11. Gene Expression

Question 0

how does the type of regulation affect enzyme kinetics?

Answer 0

allosteric regulation affects Km

transcriptional control affects Vmax

Question 1

what does every somatic cell contain?

Answer 1

the genetic material that codes for every cell in the organism

Question 2

what is a super secondary structure?

Answer 2

when a DNA-binding protein attaches to DNA

pretty much, structure somewhere between secondary & tertiary protein structure

Question 3

helix turn helix

Answer 3

a helix
b turn
b helix

MOST common DNA binding motif

Question 4

as a dimer, DNA-binding proteins can do what?

Answer 4

DNA-binding proteins can bind to both halves of a palindrome with equal specificity

Question 5

zinc finger

Answer 5

zinc chelates 2 or more histidine or cytosine residues

zinc binds to major groove of DNA

common motif in hormone receptors i.e. glucocorticoid

Question 6

leucine zipper

Answer 6

leucine repeated at every 7th AA
forms a zipper structure

creates hydrophobic domain

Question 7

combinatorial control

Answer 7

different DNA binding motifs used in combination to regulate gene expression

Question 8

binding of DNA-binding protein to specific sequences

Answer 8

DNA-binding protein interacts with DNA, hydrogen bonds form between an R group on the protein & the major groove of the DNA in tight/high affinity bonds

Question 9

what do restriction enzymes do

Answer 9

bind to a specific sequence on DNA & cut

MOST COMMON DNA-binding proteins

Question 10

what is an operon?

Answer 10

a single stretch of DNA that encodes for all of the enzymes necessary to produce a given response

Question 11

trp operon, when tryptophan is present?

Answer 11

DNA-binding protein is bound to DNA and trp operon is OFF

Question 12

DNA-binding protein functions as a ______ in the trp operon

Answer 12

repressor

when DNA-binding protein is bound to the DNA, it blocks transcription, turning trp OFF

Question 13

negative control

Answer 13

when binding of the protein to DNA inhibits transcription

Question 14

positive control

Answer 14

when binding of the protein to DNA activates transcription

Question 15

what is a gene activating protein?

Answer 15

DNA-binding protein that binds to the DNA and ACTIVATES transcription

Question 16

lac operon

Answer 16

ON when lactose is present with no glucose (glucose is ideal energy source)

controls lactose metabolism

controlled by glucose & lactose

Question 17

2 things transcription factors must do?

Answer 17

1. bind DNA

2. bind more proteins so transactivation can occur

Question 18

2 main functional domains of a transcription factor?

Answer 18

1. DNA-binding domain

2. transactivation domain

Question 19

if a transcription factor does not have a DNA-binding domain?

Answer 19

it must have two transactivation domains

Question 20

promiscuity

Answer 20

ability of 1 DNA-binding domain to bind specifically to multiple different DNA sequences

Question 21

what do promoters do?

Answer 21

give RNA pol the position and orientation info it needs in order to start transcription

Question 22

what do enhancers do?

Answer 22

regulate transcription by either enhancing or inhibiting transcription

always palindromes

Question 23

2 types of transcription factors that are enhancers?

Answer 23

1. constitutive transcription factors

2. inducible transcription factors

Question 24

inducible transcription factors

Answer 24

we can turn on/off

can be second messenger dependent, hormone receptors, or tissue specific

Question 25

what do chromatin remodeling complexes do?

Answer 25

alter chromatin structure in order to form a transcription bubble

Question 26

what does a transcription bubble do?

Answer 26

ensure only one strand is read during transcription

Question 27

what can the chromatin remodeling complex do to create a transcription bubble?

Answer 27

1. remodel nucleosomes
2. remove histones from nucleosomes
3. replace histones on nucleosomes
4. modify histones (i.e. methylation or acetylation)

Question 28

effects of eukaryotic gene repressor protein examples

Answer 28

1. block gene activator proteins from binding to DNA via competitive DNA binding
2. mask activation surface
3. directly interact with the general transcription factors
4. recruit chromatin remodeling complexes to close or silence the DNA
5. recruit histone deacetylase (remove acetly groups that have been attached to the promoter to open up the DNA for transcription)
6. recruit histone methyl transferase (which methylates & silences chromatin)

Question 29

DNA-bending protein

Answer 29

manipulates DNA so you can get the factors to form an initiation complex

Question 30

insulator sequence

Answer 30

between genes, prevent a transcription factor from cross-regulating genes, restricting their activity to the intended gene

Question 31

barrier sequences

Answer 31

between genes, block heterochromatin from spreading, preventing cross-regulation