test 3 study guide

Question 1

What is chromatin?

Answer 1

DNA + histone proteins.

Question 2

What is euchromatin?

Answer 2

Open, less condensed, transcriptionally active.

Question 3

What is heterochromatin?

Answer 3

Condensed, transcriptionally inactive.

Question 4

Constitutive heterochromatin?

Answer 4

Always heterochromatic (centromeres, telomeres).

Question 5

Facultative heterochromatin?

Answer 5

Can switch between open/closed forms.

Question 6

What is a nucleosome?

Answer 6

DNA wrapped around histone octamer.

Question 7

The histone octamer contains how many histones?

Answer 7

8 (H2A, H2B, H3, H4 — two copies each).

Question 8

What enzyme adds acetyl groups to histones?

Answer 8

HATs (histone acetyltransferases).

Question 9

Effect of histone acetylation?

Answer 9

Opens chromatin → increases transcription.

Question 10

What enzymes remove acetylation?

Answer 10

HDACs (histone deacetylases).

Question 11

Effect of HDAC activity?

Answer 11

Closes chromatin → decreases transcription.

Question 12

DNA methylation usually occurs at what sequences?

Answer 12

CpG islands.

Question 13

What is the effect of heavy DNA methylation?

Answer 13

Gene silencing.

Question 14

DNA methylation mediates what long-term process?

Answer 14

Epigenetic inheritance.

Question 15

Chromatin remodeling complexes do what?

Answer 15

Move or evict nucleosomes to regulate transcription.

Question 16

Example of a remodeling complex?

Answer 16

SWI/SNF.

Question 17

What is a DNase hypersensitivity site?

Answer 17

Region of open chromatin accessible to transcription factors.

Question 18

Are enhancer regions usually open or closed?

Answer 18

Open chromatin.

Question 19

What is imprinting?

Answer 19

Parent-specific methylation causing allele-specific expression.

Question 20

Does epigenetic modification change DNA sequence?

Answer 20

No, changes packaging/chemistry only.

Question 21

What is a promoter?

Answer 21

DNA region where RNA polymerase binds.

Question 22

What is the TATA box?

Answer 22

Core promoter sequence.

Question 23

What binds the TATA box?

Answer 23

TBP (TATA-binding protein).

Question 24

Enhancers do what?

Answer 24

Increase transcription when activators bind.

Question 25

Silencers do what?

Answer 25

Decrease transcription when repressors bind.

Question 26

Can enhancers work far from a gene?

Answer 26

Yes, upstream, downstream, introns.

Question 27

What are insulators?

Answer 27

Block enhancer–promoter interactions.

Question 28

What binds insulators?

Answer 28

CTCF protein.

Question 29

What is a transcription factor (TF)?

Answer 29

Protein that binds DNA to regulate transcription.

Question 30

TFs contain what key functional domain?

Answer 30

A DNA-binding domain.

Question 31

Examples of DNA-binding motifs?

Answer 31

Helix-turn-helix, zinc finger, leucine zipper.

Question 32

What is an activator?

Answer 32

TF that increases transcription.

Question 33

What is a repressor?

Answer 33

TF that decreases transcription.

Question 34

Coactivators mediate what interaction?

Answer 34

Activators → RNA Polymerase II.

Question 35

Main coactivator complex in eukaryotes?

Answer 35

Mediator

Question 36

What determines which genes a cell expresses?

Answer 36

The TFs present in that cell.

Question 37

Example of a hormone response element?

Answer 37

Estrogen response element (ERE).

Question 37

What are response elements?

Answer 37

TF binding sequences responsive to environmental signals.

Question 39

Do enhancers need to be close to promoters?

Answer 39

No — DNA looping brings them together.

Question 40

Can multiple TFs act on the same gene?

Answer 40

Yes, combinatorial control.

Question 41

When is the 5′ cap added?

Answer 41

During transcription

Question 42

What is the 5′ cap?

Answer 42

Modified guanine nucleotide (7-methylguanosine).

Question 43

Functions of the 5′ cap?

Answer 43

Protects mRNA, aids ribosome binding.

Question 44

What enzyme adds the poly-A tail?

Answer 44

Poly-A polymerase.

Question 45

Function of poly-A tail?

Answer 45

mRNA stability + nuclear export.

Question 46

What is a spliceosome?

Answer 46

Complex that removes introns.

Question 47

Spliceosome is made of what?

Answer 47

snRNPs

Question 48

Splice sites are defined by what sequences?

Answer 48

5′ GU, branch point A, 3′ AG.

Question 49

What is alternative splicing?

Answer 49

producing multiple mRNAs from one gene

Question 50

Why is alternative splicing important?

Answer 50

increases proteome diversity.

Question 51

RNA editing?

Answer 51

Base changes after transcription.

Question 52

What is RNA surveillance?

Answer 52

degradation of faulty mRNAs.

Question 53

Nonsense-mediated decay (NMD) removes what?

Answer 53

mRNA with premature stop codons.

Question 54

What distinguishes miRNA from siRNA?

Answer 54

miRNA = imperfect pairing; siRNA = perfect pairing.

Question 55

miRNA inhibits gene expression how?

Answer 55

Blocks translation.

Question 56

siRNA inhibits gene expression how?

Answer 56

Cleaves mRNA.

Question 57

siRNAs often come from?

Answer 57

Viruses or transposons.

Question 58

miRNAs come from where?

Answer 58

Host genome.

Question 59

RISC complex function?

Answer 59

Binds miRNA/siRNA to silence target mRNA.

Question 60

What is RNA polyadenylation signal?

Answer 60

AAUAAA.

Question 61

What is the start codon?

Answer 61

AUG.

Question 62

How many codons encode amino acids?

Answer 62

61

Question 63

How many stop codons are there?

Answer 63

3 (UAA, UAG, UGA).

Question 64

What is degeneracy of the genetic code?

Answer 64

Multiple codons encode same amino acid.

Question 65

What is wobble?

Answer 65

Flexibility in third codon position.

Question 66

What enzyme charges tRNAs?

Answer 66

Aminoacyl-tRNA synthetase.

Question 67

What is an anticodon?

Answer 67

tRNA sequence complementary to mRNA codon.

Question 68

EPA sites — which is which?

Answer 68

A = aminoacyl, P = peptide, E = exit.

Question 69

Translation initiation requires what?

Answer 69

Small ribosomal subunit + initiator tRNA.

Question 70

Eukaryotic initiation depends on what structure?

Answer 70

5′ cap.

Question 71

During elongation, what forms the peptide bond?

Answer 71

Peptidyl transferase activity of rRNA.

Question 72

What is translocation?

Answer 72

Ribosome moves 3 nt along mRNA.

Question 73

What terminates translation?

Answer 73

Release factor binding to stop codon.

Question 74

What is a polyribosome?

Answer 74

Multiple ribosomes translating same mRNA.

Question 75

Are ribosomes catalytic?

Answer 75

Yes — rRNA catalyzes peptide bonds.

Question 76

What determines mRNA half-life?

Answer 76

Poly-A tail length and RNA-binding proteins.

Question 77

What shortens mRNA lifespan?

Answer 77

AU-rich elements in 3′ UTR.

Question 78

What does ubiquitination do?

Answer 78

Marks proteins for degradation.

Question 79

What is phosphorylation used for?

Answer 79

Activating/inactivating proteins.

Question 80

What does acetylation do to proteins?

Answer 80

Modifies activity or stability.

Question 81

What is proteasome function?

Answer 81

Degrades ubiquitinated proteins.

Question 82

What is translational repression?

Answer 82

Preventing ribosomes from initiating translation.

Question 83

miRNA effect on translation?

Answer 83

Represses initiation.

Question 84

Iron-response element (IRE) regulates what?

Answer 84

Ferritin and transferrin receptor translation.

Question 85

Do bacteria have a nucleus?

Answer 85

No

Question 86

Are transcription and translation coupled in bacteria?

Answer 86

Yes.

Question 87

What is an operon?

Answer 87

Cluster of genes under one promoter.

Question 88

Are eukaryotic mRNAs polycistronic?

Answer 88

No; usually monocistronic.

Question 89

Main regulatory point in bacteria?

Answer 89

Transcription initiation.

Question 90

Main additional regulatory point in eukaryotes?

Answer 90

Chromatin structure.

Question 91

Bacteria use what sigma factor to initiate transcription?

Answer 91

σ factor.

Question 92

Eukaryotes use which polymerase for mRNA?

Answer 92

RNA Polymerase II.

Question 93

Do bacteria perform splicing?

Answer 93

No

Question 94

Do eukaryotes use histones?

Answer 94

Yes

Question 95

Lac operon is?

Answer 95

Inducible

Question 96

trp operon is?

Answer 96

Repressible

Question 97

CAP–cAMP activates lac operon when?

Answer 97

Glucose is low.

Question 98

What blocks lac operon when lactose absent?

Answer 98

Lac repressor.

Question 99

Attenuation in trp operon occurs when?

Answer 99

High tryptophan levels.

Question 100

Do eukaryotic genes have operators?

Answer 100

No — promoters + enhancers instead.