging Strand

Pol

3’

5’

Okazaki FragmentsRNAPrimer

Video

Other Proteins at Replication Fork

Pol

5’

5’

3’

3’

Leading Strand

Lagging Strand

Pol

3’

5’

Okazaki Fragments

Helicase

Single StrandedBinding Proteins

Primase

DNA Pol I

Ligase

DNA Pol III

Fig. 16-16 Overview

Origin of replication

Leading strand

Leading strand

Lagging strand

Lagging strand

Overall directions of replication

Template strand

RNA primer

Okazaki fragment

Overall direction of replication

12

3

2

1

1

1

1

2

2

51

3

3

3

3

3

3

3

3

3

5

5

5

5

5

5

5

5

5

5

53

3

Damaged DNA Nuclease Excision Repair

Nuclease

DNA Polymerase

Ligase

Replicating the Ends of DNA Molecules

• Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes

• The usual replication machinery provides no way to complete the 5 ends, so repeated rounds of replication produce shorter DNA molecules

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Replicating Ends of Linear Chromosomes

Fig. 16-19Ends of parental DNA strands

Leading strand

Lagging 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

5

3

3

3

3

3

5

5

5

5

• 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

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Telomerase

Central Dogma of Molecular Biology

Gene Structure

Promoter Terminator

Transcribed Region

RNA( )Open Reading Frame5’UTR 3’UTR

Three Parts to Transcription• Transcriptional Initiation –

– RNA polymerase binds to promoter– DNA strands separate– RNA synthesis begins as ribonucleotides complementary to template

strand are linked• Transcriptional Elongation

– RNA polymerase moves down DNA unwinding a small window of DNA.– Nucleotides are added to the growing RNA chain

• Transcriptional Termination– When the RNA polymerase reaches terminator the RNA and the RNA

polymerase are released from the DNA.

RNA Processing in Eukaryotes5’ 3’

Modification of 5’ and 3’ ends

Pre-mRNA (hnRNA)

Spicing of exons

5’CAP Poly A tailExon1 Intron1 Exon2 Intron2 Exon3 Intron3 Exon4

Genetic Code

Identifying ORF

• Locate start codon (1st ATG from 5’ end)

• Identify Codons (non overlapping units of three codons including and following start codon)

• Stop at stop codon ( remember stop codon doesn’t encode amino acid)

• Nucleotides before start codon – 5’UTR

• Nucleotides after stop codon -3’UTR

• [MetArgAsnAlaSerLeu]

GACGACGGAUGCGCAAUGCGUCUCUAUGAGACGUAGCUCAC5’

Players in Translation

mRNA – Genetic CodeRibosome – synthesizes protientRNA – adaptor moleculeAmino acidsAminoacyl tRNA synthetases

- attach amino acids to tRNAs

Fig. 17-18-4

Amino endof polypeptide

mRNA

5

3E

Psite

Asite

GTP

GDP

E

P A

E

P A

GDPGTP

Ribosome ready fornext aminoacyl tRNA

E

P A

tRNA

Ribosomes

Three parts to Translation• Initiation

– Delivery of Ribosome with first tRNA to start codon.• Elongation Cycle

– Three Parts of Elongation Cycle• Delivery of tRNA to A site• Transpeptidase Activity – Amino acids on tRNA in P site cleaved from

tRNA and attached to amino acid on tRNA in A site.• Translocation – Ribosome ratchets over on codon. The tRNA that was in

the A site is moved to the P site. The uncharged tRNA in the P site exits the ribosome through the E site.

• Termination– When ribosome reaches the stop codon a release factor

binds to the A site and triggers the release of the polypeptide. The ribosome releases the tRNA and the mRNA.

The Functional and Evolutionary Importance of Introns

• Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing

• Such variations are called alternative RNA splicing• Because of alternative splicing, the number of

different proteins an organism can produce is much greater than its number of genes

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Fig. 17-12Gene

DNAExon 1 Exon 2 Exon 3Intron Intron

Transcription

RNA processing

Translation

Domain 2

Domain 3

Domain 1

Polypeptide

Polysomes

• Polypeptide synthesis always begins in the cytosol• Synthesis finishes in the cytosol unless the

polypeptide signals the ribosome to attach to the ER

• Polypeptides destined for the ER or for secretion are marked by a signal peptide

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• A signal-recognition particle (SRP) binds to the signal peptide

• The SRP brings the signal peptide and its ribosome to the ER

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Proteins targeted to ER

Functions of RNA

• mRNA – genetic code• tRNA – adaptor molecules• rRNA- part of ribosome• snRNA – part of splicosome• SRP RNA – part of SRP• siRNA- eukaryotic gene regulation

Silent Mutations

Missense Mutations

Nonsense Mutations