Topic 2, Lecture 1

Question 1

sWhat accounted for the different between a neuron and liver cell?

Answer 1

the function of the cells come from the structure of the protein. later we learned that TF’s can alter the liver to a neuron by just 3 MASTOR REGULATORS ( transcription factors)

Question 2

What were the differences in the protein expression of two tissues?

Answer 2

each tissue has its own genome
and all tissues have the same genome but different mechanism (time- specific regulation)

Question 3

Where does regulation happen?

Answer 3

at the transcription level

Question 4

Remember the examples of the dolly and bonnie

Answer 4

due to genomic equivalence this proves that all cells have the same genome needed to control proteins (transcribed and then made)

Question 5

What are the important specific protein structure regulation thingys?

Answer 5

tissue-specific
gene-specific
Time-specific

BUT MOST IMPORTANTLY
right protein
right time
right amount

Question 6

be able to draw out drawing of the gene and +1 site with appropriate labels to help with concepts

Answer 6

DRAW THAT DUDE

Question 7

Central Dogma

Answer 7

flow of genetic information from DNA to RNA to protein

Question 8

Regulation at transcription or at translation level?

Answer 8

it is more efficient to regulate at transcription because it is easier and it saves energy

Question 9

what makes DNA an acid?

Answer 9

phosphodiester bonds (how we regulate gene transcription)
backbone is a (-) charge

Question 10

how many genes encode, how many proteins?

Answer 10

30,000 genes, 24,000 proteins

Question 11

what is the complete nucleotide of human genome

Answer 11

3.2x10^9 billion

Question 12

how many nucleotide pairs are in chromosome 22

Answer 12

48 million

Question 13

DNA laid end to end is what?

Answer 13

2 meters

Question 14

Nucleus is what diameter

Answer 14

6um

Question 15

A protein encoding gene is every

Answer 15

130 meters

Question 16

an average gene would extend

Answer 16

30 meters

Question 17

Chromatin is what?

Answer 17

fibrous, nucleoproteins (DNA/Proteins) complexed within the nucleus

Question 18

what does chromatin consists of?

Answer 18

DNA, histones, Nucleosomes, and non-histone proteins.
It is about 1/3 DNA and 2/3 proteins

Question 19

Chromosomes are

Answer 19

linear, double-stranded DNA molecule and associated proteins it is highly condensed DNA

Question 20

DNA double helix is decondensed proteins that form a what? but it is also only transcribed at what length? (beads on a string)

Answer 20

chromosome scaffold
11mm

Question 21

Chromosomes are formed from? but the way they look is determined by what?

Answer 21

formed from chromatin
look is determined by stage of cell cycle

Question 22

What is the typical structure of the histone fold?

Answer 22

H2A and H2B form dimer through an intersection called a handshake

Question 23

How many turns does the DNA helix make around the histone octomer?

Answer 23

1.7 tight turns

Question 24

Histone tails are

Answer 24

tails that stick out (8) on n- terminus
11-37 AA on n-terminus that extend from nucleosome

Question 25

Tails can under go what?

Answer 25

MODIFICATIONS

Question 26

Linker Histone is

Answer 26

the linker that keeps the tails close to the histone core

Question 27

what are the tails doing?

Answer 27

help like one nucleosome to next nucleosome beings everything together (paper clip holding paper)

Question 28

heterochromatin

Answer 28

highly condensed regions of chromosome that stain darkly transcriptionally inactive

Question 29

heterochromatin undergoes two stages

Answer 29

facultative constitutive

Question 30

facultative

Answer 30

decondensed and go back and forth from hetero to euchromatin

Question 31

constitutive

Answer 31

stays condensed as hetero and rarely if ever transcribed

Question 32

euchromatin

Answer 32

light regions less condensed regions of chromatin site of gene transcription

Question 33

If modifying histones to induce heterochromatin what formation must be tightly packed?

Answer 33

histone tails - hetero specific proteins lock heterochromatin in place, not just a matter of DNA being tightly packed but keeping it condensed to bind to proteins.

Question 34

What percent open-active chromatin in the cell (housekeeping gene encodes)?

Answer 34

20%

Question 35

what falls under constitutive heterochromatin?

Answer 35

centromere and telomere

Question 36

What do the modifications of the tails do to histones?

Answer 36

how tails pack hetero- tightly condensed euchromatin- spread out (transcribed)

Question 37

But what's the story behind modifications?

Answer 37

histone modification, morphology of nucleus, and degree of transcription are all apart of the story

Question 38

Lampbrush

Answer 38

the dark area is the scaffolding, fuzzy loops

Question 39

Lambrush loops contain how many nucleotide pairs?

Answer 39

50,000 to 200,000 nucleotide pairs

Question 40

the extended loops are

Answer 40

the active sites of transcription at 11nm

Question 41

the tight loops are

Answer 41

30nm

Question 42

nuclear neighborhoods

Answer 42

subcompartments that can accelerate complete sets of chemical reactions locked on the loop of the 30nm fiber MOLECULAR GLUE THAT KEEPS WHAT NEEDS TO BE HERE IN PLACE

Question 43

Why have a gene that would not be transcribed in a nuclear neighborhood? (active or passive approach)

Answer 43

active or passive approach to regulating gene transcription passive would NOT DO IT some want ACTIVE cannot transcribe a gene, so lock it in NUCLEAR NEIGHBORHOODS with heterochromatin REMEMBER MOLECULAR GLUE

Question 44

histones include how many nucleosome pairs of DNA

Answer 44

200 50 in between and 150 wrapped

Question 45

typical diploid human cell contains how many nucleosomes

Answer 45

30 million

Question 46

small basic portions of histones

Answer 46

H1 H2A H2B H3 H4

Question 47

how many bonds are btw dna and histone core? and how many of these form between the AA and phosphodiester backbone

Answer 47

142 and 1/2 of these form btw AA and phosphodiester backbone

Question 48

how many copies of each histone per cell in humans

Answer 48

60 million