17-1

Chapter 17: OutlineDNA

Mutation Chromosomes and

Variations Chromatin

Supercoiling Genome Structure

RNA

Transfer, Ribosomal, Messenger

Heterogeneous and Small Nuclear

Viruses

17-2

DefinitionsDNA stands for deoxyribonucleic acid.

It is the genetic code molecule for most organisms.

RNA stands for ribonucleic acid. RNA molecules are involved in converting the genetic information in DNA into proteins. In retroviruses, RNA is the genetic material.

17-3

17.1 Nucleic Acids, DNADNA 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

17-4

NucleobasesThe bases found in nucleic acids are

derived from either the purine or the pyrimidine ring systems.

NCH CH

N CHCH

NH

CCH

C

N

NCH

CH

N

pyrimidine purine

Examples follow on the next screen.

17-5

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

17-6

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

17-7

Some less common bases

NC CHN

O

CCNH2

H

CH3

NC CH2

NH

O

CH2CO

H

C NH

CHNC

NCHNH

CO

hypoxanthine

5-methylcytosine 5,6-dihydrouracil

17-8

NucleosidesA nucleoside is a

compound in which the DNA/RNA base forms a glycosidic link to the sugar molecule. The sugar molecule is numbered with primed numbers.

NCCH

C

N

NC

CH

N

NH2

OCH2

HOH

H

H

HH

OH

1'

2'3'

4'

5'

base

deoxyribose sugar

glycosidic link

17-9

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

17-10

Nucleotides-2Nucleotides are named after the parent

nucleoside. Examples follow.

C

C

N

C

C

NH

NH2

2-O3PO

OCH2

HOH

H

H

HH

CH3

O

Deoxythymidine 5’-monophosphate

17-11

Nucleotides-3

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’-monophosphate

Deoxycytidine5’-monophosphate

2-deoxy

17-12

Nucleotides-4

NCCH

C

N

NC

C

NH

O

NH2

2-O3PO

OCH2

H

OH

H

H

HH

NC CH

NH

O

CHC

O

2-O3PO

OCH2

H

OH

H

H

HH

Uridine 5’-monophosphate

Guanosine 5’-monophosphate

17-13

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 .

17-14

Segment of 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

17-15

Abbreviated DNADNA and RNA chains are abbreviated

using a structure where vertical lines represent the sugars, diagonal lines with P at the midpoint represent the 3,5-phosphodiester bonds, and horizontal lines the ends of the chain.

The structures are always written with the 5’ end to the left.

Single letter abbreviations are also used.

17-16

Abbreviated DNA-2

Or: pdGpdTpdC

Or: pd(GTC)RNA abbreviations lack the d (for deoxy)

PP P

G T CHO

5'

'3d d d

17-17

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.

17-18

DNA-Secondary Structure: 2

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

17-19

DNA-Secondary Structure: 3In addition to hydrogen bonding between

bases, other important noncovalent interactions contribute to helical stability.

2. Hydrophobic interactions among the bases.

3. Base stacking results in weak van der Waals attractions

4. Electrostatic interactions with Mg2+, histones, etc.

17-20

DNA: MutationsIf tautomers

form during replication, base mispairing can occur. E. g. purine for purine: a transition mutation

N C

CH C

N

NC

CHN

N HH

NCCHN

O

CHCN

H

H

|||||||||||

|||||||||||

A C

N C

CH C

N

NC

CHN

N

H

HNC

CHN

O

CHCN

H

H

17-21

DNA: Mutations-2Hydrolysis of purine-sugar

bond can occur and purine base is lost.

Bases can spontaneously deaminate.

(cytosine uracil)

Ionizing radiation can cause strand breaking and base modifications, esp. thymine dimers.

NC

CH

NO

CCO

CH3

H

NC

CH

NO

CCO

CH3

H

17-22

Xenobiotics1. Base analogues

Caffeine can pair with guanine causing a transition mutation.

2. Alkylating agents

Adenine and guanine are especially liable to alkylation (e. g. methylation).

Transversion mutations (purine for pyrimidine or reverse) are possible.

17-23

Xenobiotics-23. Nonalkylating agents

Nitrous acid deaminates bases.

Polyaromatic hydrocarbons are mutagenic and prevent base pairing.

4. Intercalating agents

Some planar molecules can insert between base pairs. Adjacent pairs may be deleted or new ones inserted resulting in a frame-shift mutation.

17-24

DNA: Variations on a ThemeThe Watson-Crick form of DNA (B-DNA)

is not the only one possible. A and Z forms also exist.

The forms differ in helical conformation.

17-25

B DNA segment

Sugar-phosphate backbone

Hydrogen bondedbase pairs in thecore of the helix

Chain 1

Chain 2

17-26

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

17-27

A DNA and Z DNAA second form of DNA is the A form.

It has 11 base pairs per turn of the helix and the bases lie at an angle of about 20o relative to the helix axis. It, too, is a right hand double helix.

A third form of DNA is the Z form. It is a left handed helix.

A picture of A DNA is on the next slide.

17-28

A DNA segment

Base pairs notperpendicular tohelix axis. 11 pairsper turn.

17-29

DNA, Higher Order StructureExamples of higher order structures

include cruciforms, triple helices, and supercoils.

Cruciforms are cross-like structures likely to form when the DNA sequence contains a palindrome, a sequence providing the same information read forward or backward.

E. g. MADAM I’M ADAM

17-30

CruciformsInverted repeats form palindromes within

DNA. Palindromes play an important role in the function of restriction enzymes.

ATATCGACTCCGATATTATAGCTGAGGCTATA

CGATAT ATATCG

GCTATA TATAGCA

C

T C G A

GT

17-31

Triple HelixA polypurine strand hydrogen-bonded to a

poly pyrimidine strand can form a triple helix (H-DNA) involving Hoogsteen base pairing.

17-32

SupercoilingProkaryotic DNA is circular. If the

circular loop of right-handed DNA is twisted in a left-handed manner the DNA is said to be negatively supercoiled. Cruciforms and H-DNA can result.

Extra right-handed twists results in a positively supercoiled loop of DNA. This is found when DNA coils around a protein core to form a supercoil.

17-33

Chromosomes (Prokaryote)In the nucloid the E. coli chromosome

(circular DNA) is attached to a protein core in at least 40 places.

The protein HU binds DNA. Polyamines (+ charge) bound to DNA help neutralize DNA charge for denser packing of the DNA.

A diagram of the E. coli chromosome is on the next slide.

17-34

The E. coli Chromosome

Fig 17.16

17-35

Chromosomes (Eukaryote)Eukaryotic chromosomes have two

unique structural elements:

Centromere: AT-rich, associated with nonhistome protein to form kinetochore which interacts with spindle fibers during cell division.

Telomeres: CCCA repeats at the end of DNA that postpone loss of coding on replication.

17-36

Chromosomes (Eukaryote)-2Each chromosome has one linear DNA

complexed with histone proteins to form nucleosomes. Histones regulate access to DNA of transcription factors.

Cells not undergoing cell division have partially decondensed chromosomes called chromatin which looks like a beaded chain.

As chromatin packs to form chromo-somes, 30nm and 200 nm fibers appear. Chromosomes have multiple levels of supercoiling.

17-37

Chromosomes (Eukaryote)-3

The figure below shows levels of coiled structure for nuclear chromatin.

17-38

GenomeThe genome of each living organism is

the full set of inherited instructions required to sustain all living processes.

Size varies: 1x106 to 1x1010 base pairs

Eukaryotes have larger and more complex information-coding capacity than prokaryotes.

17-39

Genome: Prokaryotes1. Size. Most prokaryotic genomes are

smaller: E. g. E. coli 4.6 Mb, 4300 genes.

2. Coding capacity. Genes are compact and continuous. Little, if any, noncoding DNA.

3. Gene expression. Higher percentage of operons, sets of linked genes.

Prokaryotes often contain plasmids, nonchromosome DNA.

17-40

Genome: Eukaryotes1. Genomic size. Larger than

prokaryotes but many have vast amounts of noncoding DNA.

2. Coding capacity. Enormous capacity but only about 1.5% codes for proteins.

3. Coding continuity. Most are dis-continuous and contain noncoding introns.

17-41

Genome: Eukaryotes-2About 45% of human genome is

“repeated sequences.”Tandem repeats (satellite DNA) have

multiple copies arranged next to each other and can vary from 10 to 2000 bp repeating to 105 to 107 bp.

Interspersed genome-wide repeats are scattered in the genome. Many result from transposition whereby DNA sequences are duplicated and moved in the genome.