Biochem Exam 2.1

Front 1

transduction

Back 1

transfer of info (dna) from phage to bacteria

Front 2

transformation

Back 2

acquisition of an inheritable trait by bacteria mediated by dna
'formation, 'found info

Front 3

conjugation

Back 3

transfer of dna by sex pili

Front 4

diameter of DNA molecule

Back 4

20 angstroms

Front 5

how many bp per one turn (360 degrees)

Back 5

10.5 base pairs per turn

Front 6

bases sepperated by (distance. how many ang?)

Back 6

3.4 angstroms

Front 7

adenine - thymine has how many h-bonds?

Back 7

two hydrogen bonds. C-G bonding has three

Front 8

structural variation in dna determined by:

Back 8

1. conformation of deoxyribose (different puckering of ring)

2. rotation about the bonds making up the backbones

3. free rotation about the C-1'-N-glycosyl bonds

Front 9

What alters DNA structure from typical b-type DNA?

Back 9

local sequences, effect of DNA binding proteins, and extent of supercoiling

Front 10

A-form DNA:

Back 10

occurs in dehydrated DNA fibers,
wider and shorter helix
A-form A-typical (atypical)

Front 11

True / False : dsRNA forms A and B like structure

Back 11

False: dsRNA only forms A-like structure

Front 12

Linking number

Back 12

number of times one strand of circular DNA winds around the other in a right-handed direction

Front 13

Twisting number

Back 13

number of turns of the watson crick double helix

bp / 10.5 = Tw

Front 14

writhing number

Back 14

number of turns of super helix
Lk = Tw + Wr

Front 15

Topoisomerase I

Back 15

requires no energy
makes single strand breaks
removes negative supercoils
changes Lk by one

Front 16

Topoisomerase II

Back 16

requires atp

makes double strand breaks

changes Lk by two

introduces negative supercoils

Front 17

what direction is chain growth in dna synth?

Back 17

always 5' to 3' which means strand is copied from 3' to 5'

Front 18

what does DNA polymerase do?

Back 18

catalyzes phosphodiester-linkage formation

Front 19

[E. coli]

which polymerase is most commonly used?

describe it's activity

Back 19

DNA polymerase III

heteroligomer containint 10 types of subunits

two core domains

clam assemblies for high processivity

proof-reading activity

3' to 5' exonuclease for if mistakes (rare)

Front 20

Describe helicase activity

Back 20

domains A1 and B1 bind single strand DNA

ATP binds, clft between domains close

A1 slides along DNA

ATP hydrolysis, cleft opens, pulls dna from B1 to A1.

repeat

Front 21

Final steps in DNA synth

Back 21

DNA polymerase I removes RNA primers and fills in gaps with dNTPs

DNA ligase closes the remaining nick

Front 22

differences in DNA synth (replication) from proks to euks

Back 22

Eukaryoes:
multiple origins of replication
replicons (replication unit/origin) only replicated once per cell cycle - licensing factors

Front 23

Teleomeres

Back 23

hundreds of tangem repeats of AGGGTT

one strand is g-rich at 3' end and is longer

forms loop

Teleomerase uses innate RNA to extend leading strand

Front 24

transversion (type of mutation)

Back 24

pyrimidine replace by purine or purine by pyrimidine

Front 25

transition (type of point mutation)

Back 25

purine for purine, pyrimidine for pyrimiding

Front 26

Shortest lived RNA's?

Back 26

mRNAs are short-lived. carry info directly to protein synth. Produced for each gene

Front 27

tRNA

Back 27

do not carry information

act as 'adaptors' to pair amino acids n codons

at least 1 tRNA for each of the 20 amino acids

Front 28

rRNA

Back 28

structural and enzymatic

component of ribosomes

catalyze synth of proteins

Front 29

RNA polymerase (proks)

Back 29

(prok) one type for all RNA classes

one strand of DNA as template

plymerizes ATP, GTP, CTP, and UTP in 5' to 3'

antiparallele to DNA template

Front 30

DNA sense and antisense strands

Back 30

template is antisense strand (used to direct RNA synth)

non-template is sense or coding strand

Front 31

inhibition of RNA polymerase

Back 31

Proks: rifampicin

proks and euks: actinomycin D

Front 32

RNA polymerase (euks)

Back 32

(euk) one type of RNA pol for each class of RNA (3 types)

9-11 subunits

Front 33

sense strand numbering

Back 33

first nucleotide of sence that is transcribed is position +1

nucleotide prior to start of transcription is -1

*neg numbers are 'upstream' of transcription start site

Front 34

T/F: promoters have approx equal binding strength

Back 34

False: Not all promotors are created equal in strength and frequency of binding by RNA polymerase

Front 35

consensus sequence of prok promotor

Back 35

two sequences of 6 nucs. -10 to -35. pribnow box TATAAT

Front 36

consensus sequence of euk promotor

Back 36

(euk) RNA pol II binds to TATA box (TATAAA) aka Hogness box

Front 37

Sigma factors

Back 37

catalytically assist polymerase in finding correct promoter site. dissociate from active enzyme and repeat

Front 38

transcription factors (when/where needed?)

Back 38

All euks need factors!

RNA pol II binding to TATA requires TATA factor

Binding to GC box require Sp1

Binding to CAAT box require CTF

Proks do not need transcription factors

Front 39

enhancer sequence

Back 39

can activate transcription

act upstream, downstream, within transcribed regions

eg: steroid receptor complex to glucocorticoid enhancer

Front 40

synthesis of mRNA precursor steps

Back 40

1. start of elongation phase (no primer, purine first, 5' to 3', RNA no Hbond to DNA)

2. cap 5' end: 7-methylguanylate

3. endonuclease sees AAUAAA, cuts precursor

4. addition of poly A tail (250 A to 3' end)

Front 41

Rho protein

Back 41

contains ATPase activity, fast, binds to 72 nucleotides on RNA, zips away and finds/stops RNA pol

Front 42

rRNA generation

Back 42

Precursor molecule, nucleotide modification (methyl groups and pseudouridine), cleavage = mature rRNA

to 18S 5.8S and 28S in mamals

Front 43

split genes not in prokaryotes

Back 43

eg procollagen gene contains 52 introns.

Front 44

mechanism of splicing mRNA precursors

Back 44

1. 2' OH of A breaks bond between upstream exon and 5' of intron

2. 3' OH of upstream exon b bond between upstream intron

3. exon 1 and 2 joined, intron lariat relased, transesterification

Front 45

mRNAs read in what direction for translation

Back 45

mRNAs read 5' to 3'

Front 46

number of codons, and tRNAs

Back 46

64 possible, 61 codons, less tRNAs due to wobble position

Front 47

Translation of mRNA (prok vs euk)

Back 47

Eukaryotes contain monocistronic mRNA

Proks contain polycistronic mRNA (many genes)

Front 48

5 stages of protein synth:

Back 48

1. loading: aminoacyl tRNsynthetases, one per each amino acid (no proof reading)

2. initation of polypeptide synth: IF3

3. elongation

4. termination. RF1 or 2 bind to A site, OH it

Front 49

Maximum density of ribosomes on mRNA

Back 49

1 ribosome per 80 nucleotides

Front 50

Energy required for synth of N# of amino acids

Back 50

sum = 4N ATPs/GTPs

prot of 300 amino acids long: 4*(300) = 1200 phosphates. 1200x7.3= 8760 kcal/mol

Front 51

What causes spontaneous folding of proteins?

Back 51

h-bonds, van der Waals, ionic, hydrophobic.

Front 52

folding and processing of proteins?

Back 52

1. spontaneous

2. molecular chaperones

3. post-translational modifications: amino, carboxy, or carbohydrate side chain attach