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Cmmb 411 > Topic 2 Protein DNA Interaction And Gene Control > Flashcards

Topic 2 Protein DNA Interaction And Gene Control Flashcards

1
Q

What is a nucleoside vs nucleotide

A

Nucleoside: sugar and the base

Nucleotide: sugar base phosphate

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2
Q

What carbon of the sugar is the phosphoester bond on

What about the base glycosidic bind

What carbon of the deoxyribos has h instead of oh

A

C5

C1

C2

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3
Q

What is the special carbon and group of adenine

Guanine

Cytosine

Thymine

A

Adenine : 6’ nh2 (amino group)

Guanine : 6’ oxy (c=o), 2’ amino

Cytosine: 4’ amino

Thymine: 4’ oxy

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4
Q

The opposite side of the dna major groove has

A

A minor groove

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5
Q

What is the major and minor groove of dna

A

Major groove is 210 degrees to each glycosidic bind to the back bone

Minor is 150

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6
Q

Groovy dna slide

A

9

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7
Q

What is the sequence of operator sites recognized by the lambda repressor and cro

A

Via palindromic sequences that are 17bp long

Slide 11 and 12 idk

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8
Q

What determines the specific characteristic of an amino acid

A

The r group, side chain

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9
Q

Neutral polar, neutral nonpolar, acidic, basic amino acids

A

Slide 15

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10
Q

How many peptide bonds can and amino acid form,

A

2

One on n term and one on c term

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11
Q

How many peptide bonds can and amino acid form,

A

2

One on n term and one on c term

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12
Q

In contrast to dna , where is the peptide backbone of a polypeptide chain

A

On the inside

Sugar phosphate backbone in dna is on the outside

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13
Q

In contrast to dna where are the r groups of the polypeptide

A

On the outside

Bases are on inside

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14
Q

What does 3D fording of the polypeptide determine

A

The function/activity of a protein

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15
Q

Primary

Secondary

Tertiary structure

Quaternary

A

1D string of amino acid residues

3D structure of short stretch of amino acid residues

One 3D secondary structure folding in in itself (found in physiological conditions)

Multiple subunits of alpha helix and beta sheets

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16
Q

Diff in alpha helix and beta sheet

A

Side chains protrude out

Beta sheets side chains project alternately to either side of the backbone

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17
Q

What are domains

Give an example

A

Specific discrete modules in the protein

In the n term of the lambda repressor, there are five alpha helix domains

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18
Q

What components of the lambda repressor actually help in bind to the dna OR sites

A

Recognition helix (helix 3, recognizes the DNA major groove and interacts with it)

Helix turn helix (HLH) motif (helix 2 to three, helps position the dna binding domain of the repressor to the major groove of the OR dna site )

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19
Q

What is the characteristic of the one of the alpha helix domains in a lambda repressor

A

The side chains protrude outward which suggests that the R groups have an important role for it binding

The side chains of the repressor fit into the major groove on the operator

20
Q

What does helix 3 do in binding

A

Recognizes and fits into the major groove

21
Q

What does helix 2 do in binding

A

Helps position helix 3 in the major groove of the dna

22
Q

What does the lambda repressor dimer being symmetric help with

A

It’s let’s each individual helix 3 bind to an individual major groove on the dna

23
Q

What in the lambda repressor enhance the binding to the dna

A

The repressor arms (loops) wrap around the operator

24
Q

What in the lambda repressor enhance the binding to the dna

A

The repressor arms (loops) wrap around the operator

25
Q

What is the tertiary structure of cro

A

3 alpha helix and 3 beta sheets

26
Q

Why is there competition for binding with the cro binding to or and lambs binding

A

Because the cro binds to the same Or site as the repressor in the same major groove

27
Q

What actually determines the lands repressor or cro affinity for OR sites

A

The amino acid residues of the lambda repressor or cro proteins

They both use conserved amino acids for dna bases contact

28
Q

What important conserved amino acids are in the lambda repressor

In cro

A

Gln, ser, ala

Gln, ser, asn, lys

29
Q

What role does each conserved amino acid in the lambda repressor helix 3 play in binding to the or site

A

Glutamine: has long side chains, can have h bonding, is polar which helps it bind to the adenine in dna

Serine: has a ch3-OH group which is polar uncharged , binds to dna tightly

Alanine: nonpolar, helps bring helix 3 closer by making hydrophobic environment around helix 3 and the DNA. Pushes the water out and causes aggregation of it to dna (HYDROPHOBIC ENVIRONMENT)

30
Q

What role does each conserved amino acid in the cro protein helix 3 play in binding to the or site

A

Gln and serine are same

Asparagine: polar uncharged, helps form H bonding interactions

Lysine: has a + charged side chain, lets it interact with negative charged dna. Also has long side chains so wide reach

31
Q

What type of bonding does glutamine in cro and repressor do to bind to dna

A

2 h bonds between the side chain of gln and the adenine base in the major groove

1 with The c=O in the side chain and 1 in the nH2 of the side chain

32
Q

What residues in helix 2 lambda and cro repressor help it position helix 3

A

Alanine on helix two lambda interacts with valine on helix 3

Alanine of helix 2 of cro interacts with isoleucine of helix 3

Glutamine in both cro and lambda helix 2 interacts with the DNA phosphate backbone

33
Q

Why does Glutamine in both cro and lambda helix 2 interact with the DNA phosphate backbone

A

Because glutamine is partial positive and the backbone is negatively charged so they are both interacting to bring each other closer and push helix three further into the groove

34
Q

How do the ala and Val in the cro and repressor helices interact?

A

Since they’re both non polar, they interact through the hydrophobic effect and aggregate together

This gets helix two and three stuck deep in the groove

35
Q

Slide 37

A

Okay

36
Q

What are the two important regions in the dna promoter region

What are they called

A

-10 and -35

-10 is usually called the TATA BOX (eukaryotic cells)

-10 is Pribnow box in (prokaryotes)

37
Q

What are the two important regions in the dna promoter region

What are they called

A

-10 and -35

-10 is usually called the TATA BOX (eukaryotic cells)

-10 is Pribnow box in (prokaryotes)

38
Q

What molecule recognizes the tata box/pribnow box

What does it do

A

Sigma factor

Recruits rna pol to the promoter

39
Q

Why is rna pol bound only to either the Prm or Pr poronoter

A
40
Q

When the repressor binds to the Pr promoter, what is it doing

When the cro protein binds to the Prmpromoter, what is it doing

A

Is block the sigma factor from binding to the tata/pribnow box of the Pr promoter

This results in rna pol not binding to the pr promoter and now not transcribing the cro gene

Is block the sigma factor from binding to the tata/pribnow box of the Prm promoter

This results in rna pol not binding to the prm promoter and now not transcribing the lambda repressor gene

This is why the affinities are the way they are

41
Q

What element of broth promoters is in the or2 region

A

The -35 elements

42
Q

What element of broth promoters is in the or2 region

A

The -35 elements

43
Q

in the Or2 how long is the -35 element from the pr promoter how many nucleotides are actually in the or2)

in the Or2 how long is the -35 element from the prM promoter

A

3 nucleotides

2 nucleotides

44
Q

Why does affinity binding of the lambda repressor to the OR2 help repress cro transcription

A

The pr -35 element in the or2 has 3 nucleotides

if the lambda binds there, there is extra nucleotide blockage

Leads to suppression of pr promoter but activation of Prm (so making lambda repressor

45
Q

Why does affinity binding of the lambda repressor to the OR2 help repress cro transcription

A

The pr -35 element in the or2 has 3 nucleotides

if the lambda binds there, there is extra nucleotide blockage

Leads to suppression of pr promoter but activation of Prm (so making lambda repressor

46
Q

How does the lambda repressor work as a transcription activator

A

The amino acids residue on helix 2 and the loop between helix 2 and 3 interact with rna pol to position is better and positively promote transcription initiation

Promote lamda gene transcription

Cmmb 411 (6 decks)

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