Lecture 3 - Overview of DNA replication and chromosome structure

Question 1

DNA replication is __________

Answer 1

semiconservative

Question 2

DNA replication initiates at specific _________. These are bound by ________________ which form the _____________ and _________ replication

Answer 2

sequences, prereplicative complexes, preinitiation complex and initiate replication.

Question 3

After replication initiation, ____________ are formed and _________ occurs

Answer 3

replication forks, elongation

Question 4

What did the experiment with plasmid vectors with only His gene and His gene + Ars gene that were introduced to yeast cells show

Answer 4

Introduction in yeast w/o His gene (needed for development). Ars is an autonomously replicating sequence so plasmid vector was able to replicate in yeast cells (with His gene) and His gene could be transfered to furthur generations)

Question 5

About Ars (3)

Answer 5

1) AT rich 2) Attracts origin proteins 3) Necessary for replication

Question 6

Different chromosomal regions are replicated at __________ times during ____ phase. Origins of replication do not start _________ at the same ___________. It depends on _________ state (___ or ____)

Answer 6

different. S phase. replication. time. chromatin. (open or closed)

Question 7

Some RNA can ____ and form structure with _____________

Answer 7

fold. catalytical properties

Question 8

During __________ (,,_), cell ______ its DNA in preparation for _______

Answer 8

interphase (G1, S, G2), copies, mitosis.

Question 9

Chromatin where/where is telomere, chromatid, centromere

Answer 9

telomere = tip of chromosome, chromatid = huge chunk, centromere = middle

Question 10

_________ chromatin is not transcriptionaly active, as oposed to more ____, less _______ chromatin

Answer 10

Condensed, (not). more open. less condensed can be active

Question 11

Way of regulating transcriptional gene expression

Answer 11

Controlling chromatin condensation/decondensation

Question 12

Females have 2 ___ chromosomes so one of them is _____________ by __________ which converts the targeted ___ chromosome into densely-packed _____________ which is transcriptionally ________

Answer 12

X. transcriptionally silenced. inactivation mechanism. X. heterochromatin . inactive.

Question 13

Chromatin decondenses when the cell enters ________ (a certain phase) in order for __________ to happen but DNA is not completely ________

Answer 13

interphase. mitose. naked

Question 14

Inactive, condensed chromatin is called ____. Active, open chromatin is called _____. Specialized regions of the chromosome such as ______ and ________ contain ____ genes and do not fully ________ in interphase. (they are part of __________ (which type of chromatin))

Answer 14

heterochromatin. euchromatin. telomers, centromers, few, decondense, heterochromatin.

Question 15

Eukaryotic chromatin consists of ______ and ____________. The major chromatin proteins are _________.

Answer 15

DNA and closely-associated proteins. Histones.

Question 16

Histones are ____ and highly ________ proteins that are extremely _______________ in evolution. They play a key role in DNA _________. How they interact with DNA : ___________

Answer 16

small. basic. conserved. packaging. positively charged histones interact with negatively charged DNA backbone (phosphate)

Question 17

DNA coiled around a histone is called a __________. The protein core is a ____________. (8 histones which are ___..)

Answer 17

nucleosome. histone octamer. 2 H2As 2 H2Bs 2 H3s and 2 H4s

Question 18

Nucleosomes are linked by _______ bp of DNA. Additional histones like _____ are not __________

Answer 18

10-90, H1, part of the octamer.

Question 19

model for the 30 nm chromatin fiber

Answer 19

Chain of nucleosomes -> Zig-zag ribbon -> two-start helix (solenoid)

Question 20

Histone ___ and ___ terminal _____ protrude from the __________. During PTMs, _________ in histone tails are ____ modified

Answer 20

C- and N- tails. nucleosome. some amino acid side chains , covalently modified.

Question 21

Modifications of a.a side chains on histone tails include :

Answer 21

Methylation of lysine or aginine (mono, di or tri methylation). Acetylation of lysine. Phosphorylation of serine or threonine, etc.

Question 22

Histone tail modifications are ________ and highly ______. 3 reactions and their enzymes

Answer 22

reversible. regulated. Unmethylated - > methylated (methyl transferase), opposite = demethylase. Unacetylated -> acetylated (acetyl transferase) opposite = deacetylase. Unphosphorylated -> phosphorylated (protein kinase) opposite = protein phosphatase

Question 23

Modifications of histone tails affect their _______ which affects their ______ interactions with DNA, (explain lysine ex.)

Answer 23

charge. electrostatic. Acetylation of lysine side chain changes its positive charge to a neutral charge which reduces interaction with DNA.

Question 24

closed chromatin :_______ of _______ (a.a) on histone tails form a binding site for the __________ (a protein domain). Proteins with this domain can bind and affect __________. (ex : ______)

Answer 24

Methylations. Lysine. Chromodomain. nucleosomes. Heterochromatin protein 1 (HP1)

Question 25

open chromatin : _______ of _______ (a.a) on histone tails form a binding site for the ___________ (a protein domain). Proteins with this domain can bind and affect ___________. (ex: _______)

Answer 25

Acetylations. Lysine. Bromodomains. nucleosomes. general transcription factor TFIID.