Eukaryotic Gene Expression

Question 1

Histones

Answer 1

• proteins that wrap around DNA
• about 100 AAs per histone
• positive AAs bind tightly around histones to the negatively charged DNA
• highly conserved protein across species

Question 2

What are the 4 common types of histones?

Answer 2

• H2A
• H2B
• H3
• H4

Question 3

Nucleosomes

Answer 3

• 10nm fiber
• “beads on a string”
• DNA that is wound 2x around an octamer of histones (2 histones of each type)

Question 4

Histone tails protrude outwards from a ____

Answer 4

nucleosome

Question 5

Histone Tails

Answer 5

• consist of amino acids that are available for chemical modification
• the N terminus of an AA

Question 6

Histones only briefly leave DNA during ___

Answer 6

replication

Question 7

30nm Fiber

Answer 7

• consists of interactions between histone tails and linker DNA (DNA “strings” between nucleosomes)
• H1 involved here
• takes the 10nm fiber and folds it into a chromatin fiber
• seen in interphase of cell cycle when the chromosomes are decondensed

Question 8

300nm Fiber

Answer 8

• looped domains

- formed when the 30nm fibers form loops that attach to a chromosome scaffold made of proteins

Question 9

Chromosome scaffold is rich in ___ and ___

Answer 9

topoisomerase and H1

Question 10

Metaphase/Mitotic Chromosome

Answer 10

• most tightly folded

- occurs during metaphase when the looped domains fold to form sister chromatids

Question 11

Centromere

Answer 11

• middle of the mitotic chromosome that binds to the mitotic spindle
• present during metaphase

Question 12

Chromatin

Answer 12

• complex of DNA and protein

- changes depending on the stage of the cell cycle

Question 13

In interphase, there are regions of DNA that are more ___ than others

Answer 13

condensed

Question 14

Heterochromatin

Answer 14

• tightly packed

- contains less frequently transcribed genes

Question 15

Euchromatin

Answer 15

• loosely packed
• contains “housekeeping genes” – genes that need to be transcribed all the time
• genes are more accessible

Question 16

Supercoiling

Answer 16

helps keep DNA wound tightly

Question 17

Single Copy DNA

Answer 17

one gene with no duplications

Question 18

Repetitive DNA

Answer 18

• gene families
• lots of copies of the same gene – these duplicates have evolved throughout time
• lots of these are found on the X chromosome
• ex. smell receptors

Question 19

With age, our ___ get shorter

Answer 19

telomeres

Question 20

Cancer has a way of replacing ___ so that they can have uncontrolled cell growth

Answer 20

telomeres

Question 21

Acetylation of histone tails leads to ___ of DNA folding

Answer 21

loosening

tail goes from positively charged to neutral

Question 22

Lots of acetylation means ___ transcription

Answer 22

increased

Question 23

Deacetylation of histone tails leads to ___ of DNA folding

Answer 23

tightening

Question 24

In general (depends on the AAs present), methylation of histone tails leads to ___ of DNA folding

Answer 24

loosening

Question 25

Phosphorylation of histone tails (addition of negative charges) leads to ___ of DNA folding

Answer 25

loosening | negative charge of DNA and PO4 repel each other

Question 26

How can you regulate the step between DNA and pre-mRNA

Answer 26

-regulating transcription initiation

Question 27

How can you regulate at the level of RNA processing (pre mRNA to mature mRNA)?

Answer 27

-alternative splicing (produce different isoforms by varying the exons that we put together during RNA processing)

Question 28

Where does translation of mRNA occur?

Answer 28

cytosol

Question 29

What happens to mRNA if it is not translated?

Answer 29

it is degraded in the cytosol

Question 30

What processing occurs between polypeptide and active protein formation in the cytosol?

Answer 30

protein processing (can be either by chemical modification or cleavage)

Question 31

Histone tails contain a lot of positively charged, ___ and ___ amino acids

Answer 31

lysine and arginine

Question 32

Where does methylation of DNA occur?

Answer 32

on the bases A, G, T, and C (mostly C)

Question 33

Long stretches of inactive DNA are usually ___

Answer 33

methylated

Question 34

Barr Bodies

Answer 34

- inactive X chromosomes | - contain heavily methylated DNA

Question 35

Females have one ____ X chromosome

Answer 35

inactive

Question 36

Transcription Factors

Answer 36

- can bind to DNA - torque DNA to open it up which allows RNA Polymerase to bind and start transcription - regulated by cellular signals

Question 37

Where do transcription factors bind? (2)

Answer 37

-proximal control elements (directly upstream of promoter) -distal control elements or enhancer (located thousands of nucleotides upstream of promoter)

Question 38

What happens when transcription factors bind to the enhancer?

Answer 38

the rate of transcription is greatly increased b/c the enhancer can fold over and interact by the promoter which helps RNA Polymerase bind

Question 39

What regulation occurs at the RNA level?

Answer 39

1. alternate splicing | 2. regulate degradation of mRNA -- if mRNA has a short half life then less translation occurs

Question 40

What regulation occurs at the protein level?

Answer 40

1. addition of sugar to protein 2. phosphorylation 3. regulation of the half life of a protein by tagging it with ubiquitin which targets it for destruction by a proteasome