Lecture 1-2: DNA, Chromosomes and Genomes

Question 1

Examples of Epigenetics (3)

Answer 1

DNA methylation Chromatin structure Histone modification

Question 2

ATP-dependent chromatin remodeling protein is located where

Answer 2

On reader writer complex. Uses ATP to either condense or decondense long stretches of chromatin

Question 3

Chromatin consists of

Answer 3

Nuclear DNA + Protein

Question 4

Purifying Selection

Answer 4

Elimination of mutations that interfere with important genetic functions

Question 5

Phosphorylation of serine (covalent modification)

Answer 5

Gene activates

Question 6

SNPs

Answer 6

Single nucleotide polymorphism Points in genome where one group has one nucleotide and another group has another

Question 7

Acetylation of lysines (covalent modification)

Answer 7

Loosens chromatin structure (added by histone acetyl transferases, removed by histone deacetylase complexes)

Question 8

Duplication and divergence

Answer 8

Both copies of gene maintain functional while diverging in sequence and pattern of expression

Question 9

Pseudogenes

Answer 9

A duplicated gene that has become irreversibly inactivated by mutations

Question 10

HS4 region

Answer 10

Contains cluster of histone acetylase binding sites, protects beta-globulin locus from silencing

Question 11

Nucleosome consists of

Answer 11

8 histone proteins (histone octamer) DS-DNA that is 147 nucleotide pairs long

Question 12

Condensation of chromosomes function

Answer 12

Disentanglement of sister chromatids Protection of fragile DNA molecule as separation occurs

Question 13

Epigenetics

Answer 13

A form of inheritance that is superimposed on the genetic inheritance based on DNA

Question 14

Interactions between DNA and histone

Answer 14

H-bonds Hydrophobic interactions Salt linkages (1/5 of histone residues are lysine or argenine +)

Question 15

Barrier sequence function

Answer 15

Halt the spread of chromatin modifications

Question 16

Chromatin remodeling complex

Answer 16

Allow further loosening of DNA/histone contact Changes structure of DNA temporarily, making DNA less tightly bound

Question 17

Zone of inactivation

Answer 17

Area around heterochromatin, can spread different distances in different cells

Question 18

DNA condensation is a ____ situation

Answer 18

Dynamic

Question 19

Nucleosome

Answer 19

Most basic unit of chromosome packing

Question 20

Final level in chromosome packing is during

Answer 20

Mitosis, very condensed

Question 21

of hydrogen bonds formed between histone core and DNA in each nucleosome

Answer 21

142 H-bonds

Question 22

Chromosome requirements (3)

Answer 22

DNA replication origin Centromeres Telomeres

Question 23

Nucleotides are made of

Answer 23

5-carbon sugar and nitrogenous base covalently linked via glycosidic bond

Question 24

Chromosomes during interphase:

Answer 24

Chromosomes are replicated; they are decondensed and difficult to distinguish

Question 25

Position effect variegation

Answer 25

Breakage events that bring heterochromatin near active genes tends to silence them

Question 26

Position effect

Answer 26

Activity of a gene depends on position on the chromosome

Question 27

Lysine methylation (covalent modification)

Answer 27

Silences genes (added by methyl transferases, removed by demethylases)

Question 28

Histone code read by

Answer 28

Code reader complex Involves joint recognition of histone tail and covalent modification

Question 29

Nucleosome packing

Answer 29

Forms dense fibrous structure with diameter of 30nm

Question 30

Heterochromatin is very concentrated near

Answer 30

Telomeres and centromeres

Question 31

Histone code determines

Answer 31

Determines how/when DNA is packaged in nucleosome

Question 32

Histone H1

Answer 32

Linker histone Contacts both DNA and protein Changes path of DNA as it exits nucleosome

Question 33

Heterochromatin location in nucleus

Answer 33

Usually associates with nuclear lamina

Question 34

Types of barrier sequences

Answer 34

Physical barriers Enzymatic barriers

Question 35

8 Histone proteins include

Answer 35

2 molecules each of H2A, H2B, H3, H4

Question 36

How can various possible chromatin structures arise

Answer 36

Specialized variant histones

Question 37

Centromeric sequences

Answer 37

Consist of short repetitive DNA sequences called alpha satellite DNA Defined by assembly of proteins (i.e., H3 histone), not DNA sequence Centromeres can form spontaneously w/o alpha satellite DNA sequence

Question 38

Interphase chromosome structure

Answer 38

Lampbrush- series of large chromatin loops emanating from a linear chromosome axis

Question 39

Translocation of chromosome 9&22 form

Answer 39

Philadelphia chromosome on chromosome 22. Commonly found in CML

Question 40

Homologues

Answer 40

Genes that are similar in both sequence and function due to common ancestry

Question 41

Building blocks of DNA

Answer 41

Nucleic acids

Question 42

How are different activities localized in the nucleus

Answer 42

Different neighborhoods have effects on gene expression.

Question 43

Nucleotides are joined together via

Answer 43

Phosphodiester linkage between 5' and 3' carbon atoms

Question 44

CNVs

Answer 44

Copy number variants Presence of many duplications and deletions of large blocks of DNA

Question 45

Chromosomes during mitosis

Answer 45

Chromosomes are highly condensed and separated into two daughter nuclei

Question 46

Histone tails

Answer 46

Help to condense chromatin Largely unstructured, highly flexible Can form interactions with adjacent nucleosomes

Question 47

Heterochromatin

Answer 47

Very condensed chromatin, stains darkly throughout the cell cycle, even interphase

Question 48

Condensins

Answer 48

Use ATP hydrolysis to coil DNA molecules into chromatids

Question 49

Major histones are synthesized and assembled when

Answer 49

Synthesized during S-phase Assembled into nucleosomes on daughter DNA helices just behind replication fork

Question 50

Code reader-writer complex

Answer 50

Reads modifications and spreads them to nearby nucleosomes

Question 51

Percentage of DNA sequence in exons

Answer 51

1.5%

Question 52

Nucleosomes repeat every \_#\_ nucleotides

Answer 52

~200 nucleotides between

Question 53

Varient histones synthesized and inserted when

Answer 53

Synthesized during interphase Inserted into already-fromed chromatin, REQUIRES histone exchange process catalyzed by chromatin remodeling complex

Question 54

How do genomic changes occur

Answer 54

Mistakes in DNA replication and repair Movement of transposable elements

Question 55

Reasons for sequence conservation

Answer 55

Not having enough time for mutations to occur since lineages separted Purifying selection