Biochem Test 3

Front 1

Components of a nucleotide

nucleoside

Back 1

5 carbon sugar, phosphate group, nitrogenous base

base + sugar

Front 2

Difference between DNA and RNA

Back 2

DNA - DEoxy - no oxygen atom at 2' carbon on pentose sugar
RNA - has hydroxyl group at 2' carbon on pentose sugar

Front 3

Glycosidic bond

Back 3

linkage between the N-9 of a purine or the N-1 of a pyrimidine w/ C-1 of pentose sugar

Front 4

dNTP's

Back 4

deoxynucleoside 5' triphosphates.
precursors of DNA synthesis.

Front 5

What kind of bond forms between nucleosides and phosphate groups?

Back 5

phosphodiester bond

Front 6

Hyperchromic affect

Back 6

When DNA denatures, single strands absorb more UV light than double strands.

Front 7

1. GC content goes up, Tm goes .... curve shifts....
2. GC content goes down, Tm goes... curve shifts...

Back 7

1. up, right
2. down, left

Front 8

what is the significance of rna being single stranded?

Back 8

It can form 3d structures, and become a functional unit.

Front 9

Various RNA structural motifs (structures)

Back 9

Hairpins, stem loops, pseudoknots

Front 10

snRNA

Back 10

small nuclear RNA. RNA splicing of pre-mRNA

Front 11

siRNA

Back 11

small interfering RNA. binds to mRNA and helps with degradation of message.

Front 12

miRNA

Back 12

micro RNA - binds to complementary mRNA, inhibits translation

Front 13

Is the genetic code universal?

Back 13

Almost. there are small differences in code between eukaryotes and prokaryotes...and in mitochondrial dna

Front 14

DNA types, screw sense, major and minor grooves
1. A
2. B
3. Z

Back 14

1. right. narrow, deep. broad, shallow
2. right. wide, deep. narrow, deep.
3. left. flat. narrow, deep.

Front 15

why are there major and minor grooves?

Back 15

glycosidic bonds and not diametrically opposite each other

Front 16

Four requirements for DNA to be genetic material:

Back 16

carry info
exchange info
replicate
govern phenotype expression

Front 17

The messelson stahl experiment was significant because...

Back 17

it proved semi conservative replication to be the mechanism of dna replication. Used radioactive isotope of nitrogen. N15.

Front 18

3 steps of replication
1.
2.
3.

Back 18

1. initiation - proteins bind to DNA and open up helix. Prepare DNA for base pairing.
2. Elongation - Proteins connect the correct sequences of nucleotides into a new strand of DNA.
3. termination - it...ends

Front 19

circular chromosome replication
1. what direction
2. how many replication forks
3. symbol

Back 19

1. bi-directional
2. two
3. theta

Front 20

DNA POL I function:

DNA POL II Function:

DNA POL III function:

Back 20

1. removes primer from lagging strand, fills in with nucleotides. proofreading.
2. DNA repair
3. Main polymerase of dna replication.

Front 21

Enzymes involved in replication:
1. Pol I
2. Pol III
3. Topoisomerase
4. DNA helicase
5. SSbp
6. Primase
7. Ligase

Back 21

1. fills in gaps
2. main DNA synthesizer
3. changes DNA supercoiling by inserting or removing a supercoil
4. unwinds double helix
5. single stranded binding protein. keeps helix open
6. creates RNA primers to initiate synthesis
7. welds together okazaki fragments

Front 22

DNA polymerase holoenzyme.
consists of...

Back 22

2 copies of the polymerase core enzyme, made of:
alpha catalytic subunit - synthesis dna
beta subunit (2 copies to make a donut) - processivity factor - prevents holoenzyme from dissociating from DNA
epsilon subunit - 3to5 exonuclease activity (proof reading)
theta subunit

Central structure, made of:
clamp loader complex and hexameric helicase DnaB.

Front 23

Type I topoisomerase

mechanism

Back 23

produce break in only one strand of DNA backbone. Allows one of the phosphodiester bonds to rotate freely around the other, relieving stress.

OH group of Tyr acts as a nucleophile attacking the phosphate group. forms bond. frees OH group. spin spin spin spin spin..... free hydroxyl group on spinning dna strand attacks phosphate backbone to reseal.

Front 24

Type II topoisomerase

mechanism

Back 24

produces double stranded breaks in the DNA backbone at the same time. requires ATP. l
ike two connected donuts. donuts are dimers

TOPO II first binds dna double helix (G for gate). Then both strands are cut. Then another double helix is bound (t for transport). Then T segment moves through break in G segment and out of the bottom of the enzyme.

Front 25

Bacterial helicase PcrA structure


mechanism

Back 25

4 domains: A1, B1, A2, B2.

both A1 and B1 domains bind ss dna. upon dna binding, cleft closes, a1 slides along dna. ATP hydrolysis, cleft opens. A1 has a tighter grip than b1 and pulls dna. Translocation occurs 3 to 5 direction.

Front 26

Ligase:

mechanism

Back 26

seals break in DS dna. DNA ligase catalyzes the formation of a phosphodiester bond between the 3' OH group at one end of one DNA chain, and the 5' phosphate group at the end of the other. requires energy.

Front 27

Origin of replication (E. coli)
1. code word
2. what is it (exactly)
3. what is its function
4. repeats are flanked by....
5. unwounded to allow for...

Back 27

1. Ori C
2. defined segment of DNA made by multiple repeats. 3 identical repeats at first, each made of 13 bp. Then - 5 identical repeats used for binding sites to the hexameric protein, dnaA.
3. serves as binding site for multimeric protein, DnaA
4. A-T rich DNA
5. strand separation

Front 28

During replication, the double helix denatures into single strands, exposing the bases. This area of exposed bases is called the

Back 28

replication bubble

Front 29

DNA termination
1. replication terminates at what region
2. location of termination region
3. Ter region is comprised of a...
4. termination requires bind of...

Back 29

1. ter region
2. opposite of oriC locus
3. number of short DNA sequences with consensus 5' GTGTGTTGT 3'
these sequences act as terminators
4. tus protein to TRT(?)

Front 30

Tus - how does it stop the replication

Back 30

it is a contra-helicase, meaning it prevents the DNA duplex from unwinding by blocking progression of the replication fork and inhibiting DnaB helicase activity.

Front 31

Primase

Back 31

enzyme that consists of rna template and a protein.

Front 32

what phase of the cell cycle does dna replication occur in?

Back 32

S phase

Front 33

Telomeres
1. what
2. length varies but is controlled...
3. enzyme that replicates telemere dna
4. what kind of activity?

Back 33

1. G rich series of repeats at end of chromosome
2. in a species specific manner
3. telomerase.
4. reverse transcriptase

Front 34

is dna replication of eukaryotes much more complex than prokaryote?

Back 34

YES

Front 35

what is the only biological macromolecule that is repaired?

Back 35

dna

Front 36

what are the promoter sequences for prokaryotic transcription?

Back 36

consensus sequences at the -10 and -35 areas, upstream of the start, or TSS

Front 37

Rho dependent termination:
1. how the rho protein detects start site
2. structure of rho

Back 37

1. find a sequence on nascent rna that is rich in C, poor in C
2. atp dependent helicase. a hexamer. evolutionarily similar to atp synthase.

Front 38

Rho independent termination:
1. what sequence causes it
2. what does the sequence turn into
3. what effect does this have on the polymerase

Back 38

1. palindromic g-c rich sequences
2. a stem loop structure
3. causes it to pause, and then dissociate

Front 39

What enzyme(s) produce prokaryotic RNA?

Back 39

RNA polymerase. that's it.

Front 40

Enzymes of eukaryotic RNA production.
1. RNA polymerase I
2. RNA polymerase II
3. RNA polymerase III

Back 40

1. synthesizes rRNA
2. synthesizes mRNA and snRNA
3. synthesizes tRNA and 5s rna

Front 41

Poisonous mushrooms?
1. name of it
2. name of toxin
3. what it inhibits, or which enzyme it affects

Back 41

1. Amanita phalloides
2. alpha amanitin
3. binds tightly to RNA Pol II, inhibiting it.
inhibits pol III at high concentrations.
Has no affect on Pol I

Front 42

Four elements of Pol II promotors

which is the most important?

Back 42

TATA box

Inr - initiator element

DPE - downstream core promoter element

CAAT box/ GC box
promotor sequences
Positions vary
can be effective when on antisense (template) strand

TATA BOX IS MOST IMPORTANT

Front 43

what is a technique that will tell you if protein is bound to DNA?

Back 43

dna footprinting

Front 44

Eukaryotic vs. Prokaryotic transcription
1. protein number during transcription
2. regions of repetitive dna
3. coding/noncoding genes
4. structure of dna

Back 44

1. Eukaryotic - 1 gene = 1 protein
Prokaryotic - 1 gene can make many different proteins. Polycistronic.
2. eukaryotic - large regions of repetitive dna
prokaryotic - no repetitive dna
3. eukaryotic is around 98% non coding genes
prokaryotic, 95% are coding
4. compact complex with histones

Front 45

DNA binding domains / structural motifs

Back 45

1. HTH motifs
2. zinc fingers
3. leucine zipper motifs

Front 46

5' cap contains what special base?

Back 46

methylated guanosine

Front 47

Poly A adenylation:
1. what is the cleavage signal
2. what is the donor molecule after that?

Back 47

1. AAUAAA
so its cleaved by specific endonuclease
2. ATP adds adenosines

Front 48

what is the reaction occuring during mrna splicing?

Back 48

transesterification.

Front 49

Splicing mechanism

Back 49

attacking group is 2' OH.
swings out and attacks 5' end of intron. transesterification.
this frees the exon. forms lariat intermediate.
The free 3' has hydroxyl group, which attacks phospho bond between intron and exon 2. frees the exon. lariat form of intron is left over.

Front 50

Splice sites of introns:

Back 50

begins with gu, ends with ag.

Front 51

snRNP (snurps)
1. U1
2. U2
3. U5
4. U4
5. U6

Back 51

1. binds the 5' splice site and then the 3' splice site
2. binds the branch site, forms part of the catalytic center
3. binds the 5' splice site
4. masks the catalytic activity of U6
5. catalyzes splicing

Front 52

what causes thalassemia?

Back 52

splicing mutation. A to G mutation creates another stop sequence.

Front 53

what causes cystic fibrosis?

Back 53

alternative splicing mutation

Front 54

Group I intron self splicing mechanism
1. requires what?
2. results in what?
3. what type of rna?

Back 54

1. guanosine cofactor
2. catalytically active L19 rna
3. nuclear rRNA

Front 55

Base stacking: important in two ways

Back 55

1. hydrophobic bases congregate in middle, hydrophilic phosphate backbone faces water. stabilized molecule.
2. base stacking in DNA is favored by conformations of somewhat rigid pentose sugars.