Genetics 3

Front 1

Decondensed chromatin where transcription occurs

Back 1

Euchromatin

Front 2

Condensed chromatin where transcription DOES NOT occur

Back 2

Heterochromatin

Front 3

Explain what "Epigenetic" means

Back 3

A code that is heritable due to coordination between histone modification and methylation of DNA that doesn't involve changes in the sequence of DNA

Front 4

Name 6 Nuclear compartments

Back 4

Nucleoli
Cajal Bodies
SMN gems
Splicing factor domains
PML bodies
Lamina

Front 5

Name the 3 DNA components compacted by histones

Back 5

Base Pair
Nucleosome
Chromatin Fiber

Front 6

Name the 3 DNA components compacted by chromosome scaffolding/nuclear matrix

Back 6

DNA domain
Mitotic chromosome
Nucleus

Front 7

Describe Chromatin Structure

Back 7

DNA wraps around histones which turn on themselves.... These turns then loop on scaffolding which then coils on itself?

Front 8

Describe FISH

Back 8

dsDNA is denatured --> add labeled DNA probe--> Hybridize for fluorescence imaging

Front 9

What does the Nucleosome consist of?

Back 9

Histone core with DNA wrapped around it (~150 bp)

Front 10

True or False:
The basic structure of ALL core histones is the same.

Back 10

True

Front 11

Describe the structure of histones

Back 11

1 long hydropho alpha helix bordered by 2 short hydropho alpha helices that form pairs:
H2A-H2B and H3-H4 which interact

Front 12

Histone Octamer

Back 12

H3+H4 --> H3-H4 Dimer x 2 --> H3-H4 Tetramer
+
H2A+H2B --> H2A-H2B dimer x 2

Front 13

True or False:
Histone tails are highly charged and reactive

Back 13

True

Front 14

What do histone modifications affect?

Back 14

Chromatin structure

Front 15

What structure essentially forms a "ramp" for DNA?

Back 15

Histone octamer

Front 16

Each core histone dimer has how many DNA binding surfaces?

Back 16

6

Front 17

Each core histone DIMER organizes __ DNA turns?

Back 17

3

Front 18

Each histone OCTAMER organizes __ helical turns of DNA?

Back 18

1 3/4

Front 19

H1 is also known as...

Back 19

Linker histone

Front 20

What does H1 do?

Back 20

Promotes "higher order" folding
Organizes exiting DNA
Stabilizes interaction between nucleosomes in compacted chromatin

Front 21

High [salt] promotes what kind of chromatin fiber structure?

Back 21

Compacted (Solenoid)

*low salt --> loose*

Front 22

How does high levels of H1 affect gene transcription?

Back 22

There is NO gene transcription

Front 23

What is a chromatosome?

Back 23

Core histone octamer + 1 Linker histone + 2 full turns of DNA
OR

Nucleosome + Linker protein

Front 24

True or False:
Histone acetylation is an irreversible modification of lysines in the N-termini of the core histones

Back 24

False: it is REVERSIBLE

Front 25

What are the results of histone acetylation

Back 25

Reduced binding to DNA

Destabilization of chromatin

Front 26

Describe some histone modifications

Back 26

Acetylation
Acetylation/Methylation
Methylation (asymmetric or symmetric)
Phosphorylation

Front 27

What changes lysine into N-Acetyl-Lysine?

Back 27

HAT (Histone Acetyl-Transferase)

Front 28

The N-termini and acetylation patters of which histones are absolutely conserved?

Back 28

H4 and H3

Front 29

What happens when the S phase gene is off?

Back 29

Histone Deacetylase activates

Front 30

What happens when the S phase gene is on?

Back 30

HAT activates (and DNA pol II starts?)

Front 31

When must chromatin remodeling occur?

Back 31

During replication

Front 32

Describe Chromatin transcription: Skip

Histone dissociation?

Back 32

Essentially "stepping around on a DNA loop" (pulling DNA off histone piece by piece)

No dissociation

Front 33

Describe Chromatin transcription: Split

Histone Dissociation?

Back 33

Genetranscription exposes the 2 buried H3 cysteines...? Half nucleosome repeats seen upon DNase I digestion

No dissociation

Front 34

Describe Chromatin transcription: Strip

Histone Dissociation?

Back 34

Histone is synthesized as poly goes through and histone has turnover

Front 35

What are CpG islands?

Back 35

Found in the promotor, CG rich regions where methylation of cytosine bases determines active and inactive transcription

Front 36

Methyltransferases us ______ as the methyl donor?

Back 36

S-adenosylmethionine

Front 37

Methylation potentially does what to gene transcription?

Back 37

Silences it. Evidence supports the idea that transcriptionally active genes are less methylated than their inactive counterparts.

Front 38

Describe the structure of DNA

Back 38

Double stranded helix

Front 39

Describe the structure of RNA and why it's important

Back 39

Single stranded... Allows folding into particular shapes similar to polypep chain... Allows for precise structural and catalytic functions

Front 40

Which direction is RNA made?

Back 40

5'-3'

Front 41

Name the 3 classes of Prokaryotic RNA

Back 41

rRNA
tRNA
mRNA

Front 42

What is the Shine-Dalgarno sequence?

Back 42

The SD sequence (Purine rich) base-pairs with a pyrimidine-rich (CU) sequence in 16S rRNA to facilitate the initiation of protein synthesis

Front 43

Describe the structure of prokaryotic mRNA

Back 43

5'---SD sequence---Initiation AUG-------Translated region---- Termination AAU----3'

Front 44

Differences between Eukaryote and Prokaryote transcription and translation

Back 44

Eukaryote: has introns & exons... 5' Capping RNA splicing and 3' polyadenylation... Transcription--> nucleus, Translation--> cytoplasm

Prokaryote: Transcription & translation in cytoplasm... none of the other stuff

Front 45

Compare prokaryote and eukaryote mRNA molecules

Back 45

Pro: intermittent coding and non coding sequences creating separate proteins

Euk: one lump coding sequence making one protein

Front 46

What is required to transcribe DNA into RNA?

Back 46

DNA template
4 Ribonucleotide 5' triphosphates
Mg+2

Front 47

For De Novo synthesis of RNA, what is not required?

Back 47

Doesn't require a primer

(low fidelity compared to DNA poly)

Front 48

The template strand of DNA during transcription is also known as...?

Back 48

The non-coding strand

Front 49

When is transcription of DNA into RNA regulated in vivo?

Back 49

initiation, elongation, termination

Front 50

True or false:
During transcription, the nucleotide at the 5' end loses some of its phosphate groups.

Back 50

False: The nucleotide retains all 3 P groups, all subsequent nucleotides release PPi when added to the chain and retain only their alpha phosphate

Front 51

What happens to the released PPi during transcription?

Back 51

It is subsequently hydrolyzed by pyrophosphatase to Pi, driving the equilibrium of the rxn toward chain elongation

Front 52

Describe transcription in prokaryotes

Back 52

1 RNA poly from ecoli
A multisubuint structure alpha2, beta beta', omega, sigma
The holoenzyme loses the sigma subunit to give the core enzyme

Front 53

What is the function of the sigma unit in prokaryote transcription?

Back 53

to recognize the promoter locus

Front 54

What is the function of the alpha subunit in the ecoli RNA poly holoenzyme?

Back 54

binds reg sequences/proteins

Front 55

What is the function of the Beta subunit in the ecoli RNA poly holoenzyme?

Back 55

Forms phosphodiester bonds/ binds ribonucleoside P3 substrates

Front 56

What is the function of the Beta' subunit in the ecoli RNA poly holoenzyme?

Back 56

Bind DNA template

Front 57

What is the function of the omega subunit in the ecoli RNA poly holoenzyme?

Back 57

RNAP assembly

Front 58

A single RNA poly makes multiple types of RNAs in prokaryotes

Back 58

Processive

Front 59

What does rifampicin target?

Back 59

Beta of the ecoli RNA pol holoenzyme

Front 60

Where is the initiation consensus sequences in prokaryotes found?

Back 60

often 25 and 10 bp upstream of the start of transcription
-30 box and -10 (Pribnow) box
TTGACA TATAAT
+1 will be the start site

Front 61

Where is the initiation consensus sequence found in eukaryotes?

Back 61

TATA box likes 25 bp upstream

Front 62

A DNA segment that signals the start of RNA synth

Back 62

Promoter locus

Front 63

Where is the promoter locus found?

Back 63

Upstream (toward the 3' end) of the DNA seg where the gene coding for RNA actually begins

Front 64

Consensus sequences of prok promoter regions are rich in...?

Back 64

A-T bp

Front 65

Describe transcription initiation by prok RNA pol

Back 65

Holoenzyme complex slides and scans to promoter region... releases sigma to make open complex... initiation

Front 66

How many RNA pols do euk have?

Back 66

3

Front 67

Prok RNA pol is similar to which Euk RNA pol?

Back 67

RNA pol II, althoug euk is larger

Front 68

What is the function of lac operon in ecoli?

Back 68

To produce the enzymes required to metabolize lactose for energy when it is required by the cell

Front 69

What does the promoter bind in the lac operon?

The operator...?

Back 69

Promoter binds CAP and RNA pol

Operator binds the lac repressor

Front 70

Describe regulation of the lac operon- negative control

Back 70

The repressor tetramer (from lac I) binds to the operator, prevents RNA pol from biding the promoter--> no transcription

Front 71

How is negative control regulation of the lac operon alleviated?

Back 71

Lactose hydrolyzed to allolactose... one allolactose binds to each of the repressor subunits (4)... results in a conformational change.... dissociation of repressor from DNA

Front 72

True or false:
Transcription begins after the lac operon repressor disassociates from DNA

Back 72

False: RNA pol can't form a stable complex with the promoter

Front 73

Describe the beginning of regulation of lac operon- positive control

Back 73

In the presence of both lactose and glucose, not necessary for cell to metabolize lactose for E... in the absence of glucose but with lactose advantageous to...

Front 74

Describe the regulation of lac operon-positive control beginning with cAMP

Back 74

W/o glucose, cells make cAMP... this serves as a + regulator... cAMP binds the dimeric cAMP binding protein (CAP)2... binding increases the affinity of CAP for promoter... binding of CAP to promoter facilitates biding of RNA pol... Transcrip & transla occur

Front 75

lac I...?
lac Z...?
lac Y...?
lac A...?

Back 75

lac repressor
B-galactosidase
permease
acetylase

Front 76

True or false:
Once trakstription has started, RNA pol proceeds smoothly

Back 76

False: it moves jerkily, pausing at some sequences and rapidly transcribing others

Front 77

What is the role of elongation factors during transcription?

Back 77

To travel with the pol to decrease the likelihood of dissociation. associate shortly after initiation

Front 78

What is a barrier to transcription elongation?

Back 78

DNA supercoiling

Front 79

Describe DNA supercoiling

Back 79

protein moving forward, - supercoil behind (helix opening facilitated), + supercoiling ahead (helix opening hindered)

Front 80

What is the "RNA factory" concept for euk RNA pol II?

Back 80

The RNA pol II also carries pre-mRNA processing proteins on its tail which are transferred to nascent RNA

Front 81

What is the overview of mRNA synthesis?

Back 81

initiation --> capping and elongation--> splicing--> polyadenylation nuclear export

Front 82

What is the 5' cap essential for?

Back 82

pre-mRNA splicing, export, stability, and translation initiation
*Protects RNA from 5' exonucleolytic cleavage*

Front 83

What 3 separate enzyme activities are required for 5' cap formation?

Back 83

Phosphatase
Guanyl transferase
Methyl transferase

Front 84

What structures are involved in RNA splicing?

Back 84

Exons, Introns, Spliceosome, and exonic/intronic cis elements (splicing enhancers and silencers)

Front 85

What is polyadenylation and why is it important?

Back 85

The final step in mRNA synth with the ligation of the poy-A tail. Addition of the poly-A tail is essential to protect the RNA from 3' hydrolytic enzymes