Topic 2 Protein DNA Interaction And Gene Control Flashcards
What is a nucleoside vs nucleotide
Nucleoside: sugar and the base
Nucleotide: sugar base phosphate
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
C5
C1
C2
What is the special carbon and group of adenine
Guanine
Cytosine
Thymine
Adenine : 6’ nh2 (amino group)
Guanine : 6’ oxy (c=o), 2’ amino
Cytosine: 4’ amino
Thymine: 4’ oxy
The opposite side of the dna major groove has
A minor groove
What is the major and minor groove of dna
Major groove is 210 degrees to each glycosidic bind to the back bone
Minor is 150
Groovy dna slide
9
What is the sequence of operator sites recognized by the lambda repressor and cro
Via palindromic sequences that are 17bp long
Slide 11 and 12 idk
What determines the specific characteristic of an amino acid
The r group, side chain
Neutral polar, neutral nonpolar, acidic, basic amino acids
Slide 15
How many peptide bonds can and amino acid form,
2
One on n term and one on c term
How many peptide bonds can and amino acid form,
2
One on n term and one on c term
In contrast to dna , where is the peptide backbone of a polypeptide chain
On the inside
Sugar phosphate backbone in dna is on the outside
In contrast to dna where are the r groups of the polypeptide
On the outside
Bases are on inside
What does 3D fording of the polypeptide determine
The function/activity of a protein
Primary
Secondary
Tertiary structure
Quaternary
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
Diff in alpha helix and beta sheet
Side chains protrude out
Beta sheets side chains project alternately to either side of the backbone
What are domains
Give an example
Specific discrete modules in the protein
In the n term of the lambda repressor, there are five alpha helix domains
What components of the lambda repressor actually help in bind to the dna OR sites
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 )
What is the characteristic of the one of the alpha helix domains in a lambda repressor
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
What does helix 3 do in binding
Recognizes and fits into the major groove
What does helix 2 do in binding
Helps position helix 3 in the major groove of the dna
What does the lambda repressor dimer being symmetric help with
It’s let’s each individual helix 3 bind to an individual major groove on the dna
What in the lambda repressor enhance the binding to the dna
The repressor arms (loops) wrap around the operator
What in the lambda repressor enhance the binding to the dna
The repressor arms (loops) wrap around the operator
What is the tertiary structure of cro
3 alpha helix and 3 beta sheets
Why is there competition for binding with the cro binding to or and lambs binding
Because the cro binds to the same Or site as the repressor in the same major groove
What actually determines the lands repressor or cro affinity for OR sites
The amino acid residues of the lambda repressor or cro proteins
They both use conserved amino acids for dna bases contact
What important conserved amino acids are in the lambda repressor
In cro
Gln, ser, ala
Gln, ser, asn, lys
What role does each conserved amino acid in the lambda repressor helix 3 play in binding to the or site
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)
What role does each conserved amino acid in the cro protein helix 3 play in binding to the or site
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
What type of bonding does glutamine in cro and repressor do to bind to dna
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
What residues in helix 2 lambda and cro repressor help it position helix 3
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
Why does Glutamine in both cro and lambda helix 2 interact with the DNA phosphate backbone
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
How do the ala and Val in the cro and repressor helices interact?
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
Slide 37
Okay
What are the two important regions in the dna promoter region
What are they called
-10 and -35
-10 is usually called the TATA BOX (eukaryotic cells)
-10 is Pribnow box in (prokaryotes)
What are the two important regions in the dna promoter region
What are they called
-10 and -35
-10 is usually called the TATA BOX (eukaryotic cells)
-10 is Pribnow box in (prokaryotes)
What molecule recognizes the tata box/pribnow box
What does it do
Sigma factor
Recruits rna pol to the promoter
Why is rna pol bound only to either the Prm or Pr poronoter
When the repressor binds to the Pr promoter, what is it doing
When the cro protein binds to the Prmpromoter, what is it doing
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
What element of broth promoters is in the or2 region
The -35 elements
What element of broth promoters is in the or2 region
The -35 elements
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
3 nucleotides
2 nucleotides
Why does affinity binding of the lambda repressor to the OR2 help repress cro transcription
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
Why does affinity binding of the lambda repressor to the OR2 help repress cro transcription
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
How does the lambda repressor work as a transcription activator
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
