Lecture 2: DNA basics

Question 1

Epigenetic + examples

Answer 1

a form of inheritance based on inherited chromatin structure rather than DNA sequence

DNA methylation; chromatin structure; histone modification

in other words, DNA is identical, it’s the particularities of the chromatin structure that are “superimposed” on the genetic inheritance based on DNA

Example:

Gene-A (activated) —> Chromatin-alteration-Gene A (now deactivation) —> clones of chromatin-altered Gene-A (deactivated)

Question 2

Define chromatin

Answer 2

DNA + histones + non-histone proteins contributing to mass of chromosome

Question 3

Heterochromatin

Answer 3

Chromatin that is very condensed, stains darkly in cell cycle, even in interphase

Question 4

Heterochromatin characteristics

Answer 4

• very condensed
• genetically inactive
• late replicating

highly concentrated @ centromeres + telomeres
contains few genes: those that are present resist expression

Also has an effect on neighboring genes: location influences relative expression

genes near heterochromatin will be silenced

less condensed chromatin is called euchromatin

Question 5

Histone modifications

Answer 5

histone side chains are subject a variety of covalent modifications, CORE and TAIL

acetylation of lysines: loosens chromatin structure
mono, di, tri-methylation lysines
phosphorylation of serines

Question 6

Acetylation of lysines

Answer 6

loosens chromatin structure

added by histone acetyl transferase (HATs); removed by deacetylase complexes (HDACs)

Question 7

Mono, di, and tri methylation of lysines

Answer 7

added by methyl transferase; removed by histone demethylases

Question 8

Recruitment of histone modification enzymes

Answer 8

depends on gene regulatory proteins

they’re all reversible, but last long after proteins have disappeared

Question 9

Variants

Answer 9

variants for each histone exist except for H4

present in much smaller amounts than core histones

Question 10

Variants: how they effect histones and their relation to DNA

Answer 10

histones can be modified at the core or tail, usually requiring one enzyme to add and another to remove a chemical group

These additions/removals are regulated by specific sequences on the DNA, which require specific regulatory proteins. These proteins are expressed at different times and places in the life of a cell. DNA ultimately determines the modifications of histones.

some times the modifications last longer than the regulatory proteins who made them, and these modifications provide the cell a memory of its own modifications

Question 11

major histones are synthesized during ____, assembled where?

Answer 11

S phase, assembled onto nucleosomes on daughter DNA helices just behind replication fork

Question 12

Major histones versus varient histones

Answer 12

major histones are synthesized during S phase; variant histones are synthesized during interphase and insterted into already formed chromatin

requires histone exchanges process catalyzed by chromatin remodeling complex