01/30/2025

Question 1

to fit DNA into a bacterial cell, how much must DNA be compacted

Answer 1

1000 fold

Question 2

what helps the compaction of DNA in a bacterial cell

Answer 2

the formation of loop domains

Question 3

what helps form the loop domains in a bacterial cell chromosome

Answer 3

binding proteins help pinch it in

Question 4

what is the native supercoiling of bacterial DNA? What enzyme facilitates this?

Answer 4

negative supercoiling is native, gyrase is what causes these supercoils and compacts the chromosome

Question 5

what is negative supercoiling

Answer 5

underwinding of the helix, it goes in the opposite direction and may open strands of DNA

Question 6

what is positive supercoiling

Answer 6

overwinding of the helix, it tightens the DNA in the same direction it spins and may cause breakage if not relieved

Question 7

what is the purpose of gyrase/ topoisomerase II

Answer 7

gyrase acts to introduce negative supercoils (underwinding) and will relax positive super coils

Question 8

what is the purpose of DNA topoisomerase I

Answer 8

it acts to induce positive supercoils (overwinding) and relaxes negative supercoils

Question 9

what is the role of topoisomerase I in the compaction of bacterial chromosomes

Answer 9

since bacteria are negatively supercoiled by gyrase, topoisomerase acts to relax these supercoils by inducing positive supercoils and bringing it back to to neutral, this may facilitate DNA replication

Question 10

what are the two major effects of negative supercoiling

Answer 10

1. helps in the compaction of the chromosomes
2. creates tension that may be released by DNA strand separation

Question 11

what does negative supercoiling enhance and why

Answer 11

it enhances DNA replication and transcription by strand separation

Question 12

the ability of gyrase to introduce negative supercoils into DNA is crucial for bacterial survival, why might this be important for therapeutic processes?

Answer 12

blocking these enzymes can aid in bacterial diseases

Question 13

what are drugs that inhibit gyrase and other bacterial topoisomerases? do these affect eukaryotic topoisomerases?

Answer 13

quinolones and coumarins, these do not affect eukaryotic topoisomerases

Question 14

why do eukaryotic genomes vary substantially by size?

Answer 14

the difference in genome size is due to the accumulation of repetitive DNA sequences

Question 15

why do bacteria have less repetitive DNA sequence

Answer 15

they need to be more streamlined and efficient

Question 16

what is the C value paradox

Answer 16

the C value paradox describes that, while we assume that the gene content will double as the DNA content doubles, that is not the case and this is because of repetitive sequences

Question 17

what % of DNA sequences are actually coding for exons/ proteins

Answer 17

only 2%

Question 18

what % of DNA sequences are coding for repetitive sequences

Answer 18

60%

Question 19

do repetitive sequences play any functional role

Answer 19

yes, if we did not have telomeres, origins of replication, or centromeres, there would be problems

Question 20

if Gyrase was used on the Z DNA, what would occur

Answer 20

it would be overwound

Question 21

If you are comparing two amphibian species and one has double the genetic information (haploiud amount), then it is likely that the species with more DNA has double the amount of genes

True or false

Answer 21

false

Question 22

what is the lowest level of chromosome compaction

Answer 22

nucleosomes

Question 23

what is a nucleosome

Answer 23

it is DNA wrapped around an octamer of histone proteins, there are two copies of four different histone proteins

Question 24

what fold reduction does beads on a string have for DNA

Answer 24

seven-fold reduction

Question 25

how do histone proteins interact with DNA

Answer 25

they interact by charge instead of from recognition proteins

Question 26

why do histone proteins interact with negatively charged DNA

Answer 26

because they contain positively charged amino-acids

Question 27

what is the role of H1

Answer 27

it binds to linker DNA and nucleosomes and plays a role in chromosome compaction

Question 28

what are some examples of repetitive sequences that serve a purpose

Answer 28

origins of replication, centromeres, telomeres at the end

Question 29

what is the purpose of a centromere

Answer 29

it forms a recognition site for the kinetochore proteins

Question 30

why are eukaryotes able to have repetitive sequences

Answer 30

eukaryotes have a separate nucleus from the cytoplasm so we can process out the non-important sequences

Question 31

how do nucleosomes affect the compaction of DNA

Answer 31

they shorten it by wrapping the DNA around histone proteins

Question 32

why is the spacing between nucleosomes important

Answer 32

shorter spacing (shorter linker) makes the DNA less available for proteins to interact with the genes longer spacing (long linker) makes the DNA more available for gene expression

Question 33

what is the link region

Answer 33

the linker is the region of space between the nucleosomes of DNA

Question 34

what fold of reduction length in DNA does the "beads on a string"level have

Answer 34

seven-fold reduction of DNA length

Question 35

what is the second level of chromosome compaction in eukaryotes

Answer 35

the 30nm fiber facilitated by H1 histone protein

Question 36

to what length does the 30nm fiber shorten dna

Answer 36

another 7 fold from the beads on a string

Question 37

what facilitates the compaction of beads on a sstring to the 30 nm fiber

Answer 37

the H1 histone protein

Question 38

what is the third level of compaction of a eukaryotic chromosome

Answer 38

the 30 nm fiber interacts with the nuclear matrix to form radial loops

Question 39

what is the attachment site of the radial loops for chromosome compaction

Answer 39

the Matrix-attachment regions (MARS) or Scaffold-attachment regions (SARS) these will be anchored to the nuclear matrix

Question 40

what is the nuclear matrix composed of

Answer 40

it is composed of the nuclear lamina and the internal matrix proteins/scaffolding proteins that the DNA binds to

Question 41

what is the nuclear lamina

Answer 41

they are fibers that line the inner membrane of the nucleus, they facilitate what can enter and leave the nucleus

Question 42

what are nuclear matrix proteins

Answer 42

they are connected to the nuclear lamina and fill the interior of the nucleus, also called scaffolding proteins

Question 43

what are the specific regions for chromosomes in the nucleus called

Answer 43

chromosome territories

Question 44

what are the phases of interphase

Answer 44

G1: cell division preparation, S: DNA replication, G2: where genetic material is organized and condensed for division

Question 45

when comparing chromosome compaction in interphase and mitosis, what is the key difference

Answer 45

the chromosomes in interphase are less compacted and available for transcription, in mitosis, the chromosomes are compacted tightly so they can be separated

Question 46

what are euchromatin? what phase are they found in?

Answer 46

euchromatin are found in interphase and are less condensed - more transcriptionally active - they are regions where the 30 nm fiber forms radial loop domains

Question 47

what are heterochromatin

Answer 47

they are tightly compacted regions of chromosomes that are generally transcriptionally inactive - the radial loop domains are compacted even further

Question 48

what is the highest level of chromosome compaction in interphase

Answer 48

hetereochromatin

Question 49

what are the two types of heterochromatin

Answer 49

constitutive heterochromatin, facultative heterochromatin

Question 50

what is constitutive heterochromatin

Answer 50

they are regions of chromatin that are always heterochromatic and turned off

Question 51

what is facultative heterochromatin

Answer 51

they are regions of chromatin that can alter between states of euchromatin and heterochromatin they can be turned on and off ex. neurons and skin cells

Question 52

what is a "constitutive" active gene

Answer 52

constitutive means always, so it is a gene that is always on

Question 53

list the order of chromosome compaction in interphase chromosomes for eukaryotes

Answer 53

1) DNA strand 2) beads on a string with histone octamer and H1 linker 3) 30nm fiber 4) formation of radial loops via interaction with the nuclear matrix 5) euchromatin 6) heterochromatin

Question 54

when can condensin and cohesion act on chromosomes

Answer 54

they can act during mitosis since the nuclear membrane has dissolved and proteins can can enter the nucleus and access the chromosomes

Question 55

what is the role of condensin

Answer 55

condensin binds to chromosomes and compacts the radial loops

Question 56

what is the highest form of chromosome compaction

Answer 56

cohesin, it binds sister chromatids together

Question 57

what are the structural features of dna that enable its function

Answer 57

complementarity of DNA strands two strands can come apart and each can act as a template strand

Question 58

does the template strand only encode for DNA

Answer 58

no it also encodes for RNA

Question 59

which template strand of DNA is used to code RNA

Answer 59

it depends on which strand has the gene of interest

Question 60

what is the conservative model

Answer 60

both parent strands stay together and act as a blue print

Question 61

what is the semi-conservative model

Answer 61

the double stranded DNA that is produced contains one parental and one daughter strand from replication

Question 62

what is a topoisomer

Answer 62

it is a set of DNA molecules that have the same sequence but differ in their supercoiling and twisting