Nucleic Acids, Chromosome, and Genome Structure

Question 1

purines

Answer 1

ATP/GTP

Question 2

pyrimidines

Answer 2

UTP/CTP

Question 3

Describe the hydrogen bonding between bases.

Answer 3

AT, GC base-pairing

Question 4

Chargaff’s rule

Answer 4

in any sample of dsDNA, the amount of adenine euqls the amount of thymine, the amount of guanine equals the amount of cytosine, and the total number of purines equals the total number of pyrimidines

Question 5

What are the three helical forms that DNA can take on?

Answer 5

A-, B-, and Z- forms

B-DNA is the most common

Z-DNA forms a left handed helix

Question 6

nucleoid (genophore)

Answer 6

the bacterial genome, a single circular DNA molecule

Question 7

Describe the organization of chromosomes.

Answer 7

DNA double helix -> beads on a string -> 30-nm fiber -> extended scaffold -> condensed scaffold -> chromosome

Question 8

satellite DNAs

Answer 8

one type of repetitive DNA that are clustered in discrete areas such as centromeres

Question 9

interspersed repeats

Answer 9

repetitive DNA that is distributed throughout the genome

includes SINEs, LINEs, and transposable elements

often have viral origins, transposons can cup themselves out of the genome and reinser elsewhere

Question 10

nuleosome

Answer 10

fundamental unit of packaging DNA, contains eight histone proteins (a dimer of H2A, H2B, H3, and H4)

about 146 base pairs of dsDNA is wound around each histone with a short length inbetween histones

linker region bound by histone H1 to create 3D structure

Question 11

euchromatin

Answer 11

transcriptionally active and contains most of the genes

light staining in an EM

Question 12

heterochromatin

Answer 12

transcriptionally inactive DNA, stains strongly with DNA-binding dyes

constitutive heterochromatin - always inactive

facultative heterochromatin - sometimes active sometimes inactive

comes out dark in an EM

Question 13

chromosome territory

Answer 13

the space within the nucleus where a chromosome resides

Question 14

telomere

Answer 14

specialized DNA sequences at the ends of each chromosome that stabilize the end and help prevent linear recombination with the ends of other chromosomes

stucture contains two loops called the T-loop and the D-loop, the DNA folds back on itself and inserts the tail into the previous strands

Question 15

shelterin complex

Answer 15

protein complex that associates with the telomere and maintains its structure

Question 16

centromere

Answer 16

mostly highly repetitive, constitutive heterochromatin, function in chromosome segregation during mitosis

Question 17

satellite DNA

Answer 17

repeating sequences such as those found near the centromere and the telomere

can be devided into alphoid and beta sites

ribosomal DNA are also frequently flanked by satellite DNA

Question 18

:LINEs

Answer 18

long interspersed nuclear elements, about 6kb long, transcribed using an internal promoter

encode p40 and reverse transcriptase

Question 19

SINEs

Answer 19

short interspersed nuclear elements, much shorter than LINEs and are tandemly rpeated within the individual sequence

alu dimers are the major formes

originated from tRNAs that got copied by reverse transcriptases and got inserted back into the DNA

most common sequences in the genome

Question 20

SKY FISH

Answer 20

fluorescent in situ hybridization, can be used to stain each chromosome a different color

Question 21

chromosome distribution

Answer 21

chromosome regions with very high gene density tend to be in the middle of the nucleus, regions with low gene density tend to be towards the outside of the nucleus

Question 22

functional consequences of global chromatin organization

Answer 22

transcribe genes for a particular function at the same time

different parts of the chromosome can move a little bit and localize to form a transcription pocket

spatial regulation of large parts of a chromosome