Exam 2 Study Guide

Question 1

What is epigenetics?

Answer 1

the study of how your behaviors and environment can cause changes that affect the way your genes work. Example: genetically identical mice whose mothers are on different diets have varying characteristics.

Question 2

What is chromatin?

Answer 2

DNA in the nucleus and its associated proteins during interphase (between mitosis). Chromatin is compact organization in which most DNA sequences are structurally inaccessible and functionally active.

Question 3

What is Heterochromatin?

Answer 3

Chromatin that is condensed, closed, and off. Heterochromatin is highly condensed, gene-poor, and transcriptionally silent

Question 4

What is Euchromatin?

Answer 4

Euchromatin is is less condensed, gene-rich, and more easily transcribed. Euchromatin is decondensed, open, and on.

Question 5

What is the lower order structure of chromatin?

Answer 5

Chromatin consists of a 30 nm fiber (sting) that has nucleosomes appearing throughout it (beads). The overall structure looks like beads on a string.

Question 6

What is the function of micrococcal nuclease?

Answer 6

• The micrococcal nuclease is a relatively non-specific endo-exonuclease that will preferentially cleave DNA between the nucleosomes.
• First the enzyme cuts between the nucleosomes then proceeds to digest some of the DNA of the individual nucleosome.

Question 7

What is a nucleosome?

Answer 7

The basic structural subunit of chromatin consisting of about 146-200 base pairs of DNA wrapped around an octamer histone.

Question 8

How many turns does DNA make around the nucleosome core?

Answer 8

About 1.7

Question 9

Why may the pattern of turns around the nucleosome have a possible functional consequence?

Answer 9

Sequences on the DNA that lie on different turns around the nucleosome may end up closer together. One turn around the nucleosome takes about 80 bp of DNA. So two points separated by 80 bp in the free double helix may be closer together on the nucleosome surface.

Question 10

What is the histone fold domain?

Answer 10

The histone fold domain is a conserved domain that exists in all 4 core histones. Histone variants differ in the sequences on either side of the histone-fold domain.

Question 11

What are histone variants?

Answer 11

• Histone protein sequences are highly conserved, but variants exist.
• Histone variants are any number of histones that are closely related to one of the core histones that can assemble into a nucleosome in place of the related core histone.
• Many histone variants have specialized functions.
• Core histone H4 does not have histone variants.

Question 12

What is the role of gamma-H2AX

Answer 12

gamma-H2Ax is detected by an antibody and appears at sites of DNA breakage. It is required for stabilizing binding of various repair factors at DNA breaks and to maintain checkpoint arrest.

Question 13

What is a histone code?

Answer 13

• The idea that combinations of signals may be used to define chromatin function.
• The hypothesis that combinations of specific modifications of specific histone residues act cooperatively to define chromatin function.
• Histone modifications generate a histone code that can be read by specific protein complexes.

Question 14

What is the function DNase 1?

Answer 14

Endonuclease that digests single- and double-stranded DNA. DNase 1 preferentially nicks unprotected DNA.

Question 15

What is ATAC-seq?

Answer 15

Assay for Transposase-Accessible Chromatin using sequencing. This method determines chromatin accessibility across the genome and can be used to map open chromatin.

Question 16

What is paramutation?

Answer 16

• Interaction of two alleles of the same locus, resulting in a heritable change of one allele that is induced by the other allele.
• an allelic interaction in which one allele, referred to as paramutagenic, causes a heritable change in the expression of a homologous paramutable allele

Question 17

What is DNA methylation?

Answer 17

• DNA methylation is a biochemical process where a methyl group (CH3) is added to a cytosine DNA nucleotide in CpG dinucleotides.
• DNA methylation stably alters the expression of genes in cells as cells divide and differentiate.

Question 18

What are the two DNA methylation processes?

Answer 18

1. De novo methylation: initiates new patterns of cytosine methylation (adds methyl group to sequence)
   - a process by which methyl groups are added to unmethylated DNA at specific CpG sites, catalyzed by DNMT3A and DNMT3B.
2. Maintenance methylation: copies methylation pattern during DNA replication.

Question 19

What is RNA polymerase?

Answer 19

Enzymes that synthesize RNA using a DNA template. In bacteria, a single type makes mRNA, tRNA, and rRNA. About 13,000 copies of enzyme in 1 E. coli.

Question 20

What is a promoter?

Answer 20

A region of DNA where RNA polymerase binds to initiate transcription.

Question 21

What is a startsite?

Answer 21

The position on DNA corresponding to the first base incorporated into RNA.

Question 22

What is a transcription Unit?

Answer 22

The sequence between sites of initiation and termination by RNA polymerase.

Question 23

What are the three stages of transcrition?

Answer 23

1. Initiation
   - Closed and open complex
   - Abortive transcripts
2. Elongation
   - Sigma not necessary
3. Termination
   - Sequence dependent

Question 24

What is a consensus sequence?

Answer 24

An idealized sequence in which each position represents the base most often found when many actual sequences are compared