24-1

Principles and Applications ofInorganic, Organic, and

Biological ChemistryDenniston, Topping, and Caret

4th ed

Chapter 24

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

Power Point to Accompany

24-2

24.1Structure of the NucleotideDNA and RNA are polymers whose

monomer units are called nucleotides

A nucleotide itself consists of:

1. a nitrogen containing heterocyclic base

2. a ribose or deoxyribose sugar ring

3. a phosphoric acid unit

24-3

Major Purine Bases

NCCH

C

N

NC

CH

N

NH2

HNC

CHC

N

NC

C

NH

O

HNH2

12

3 4

56 7

89

adeninein DNA and RNA

guaninein DNA and RNA

24-4

Major Pyrimidine Bases

NC CHNH

O

CCO

CH3

HN

C CHN

O

CHCNH2

HN

C CHNH

O

CHCO

H

12

3 4 5

6

cytosinein DNAand RNA

thyminein DNAand some RNA

uracilin RNA

24-5

Nucleotides-1A nucloetide is the

repeating unit of the DNA or RNA polymer. The nitrogen base is attached to the ribose (RNA) or deoxyribose (DNA) ring. The sugar is phosphorylated at carbon 5’

NCCH

C

N

NC

CH

N

NH2

2-O3PO

OCH2

HOH

H

H

HH

base

deoxyribose sugar

phosphateester

24-6

Nucleotides-2: NamesBegin with the name of the nitrogenous base.

• Remove –ine ending and replace with:

– -osine for purines or –idine for pyramidines. Uracil: -acil with –idine.

• ribose then ribonucleotide

– deoxyribose then deoxyribonucleotide

– deoxy before base name for deoxyribonucleotide

• Add prefix for number of phosphoryl groups

– Monophosphate, diphosphate, triphosphate

24-7

Nucleotides-3

C

C

N

C

C

NH

NH2

2-O3PO

OCH2

HOH

H

H

HH

CH3

ODeoxythymidine 5’-monophosphatedTMP

24-8

Nucleotides-4

NCCH

C

N

NC

CH

N

NH2

O P

O

O

OO

CH2

H

OH

H

H

HH

NC CH

N

O

CHC

NH2

O P

O

O

OO

CH2

H

OH

H

H

HH

Deoxyadenosine5’-monophosphatedAMP

Deoxycytidine5’-monophosphatedCMP

2-deoxy

24-9

Nucleotides-5Uridine 5’-monophosphateUMP

Guanosine 5’-monophosphate, GMP

NCCH

C

N

NC

C

NH

O

NH2

2-O3PO

OCH2

H

OH

H

H

HH

NC CH

NH

O

CHCO

2-O3PO

OCH2

H

OH

H

H

HH

24-10

24.2 DNA/RNA ChainsWhen nucleotides polymerize, the 5’

phosphate on one unit esterifies to the 3’ OH on another unit. The terminal 5’ unit retains the phosphate. An example of a three nucleotide DNA product is shown on the next slide .

24-11

Segment of One DNA Chain

NCCH

C

N

NC

C

N

O

NH2-2

O3POO

CH2

H

O

H

H

HH

NC CH

N

O

CC

O

CH3

O P

O

OO

CH2

H

O

H

H

HH

NC CH

N

O

CHC

NH2

O P

O

OO

CH2

H

OH

H

H

HH

5’-end

3’-end

guanine

thymine

cytosine3’-5’link

24-12

DNA-Secondary StructureThe most common form of DNA is the

form . Its structure was determined by Watson and Crick in 1953.

This DNA consists of two chains of nucleotides coiled around one another in a right handed double helix.

The chains run antiparallel and are held together by hydrogen bonding between complimentary base pairs: A=T, G=C.

24-13

Insert Fig 24.4

24-14

DNA-Secondary Structure, cont.

Hydrogen bonding between A and T or G and C helps to hold the chains in the double helix

N C

CH C

N

NC

CHN

N HH

N C

CH C

N

NC

CN

O

N H

H

H

NCCHN

O

CCO CH3

H

NCCHN

O

CHCN

H

H

|||||||||||

|||||||||||

A T

|||||||||||

|||||||||||

|||||||||||G C

The strands are said to be complimentary

24-15

B DNA segment

Sugar-phosphate backbone

Hydrogen bondedbase pairs in thecore of the helix

Chain 1

Chain 2

24-16

B DNA: 2

Outside diameter, 2 nm

Length of one turn of helix is 3.4 nm and contains 10 base pairs.

Interior diameter, 1.1 nm

Major groove

Minor groove

24-17

ChromosomesChromosomes are pieces of DNA that contain

the genetic instructions, or genes, of an organism.

Prokaryotes (single chromosome)

No true nucleus. Chromosome is a circular DNA molecule that is supercoiled, that is, the helix is coiled on itself.

At approximately 40 sites a complex of proteins is attached, forming a series of loops.

This structure is the nucleoid.

24-18

Chromosomes, cont.Eukaryotes (Number and size of

chromosomes vary.)

True nucleus. Membrane bound organelles that separate cellular functions.

Nucleosome which consists of a strand of DNA wrapped around a disk of histone proteins.

Larger structure is the 30 nm fiber.

Coiled in to a 200 nm fiber

24-19

RNA Structure

Sugar-phosphate backbone for ribonucleotides linked by 3’-5’ phosphodiester bonds.RNA molelcules usually single stranded.Ribose replaces deoxyribose.Uracil replaces thymine.

Base pairing between U and A and G and C results in portions of the single strand that become double stranded.

24-20

24.4 Information FlowDNA RNA Protein

Replication: DNA duplicates itselfTranscription: RNA is made on a DNA templateTranslation: Protein is synthesizedfrom AAs and the three RNAs.Reverse Transcription: RNA directs synthesis of DNA

24-21

Classes of RNA Structuretransfer RNA (tRNA)

Transfers amino acids to the site of protein synthesis (ribosomes). Has the anticoden.

ribosomal RNA (rRNA)rRNA forms ribosomes by reacting with

proteinsmessenger RNA (mRNA)

mRNA directs the AA sequence of proteins and is a complimentary copy of a gene. It has the codon for an AA in a protein,

24-22

tRNAThere is at least one tRNA (and often several)

for each AA to be incorporated into a protein.

tRNA is single stranded with typically about 80 nucleotides.

Intrachain hydrogen bonding (A=U and G=C) occurs to gives regions called stems with an -helix

The overall structure is called a cloverleaf in a L-shaped conformation.

24-23

tRNA

Attachment tomRNA here

AAattacheshere

Transfer RNA (tRNA) transfers AA to the site of protein synthesis. Has the anticoden

24-24

TranscriptionTranscription is catalyzed by RNA polym-

erase. Initiation binds RNA polymerase to the promoter region at the beginning of the gene. Cain elongation then occurs forming a 3’-5’ phosphodiester bond. Termination is the final step of transcription.

Will Fig 24.12 fit here??

24-25

Post Transcription Processing, mRNAProkaryote mRNA is continuous.

Eukaryote mRNA must be processed:

A 5’ cap structure is added

A 3’ poly A tail (100 to 200 units) is added

The introns (noncoding base sequences) are cut out and the introns (coding sequences) are spliced together.

Splicosomes help recognize intron-exon boundaries. They are composed of small nuclear ribonucleoproteins (snRNPs, “snurps”).

24-26

24.5 The Genetic Code (DNA)The message on DNA translated to mRNA:

1. Degenerate: more than one three base codon can code for the same AA.

2. Specific: each codon specifies one AA

3. Nonoverlapping and commaless : none of the bases are shared between consecutive codons and no noncoding bases appear in the base sequence.

4. Universal: except in a few instances, all organisms use the same code.

24-27

The Genetic Code-2All 64 codons have meaning; 61 code for an

AA and three code for the “stop” signal.

Multiple codes for an AA tend to have two bases in common.

E. g. CUU, CUC, CUA, CUG code for leu

(codons are written: 5’-> 3’ sequence.)

A partial table for the genetic code follows on the next slide. See your text for a complete table.

24-28

The Genetic Code-35’ end Middle base 3’ end

U C A G

U phe ser tyr cys U

phe ser tyr cys C

leu ser end end A

leu ser end trp G

C leu pro his arg U

leu pro his arg C

leu pro gln arg A

leu pro gln arg G

24-29

The Genetic Code-4Use the table in slide 6 to answer the

questions. Click for the answer.

1. CCU codes for: ?

2. CGA codes for: ?

3. UCA codes for: ?

proargser

24-30

24.6 Protein SynthesisProtein synthesis is called translation. It is

carried out on ribosomes, complexes of rRNA and proteins.

Protein synthesis occurs in multiple places on one mRNA. The mRNA plus the multiple ribosomes are called a polysome,

tRNA binds a specific AA aided by aminoacyl tRNA synthethase and recognizes the appropriate codon on the mRNA.

24-31

Translation Process-1Initiation

Initiation factors (proteins), mRNA, initiator tRNA, and small and large ribosomes come together.

Ribosome has two sites to bind tRNAP-site binds to the growing peptideA-site binds the aminoacyl tRNA

Chain ElongationAn aminoacyl tRNA binds to A sitePeptide bond formation occursTranslocation (movement) of ribosome

down the mRNA chain to next codon.

24-32

Translation Process-2Termination

Upon finding a “stop” codon a release factor binds a the empty A site.

The bond between the last AA and peptidyl tRNA is hydrolyzed releasing the protein.

The protein released may not be in its final form. Cleavage, association with other proteins, and bonding to carbohydrate or lipid groups may occur before a protein is fully functional.

24-33

Insert Fig 24.19

24-34

24.7 Mutation and RepairMutations are mistakes introduced into the

DNA sequence of an organism.

They can be classified as:

Point: substitution of a single nucleotide for another.

Deletion: one or more nucleotides are lost.

Insertion: one or more nucleotides are added.

Many mutagens (chemicals causing a change in the DNA sequence) are also carcinogens and cause cancer.

24-35

UV Damage and DNA RepairUV light causes formation of a pyrimidine

dimer on a DNA strand. Failure to repair this defect can lead to xeroderma pigmentosum.

People who suffer from this genetic skin disorder are very sensitive to UV light and develop multiple skin cancers.

Insert Fig 24.20

24-36

24.8 Recombinent DNARestriction enzymes are bacterial enzymes

that cut the backbone of DNA at specific nucleotide sequences.

Donor and plasmid (bacteria) DNA are cleaved by the same restriction enzyme.

Donor and plasmid DNA are mixed and donor fragment joins to a complimentary plasmid fragment due to hydrogen bonding.

Plasmid ring is restored using using DNA ligase.

Engineered plasmid (recombinent DNA) is introduced to a bacterium to be reproduced.

24-37

24.9 Polymerase Chain ReactionDNA is mixed with Taq polymerase (a heat

stable DNA polymerase), a primer DNA sequence for a specific gene, and the four nucleotide triphosphates.

A thermocycler raises the temperature to 94-96 oC to separate the DNA strands, lowers the temperature to 50-56 oC to the primers to hybridize to the DNA, and raises the temperature to 72 oC to allow the Taq polymerase to act.

Repeating the cycle doubles the new DNA strands each cycle. (12481632 etc)

24-38

24.10 Human Genome ProjectThe DNA to be sequenced is placed in four

test tubes (tt) with all the enzymes and nucleotides necessary for DNA synthesis.

In addition, each tt contains a small amount of one species of dideoxynucleotide with an H at the 3’ position. Once this is incor-porated in the growing chain, chain synthesis stops.

The DNA fragments are separated by gel electrophoresis in four wells side by side.

The sequence is read from the gel as shown in the figure on the next slide.

24-39

Insert Fig 24.26

24-40

The End

Introduction to

Molecular Genetics