Week 3

Question 1

describe the shape of the genome of e coli

Answer 1

circular

Question 2

conversion: 1000 bp = __ kb

Answer 2

1

Question 3

what does it mean that some mitochondrial genes end up in the nuclear genome

Answer 3

that there is a lot of cross talk between the organelles

Question 4

list the 3 lines of evidence for endosymbiotic theory

Answer 4

• Chloroplast genome and mitochondrial genome are circular
• Much smaller than bacterial genome (?)
• Some from mito/chloro genes wound up in nuclear genome

Question 5

in the human genome, how many bp per genome

Answer 5

~3 billion bp per genome

Question 6

how many genomes from each parent do you get

Answer 6

1 from each

Question 7

how many protein coding genes across 23 pairs of chromosomes

Answer 7

~20,000

Question 8

t/f genome size is always correlated with number of genes/organism complexity

Answer 8

false

Question 9

define haploid

Answer 9

half the normal amount of DNA (1 copy of each of the 23 pairs), haploid set 3 bill if diploid is 6 bill

Question 10

in the human genome:
____% of our genome is repetitive dna and less than ___% of our genome encodes protein (protein-coding exons)

Answer 10

50, 1

Question 11

list what comprises the unique sequences in the human genome

Answer 11

protein-coding exons, introns, nonrepetitive dna that is in neither introns nor exons (eg promotor or regulatory seq)

Question 12

list what comprises the repeated sequences in the human genom

Answer 12

mobile genetic elements (LINEs, SINEs, retrotransposons, dna-only transposon), simple repeats, segment duplications (1k-200k bp long)

Question 13

how were mobile genetic elements named

Answer 13

based on the way they are able to copy and insert themselves throughout our genome - make up more than half of the repeated seq in the genome (dna fossils - moved a lot in early evo days but don’t move around that much anymore)

Question 14

why does dna need to get packaged

Answer 14

in a non packaged state, even the small prokaryotic genome would occupy a considerable portion of the cell volume

Question 15

describe the dna packing in prokaryotes and what it forms

Answer 15

dna is condensed through folding and twisting about 1000 fold and is complexed w proteins = forms the prokaryotic nucleoid

Question 16

how many bp of dna per cell in the human genome

Answer 16

6 billion

Question 17

state the name of the solution of getting eukaryotic genome packed into cells and what it menas

Answer 17

the chromosome solution - linear chromosomes instead of circular

Question 18

what does heating dna double helices do

Answer 18

hydrogen bonds between nucleotide pairs broken leading to denaturation to make it into single strands

Question 19

describe the lab technique of hybridization - FISH (fluorescence in situ hybridisation)

Answer 19

1. probe dna
2. label w fluorescent dye
3. denature and hybridize
4. cool it slowly for renaturation to stay tgt

So many variations, a probe w a DNA or RNA sequence that has a fluorescent tag and tracks where it goes

It is called fish bc we don’t destroy the chromosome, we are trying to study it in its situation

Question 20

t/f chromatin is dynamic

Answer 20

true

Question 21

what is a karyotype

Answer 21

artificial array of chromosomes

Question 22

define what chromatin is

Answer 22

each chromosome contains a single, long, linear dna molecule and associated protein

Question 23

since chromatin is tightly packed, dna must still be accessible for what 3 processes

Answer 23

transcription, replication and repair

Question 24

define what chromatids are

Answer 24

one of the two identical halves of a chromosome that has been replicated in preparation for cell division. they come apart when cell division occurs –> 2 cells after mitosis with identical DNA to parental cell

Question 25

where on the dna are telomeres and also where on the dna is the centromere

Answer 25

telomeres are at ends and centromere is what joins chromatids together in the middle

Question 26

what is a nucleosome made up on

Answer 26

nucleosome core particle + DNA wrapped around + linker DNA

Question 27

the net result of chromatin's levels of organization is each dna molecule has been packaged into a mitotic chromosome that is ______ fold shorter than its fully extended length

Answer 27

10000

Question 28

how did scientists isolate chromatin in a cell in interphase

Answer 28

Ruptured the interphase nucleus and let the chromatin spill out and they found the 30nm fiber and then experimentally decondensed it more and applied chemical treatment so we can see the nucleosome

Question 29

what are histones

Answer 29

small proteins rich in lysine and arginine, positive charge neutralizes negative charge of dna (DNA tends to be negatively charged due to sugar phosphate backbone, the histones are positively charged so you can wrap the DNA around the histone -- can also squish the nucleosomes together bc they aren't being repelled)

Question 30

what are the 4 core histone proteins and say which are paired tgt in each octamer core

Answer 30

h2a and h2b h3 and h4

Question 31

what terminal is the tail coming off the histone and how can it be modified

Answer 31

N-terminal tail (is the squiggles coming off) which can be covalently modified and can be the addition or loss of acetyl, methyl, and phosphate groups

Question 32

t/f the structure of the nucleosome is highly conserved

Answer 32

true

Question 33

t/f the one linker histone (h1) is external to the histone core but apart of the whole nucleosome

Answer 33

true

Question 34

H1 changes the trajectory of linker DNA coming out, which allows for what

Answer 34

allows for better compaction of the dna

Question 35

what two components are involved in forming chromatin loops

Answer 35

sequence specific clamp proteins and cohesins ^ sequence specific clamp proteins recognize particular sequences on the DNA and there's a special ring protein called cohesin that pull the 30nm fiber together until the clamp proteins meet then we have a loop of chromatin

Question 36

as cells enter mitosis, __________ replace most cohesins to form double loops of chromatin to generate compact chromosome

Answer 36

as cells enter mitosis, condensins replace most cohesins to form double loops of chromatin to generate compact chromosome

Question 37

chromatin remodeling complexes and histone modifying enzymes are examples of proteins that can what

Answer 37

make changes in chromatin structure and alter access to dna for replication or transcription

Question 38

is it 40% heterochromatin and 60% euchromatin or 60% heterochromatin and 40% euchromatin

Answer 38

40% heterochromatin and 60% euchromatin

Question 39

where is heterochromatin found

Answer 39

often found by the periphery of the nucleus

Question 40

t/f the degree of chromatin condensation (heterochromatin and euchromatin) is dynamic

Answer 40

yes

Question 41

telomeres are made up of ____________ heterochromatin

Answer 41

constitutive

Question 42

quiescent is OR is not actively transcribed

Answer 42

is not

Question 43

facultative heterochromatin is ________ condensed

Answer 43

highly

Question 44

heterochromatic regions of interphase chromosomes are areas where gene expression is ______________

Answer 44

suppressed

Question 45

active euchromatic regions of interphase chromosomes are areas where genes tend to be ______________

Answer 45

expressed

Question 46

described the condensation of heterochromatin

Answer 46

high condensed - the time spent highly condensed varies (ie constitutive vs facultative)

Question 47

described the chromatin of euchromatin

Answer 47

relatively non condensed - level of activity varies (ie quiescent vs active) and degree of condensation varies

Question 48

list the types of heterochromatin

Answer 48

- meiotic and mitotic chromosomes - centromeres and telomeres

Question 49

localized covalent modification of histones, the presence of chromatin remodeling complexes and rna poly (transcription) complexes modulate the _________ switching from euchromatic to heterochromatic regions along chromosomes

Answer 49

reversible

Question 50

expressed genes are re-orientated within the chromatin during interphase, the condensed chromosomal territory tends to be where and where does the expressed gene tend to be

Answer 50

condensed chromosomal territory tends to be at the outskirts and expressed gene tended to be more in the center - loop out various parts that need to be transcribed

Question 51

is dna replication conservative or semiconservative?

Answer 51

semiconservative

Question 52

dna synthesis causes the nucleotides to be stuck to which end

Answer 52

the 3' end (so 5' to 3' direction of chain growth)

Question 53

dna is synthesized from what and rna is synthesized from what

Answer 53

dNTPs and NTPs

Question 54

what bond links nucleotides

Answer 54

phosphodiester bonds

Question 55

state the 3 main models of the direction of dna replication

Answer 55

Linear DNA viruses, plasmids that replicate a bit diff, and the bidirectional method

Question 56

describe the directional method for direction of dna replication

Answer 56

bidirectional growth from one starting point (2 forks) which begins from the replication origin. the double helix is opened with the aid of initiator proteins to make the single stranded dna templates ready for dna synthesis.

Question 57

what type of organisms use the bidirectional growth method

Answer 57

eukaryotes and bacteria

Question 58

how many origins of replication do bacteria and eukaryotes have and around how does it take

Answer 58

bacteria has single and replicates in about an hour eukaryotes have multiple and can replicate in around 8-10 hours, to replicate an entire cell's worth of dna

Question 59

describe the 2 possibilities of where dna replication starts

Answer 59

1. random start 2. always start from the same location on dna (replication origins)

Question 60

list the characteristics of replication origins

Answer 60

- easy to open - a-t rich (bc easier to break less h bonds) - recognized by initiator proteins that bind to the dna

Question 61

list the procedure of dna replication

Answer 61

1. separate dna strands 2. synthesize dna 3. proofread newly synthesized dna

Question 62

list the 6 ingredients for synthesis

Answer 62

1. origin of replication 2. primers 3. dNTPs 4. ATP as an energy source 5. dna poly 6. accessory proteins

Question 63

describe what happens at the dna replication forms

Answer 63

- the replication form is asymmetrical: you have a left and right hand fork - the leading strand is replicated continuously (5' to 3') and lagging strand is discontinuously - the most recently synthesized dna is at the end - dna polymerase is going from 5' to 3' end in an complementary anti parallel fashion - okazaki fragment sare used to fill in the lagging strand