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Chemistry 501 Handout 24 Genes and Chromosomes Chapter 24. Dep. of Chemistry & Biochemistry Prof. Indig. Lehninger. Principles of Biochemistry. by Nelson and Cox, 5 th Edition; W.H. Freeman and Company. Colinearity of the coding nucleotide sequences of DNA and mRNA

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chemistry 501 handout 24 genes and chromosomes chapter 24

Chemistry 501 Handout 24Genes and ChromosomesChapter 24

Dep. of Chemistry & Biochemistry

Prof. Indig

Lehninger. Principles of Biochemistry.

by Nelson and Cox, 5th Edition; W.H. Freeman and Company

slide2

Colinearity of the coding nucleotide sequences of DNA and mRNA

and the amino acid sequence of a polypeptide chain.

codon

slide6

Eukaryotic Chromosomes

Sister chromatids

slide7

A dividing mitochondrion

The mtDNA is replicated each time the mitochondrion divides

slide9

Types of sequences in the human genome

Short interspersed elements

100 to 300 bp

Long interspersed elements

6 to 8 kbp

(encode enzymes for transposition)

1.5 to 11 kbp

Simple sequence

repeats

Large segmental

duplications

slide11

Supercoiling of DNA

Supercoiling induced by separating the strands

of a helical structure

slide13

Most cellular DNA is underwound

DNA underwinding is defined

by topological linking number

84 bp

slide14

Superhelical density

s = DLk/Lk0 = -2/200 = -0.01

1% of the helical turns present in the

DNA (in its B form) has been removed

Linking number applied to

closed-circular DNA molecules

Negative and positive

supercoils

underwinding

overwinding

topoisomers

2,100 bp

slide15

Linking number can be broken down into two structural components

Twist (Tw) and Writhe (Wr)

Measure of the coiling of the

helix axis

Local twisting

or spatial

relationship

of neighboring

base pair

Lk = Tw + Wr

slide17

In addition of causing supercoiling and making strand separation somewhat easier,

the underwinding of DNA facilitates structural changes in the molecule

facilitates the partial strand

separation needed to promote

cruciform formation at

appropriate sequences

slide18

Topoisomerases catalyze changes in the linking number of DNA

Type 1: single strand breaks;

changes Lk in increments of 1

Type 2: double strand breaks;

changes Lk in increments of 2

Type 1

(Dt)

slide19

Bacterial type 1 topoisomerase alter linking number

Generally relax DNA by removing negative supercoils

(increasing Lk)

slide22

Proposed mechanism for the alteration of linking number by

eukaryotic type IIA topoisomerase

Two ATPs are bound and hydrolyzed during this cycle

slide23

Without topoisomerases, cells cannot replicate or package

their DNA, or express their genes, and they die.

They are important drug targets for bacterial infections and cancer

Topoisomerase inhibitors are

important pharmaceutical agents

antibiotics

Chemotherapeutic agents

slide24

DNA compaction requires a special form of supercoiling

The supercoils are right-handed in a negatively supercoiled DNA molecule, and they

tend to be extended and narrow rather than compacted, often with multiple branches.

Plectonemic supercoiling

slide25

DNA compaction requires a special form of supercoiling

Solenoidal supercoiling

provides a much greater

degree of compaction

(tight left-handed turns)

Same DNA molecule, drawn in scale

slide28

Histone cores do not bind randomly to DNA;

rather, they tend to position themselves at certain locations

In some cases seems to

depend on a local abundance

of A=T base pairs in the DNA

helix where it is in contact with

the histone

slide29

The structure of chromosomes

The chromosomal material, chromatin, consists of DNA and proteins.

Nucleosomes are the

fundamental organizational unit

of chromatin

Beginning with nucleosomes,

eukaryotic chromosomal DNA

is packed in a sucession of

higher-order structures that

ultimately yield the compact

chromosome

beads-in-a-string

Nucleosomes

slide30

DNA wrapped around the nucleosome core

Eight histone proteins

Two of each: H2A, H2B, H3, and H4

Top view

Side view

Histone complex

Nucleosome with 146 bp of bound DNA

The DNA binds in a left-handed solenoidal supercoil that

circumnavigates the histone complex 1.8 times

slide32

Compaction of DNA in a eukaryotic chromosome.

Loops of chromosomal DNA

attached to a nuclear scaffold.

Next level of organization

(after 30 nm fiber)

DNA compaction in eukaryotes

is likely to involve coils upon coils

upon coils….

slide33

Structure of SMC proteins.

(Structural Maintenance of Chromosomes)

also bound to additional

regulatory proteins (not shown)

slide35

Bacterial DNA is also highly organized.

Looped domains of the E. coli chromosome.

E. coli nucleoids.

slide37

A partially unraveled human chromosome, revealing numerous loops of DNA

attached to a scaffoldlike structure.

slide38

Several variants of histones H3, H2A, and H2B are known

Information that is passed from

one generation to another but is

not encoded in DNA is referred

to as epigenetic information.

Much of it is in the form of covalent modification of histones and/or placement of histone variants in chromosome

Histone-fold domain

(common to all core histones)

Sites of Lys/Arg residue methylation and Ser phosphorylation are indicated

slide39

ChIP-chip experiment designed to reveal the genomic DNA sequences

to which a particular histone variant binds.

slide40

The pattern of hybridization on the microarray reveals the DNA sequences

bound by the nucleosomes with the histone variant.