Exam 3 Review

Question 1

describe a feed forward circuit

Answer 1

type of network where signals pass in one direction—from input to output—without looping back. It often involves an intermediate step and helps control timing, amplify signals, or filter noise.

Question 2

describe positive feedback loop

Answer 2

regulatory mechanism where the output of a process enhances or amplifies the initial signal. In cells, this means that once a certain molecule or gene is activated, it promotes its own continued activation, often leading to a stable, self-sustaining state

Question 3

how are positive feedback loops related to cell memory

Answer 3

Positive feedback reinforces a response, and by maintaining activity after the trigger is gone, it helps cells remember and maintain long-term states.

Question 4

what is a polysome

Answer 4

cluster of ribosomes bound to a single mRNA molecule, all translating it simultaneously. This allows the cell to make multiple copies of a protein from one mRNA strand at the same time, increasing efficiency in protein synthesis.

Question 5

what is purpose of polysome

Answer 5

increase efficiency of translation

Question 6

differences between hsp70 90 and chaperonins

Answer 6

chaperonins are used when HSP aren’t sufficient to properly fold the protein, they give the protein its own compartment to properly fold without interruption, HSP works during translation, both give a correctly folded protein

Question 7

in Bulk RNA seq, what does red mean

Answer 7

activated genes

Question 8

in bulk RNA seq, when does time start

Answer 8

when serum is added

Question 9

what can BULK RNA seq not to

Answer 9

tell you individual gene expression in individual cells

Question 10

what can single cell RNA seq do

Answer 10

tell you about heterogeneity of a cell, measures mRNA 1 cell at a time for 1000s - 10000s cells

Question 11

cells close together in single cell RNA seq are what

Answer 11

similar, similar gene expression or cell type

Question 12

what can be hard to discern with single cell RNA seq

Answer 12

cell state vs type

Question 13

what does in situ hybridization do

Answer 13

tells where in organism mRNA is expressed

Question 14

what binds to target mRNA in in situ hybridization , what special about them

Answer 14

probes, they are fluorescently labeled

Question 15

what is a limit of in situ

Answer 15

can’t cover massive amounts of different mRNA

Question 16

describe prokaryote transcription

Answer 16

more efficient, multiple proteins coded per mRNA, no modification

Question 17

describe eukaryote transcription

Answer 17

more regulated, inefficient, extra coding allow for regulation

Question 18

what bind to cis reg seq

Answer 18

transciption factors

Question 19

system of survalence for viruses

Answer 19

CRISPR

Question 20

where do coactivators and co repressors bind

Answer 20

transcription factors

Question 21

RNA transcribed from CRISPR locus is bound to what

Answer 21

Cas Protein

Question 22

what is in complex with Cas protein and what does it do

Answer 22

small crRNA, seeks out and destroys viral sequence s

Question 23

list non conventional base pairs between RNA and itself

Answer 23

G-u, a-g, c-u

Question 24

what is present at active site of RNA polymerase

Answer 24

Mg2+

Question 25

how does RNA poly move

Answer 25

stepwise along DNA

Question 26

energy source for RNA poly

Answer 26

ribonucleoside triphosphate

Question 27

function in variety of nuclear processes including splicing of pre mRNA

Answer 27

snRNAs

Question 28

help to process and chemically modify rRNAs

Answer 28

snoRNAs

Question 29

not all apear to have function, some serve as scaffolds and regulate diverse cell processes

Answer 29

lncRNAs

Question 30

regulate gene exp by blocking translation of specific mRNAs and causing their degradation

Answer 30

miRNAs

Question 31

turn off gene exp by directing degradation of selective mRNAs and helping to establish repressive chromatin structures

Answer 31

siRNAs

Question 32

RNA poly 1 transcribes what genes

Answer 32

5.8S, 18S, 28S rRNA

Question 33

RNA poly 2 mainly transcribed what

Answer 33

all protein coding genes

Question 34

RNA poly 3 transcribes what

Answer 34

tRNA genes, 5S rRNA, snRNA

Question 35

in euk RNA, introns removed via what and from what

Answer 35

splicing, pre mRNA

Question 36

what happens to3' end of mRNA euk

Answer 36

3' end cleaved and poly A tail added

Question 37

describe the premRNA splicing reaction

Answer 37

1. An adenine nucleotide in the intron attacks the 5′ splice site, cutting the RNA backbone. 2. The cut 5′ end of the intron links to the adenine, forming a loop (lariat structure). 3. The free 3′-OH end of the exon reacts with the next exon, joining them together. 4. The intron is released as a lariat and later degraded into single nucleotides for recycling

Question 38

key seq for intron removal

Answer 38

in intron : GU at 5' splice site, AG at 3' splice site

Question 39

what directs direct cleavage and poly A tail addition in euk mRNA

Answer 39

sequences in the mRNA

Question 40

what is the poly a tail sequence signal

Answer 40

AAUAAA

Question 41

what is cleavage signal for euk mRNA 3'

Answer 41

CA

Question 42

GU rich element beyond cleavage site is bound by what

Answer 42

CstF

Question 43

DNA probes can bind to both RNA and DNA targets. How could you design a probe that would bind to a gene’s DNA sequence but not its mRNA sequence? How could you design a probe to bind to a gene's mRNA sequence but not its DNA sequence?

Answer 43

DNA not RNA - design a probe that binds to introns RNA not DNA - design probe that spans exon-exon junction s

Question 44

translation reads mRNA in what direction

Answer 44

5' to 3'

Question 45

match amino acids to codons in mRNA

Answer 45

tRNAs

Question 46

what base pairs with mRNA codon

Answer 46

anticodon

Question 47

amino acid attached where and to what

Answer 47

3' end of tRNA

Question 48

tRNAs contain unusual bases like what

Answer 48

pseudouridine, dihydrouridine

Question 49

what enables some tRNAs to recognize multiple codons for the same AA

Answer 49

wobble posiiton

Question 50

inosine formed by what

Answer 50

deamination of adenosine

Question 51

aminoacyl tRNA syntheses do what

Answer 51

attach amino acids to corresponding tRNAs

Question 52

steps of attaching AA to tRNA

Answer 52

Step 1: Activation – The amino acid’s carboxyl group binds to AMP, forming an adenylated amino acid. This reaction is driven by ATP hydrolysis. Step 2: Transfer to tRNA – The amino acid is transferred from AMP to the 3′ end of one the tRNAs that can code for it. This forms a high-energy ester linkage, creating aminoacyl-tRNA

Question 53

Incoming amino acid covalently linked to growing chain through

Answer 53

peptide bond

Question 54

drives peptide bond formation

Answer 54

high energy peptide tRNA bond

Question 55

what does HSP70 recognize

Answer 55

exposed hydrophobic regions

Question 56

common promotor sequence

Answer 56

TATA box

Question 57

where is TATA box located

Answer 57

about 30 nt upstream of transcription start site

Question 58

TATA box recruits what for what

Answer 58

gen transcription factors needed for initiation of transcription by RNA poly 2

Question 59

DNA sequence where general transcription factors and RNA polymerase assemble.

Answer 59

promotor

Question 60

site for transcriptional factor/regulator

Answer 60

cis regulatory sequence

Question 61

preferred nucleotides for specific transcription factor binding

Answer 61

sequence logo rep

Question 62

many transcription factors form what

Answer 62

homo or heterodimers

Question 63

euk transcription regulators form what

Answer 63

multiprotein complexes

Question 64

noncoding RNAs in multiprotein komplexes function as what

Answer 64

scaffolds to stabilize protein assemblies

Question 65

The repressor can bind near the activator on DNA and...

Answer 65

interfere with activator function, blocking coactivator recruitment

Question 66

repressor can do what

Answer 66

stabilize an intermediate in the transcription factor assembly process

Question 67

True/False: The general transcription factors are a group of DNA binding proteins that interact as homo- or hetero- dimers with cis-regulatory DNA sequences outside the TATA box. why

Answer 67

GTF help recruit RNA poly to promotor

Question 68

feed forward loop can measure what

Answer 68

duration of a signal

Question 69

a regulatory mechanism for gene silencing and posttranscriptional control in eukaryotes.

Answer 69

RNAi

Question 70

what guides RNAi

Answer 70

single strand interfering RNAs like siRNAs or miRNAs

Question 71

Single-strand interfering RNAs (like siRNAs or miRNAs) guide RNAi by...

Answer 71

bp w complimentary target RNAs

Question 72

possible outcomes of RNAi

Answer 72

Cleavage and degradation of target mRNA * Translational repression or target mRNA * Heterochromatin formation on DNA from which RNA is being transcribed

Question 73

miRNAs transcribed as what

Answer 73

primary miRNAs

Question 74

primary miRNAs for what

Answer 74

hairpin structures

Question 75

primary miRNA processed into what

Answer 75

precursor miRNA

Question 76

dicer enzyme cleaves what and forms what

Answer 76

cleaves precursor miRNA, generated mature miRNA

Question 77

key protein in RISC

Answer 77

argonaute

Question 78

RISC binds to what initially

Answer 78

both strains of the miRNA

Question 79

argonauts does what

Answer 79

cleaves and discards one strand of miRNA, uses remaining strand to guide RISC to complementary mRNA targets

Question 80

what cleaves premiRNA to get mature miRNA

Answer 80

dicer enzyme

Question 81

what determines the outcome of what RISC is doing

Answer 81

extend of bp btw miRNA and mRNA

Question 82

miRNA regulation:extensive base-pairing leads to

Answer 82

mRNA cleavage and degradation

Question 83

miRNA regulation : partial bp results in

Answer 83

inhibition of translation, eventual mRNA degradation

Question 84

what cuts dsRNA to turn it into siRNA

Answer 84

dicer

Question 85

introduction os dsRNA is for what

Answer 85

gene knockdown, gets turned to siRNA then taken up by argonauts and RISC

Question 86

Cas9 binds what

Answer 86

guide RNA

Question 87

guide RNA contains what regions

Answer 87

one required for Cas9 binding, sequence matching specific genome target

Question 88

Cas9 creates what in the targeted genomic site

Answer 88

double strand break

Question 89

double strand break by Cas9 usually repaired by what , can introduce what

Answer 89

non homologous ends joining, mutations

Question 90

what can be used in the double strand break to precisely edit, and what does this enable and require

Answer 90

homologous recombination, requires a altered repair template, which is supplied by the experimenter, enables to alter genes

Question 91

mutant Cas9 - properties and used for what

Answer 91

cannot cleave DNA, used for gene regulation

Question 92

mutant Cas9 fused to activator does what

Answer 92

turn on dormant gene

Question 93

How would you expect the usage of rare codons in a coding sequence to affect protein translation? Why?

Answer 93

Rare codons are likely to have lower translational efficiency as tRNAs may be less abundant for that codon

Question 94

What experiment would you perform to test this?How would you expect the usage of rare codons in a coding sequence to affect protein translation?

Answer 94

Make a optimal codon versus a rare codon version of the protein in an expression vector. Have cells express each version and measure resulting protein output

Question 95

Under what circumstances would using a rare codon be advantageous?

Answer 95

This could be used to reduce the output for this particular protein that is meant to be at low levels. Also could make it responsive to the upregulation of a particular tRNA. Enables modular expression of a set of proteins based on tRNA regulation

Question 96

Viruses, which rely on the translational machinery of the host cell, can evolve to infect other hosts. a)How might codon usage bias contribute to the success of a virus in a particular host?

Answer 96

Virus would use codons for efficient replication in that host by matching its codons with those most frequently used by host cells. 1 point

Question 97

How do you hypothesize codon usage could change when viruses crossover to a new host?

Answer 97

Virus would alter the codon usage to better match the new host after the acquiring the ability to infect that new host

Question 98

What experiment would you perform to test this hypothesis?: Virus would alter the codon usage to better match the new host after the acquiring the ability to infect that new host

Answer 98

Look at examples of host-species transitions in viruses and analyze sequence of the virus before and after the transition. Compare with codon frequency tables to see if codon usage shifted to more closely resemble the codon usage bias of the new host

Question 99

What factor(s) do you hypothesize can contribute to this and why: Codon usage is not equal within a species showing some are used more frequently than others. Across species, codon usage can also vary for the same amino acid

Answer 99

Differences in GC content, differences in the abundance of particular tRNAs in a cell.

Question 100

You synthesize the sequence, but the probe still does not work. Explain why the probe sequence does not effectively bind to any RNAs.

Answer 100

The probe forms a hairpin structure with itself. This prevents it from effectively binding the target region.

Question 101

If you want to use genomic DNA to PCR amplify a region for generating the probe, which regions of the gene should you target and why? Which regions should you not target?

Answer 101

You can target exonic regions but want to avoid intronic regions. Do not cross exon-intron junctions with the amplicon

Question 102

Differential exon splicing? does what

Answer 102

Generates a variety of polypeptide sequences from the same sequence

Question 103

what do bacteria not have that eukaryotes have

Answer 103

intron processing mechanisms

Question 104

polypeptide chain is synthesized from....

Answer 104

N terminus to C terminus

Question 105

determine whether cells uniformly regulate gene transcription in response to a signal or have different responses to the same input

Answer 105

single cell RNA seq

Question 106

used to identify sets of coordinately regulated genes across samples

Answer 106

bulk RNAseq

Question 107

Difference between prokaryotic and eukaryotic mRNA?

Answer 107

Prokaryotic mRNA remains unmodified at the 5’ and 3’ ends

Question 108

Know how mRNA and the ribosome interact with each other- reading from...

Answer 108

5' to 3'

Question 109

a techniques can test the sufficiency of cis-regulatory DNA sequence in promoting gene expression

Answer 109

gene reporting