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GSBS Biochem > Exam 1 review > Flashcards

Exam 1 review Flashcards

1
Q

molecules recognize each other by

A

interactions

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2
Q

van der waals interactions

A

give strong repulsions, weak “flickering” attractions

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3
Q

dipole interactions

A

between molecules with hetero atoms

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4
Q

hydrogen bonds

A

a type of dipole interaction with hydrogen that is important in biology

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5
Q

strong interactions

A

covalent bonds and ionic interactions are responsible for stable, long-lived, structures

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6
Q

water is the

A

ultimate hydrogen bonding liquid

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7
Q

as ice, water forms how many bonds

A

4 h bonds
2 accept
2 donate
tetrahedral in shape

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8
Q

as a liquid water forms how many bonds

A

4.5 h bonds
makes liquid more dense than ice

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9
Q

life requires

A

water`

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10
Q

water properties

A

liquid solvent
concentration gradients
biopolymers adopt unique shapes
hydrogen bonding networks
tetrahedral bonding
large void volume, dissolution of gasses
liquid from 273K to 373K
density maxima

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11
Q

liquids and polymers are dominated by weak forces from potential interactions around RT in size. All of biology depends on using weak forces to allow

A

biological changes

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12
Q

the purine groups are synthesized on the

A

ribophosphate
PRPP

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13
Q

that displaces the phosphate at C1 on PRPP

A

the amide group of glutamine

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14
Q

where is RNA hydrolyzed by water or base

A

2’OH

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15
Q

RNA hydrolyzation creates

A

a 2’,3’ cyclic monophosphate nucleotide and a truncated RNA

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16
Q

each base has a unique UV absorption spectrum due to the

A

electronic differences in the rings and substitutions

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17
Q

for sequencing via UV, what wavelength is used

A

260nm
blue!

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18
Q

tautomers for pyrimidine bases

A

lactam
lactim
double lactim

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19
Q

tautomers are stabulized by different environments including

A

solvent polarity and pH

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20
Q

pH causes different H-bonds to be stable and can

A

change the UV spectrum

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21
Q

different electronic states are allowed due to the

A

number of hetero atoms in conjugation in the rings coupled to tautomers

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22
Q

pH differences for UV are more prevelant in

A

pyrimidines

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23
Q

in terms of the particle in a lox, pyrimidines have a

A

smaller box
greater % change

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24
Q

attractive forces in DNA stability

A

base pair hydrogen bonds
base pi stacking

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25
Q

repulsive forces in DNA stability

A

excluded volume
phosphate-phosphate repulsions

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26
Q

2 molecules q1 and q2 interact with each other by

A

coulombs law for the potential energy U

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26
Q

water diminishes (screens) the interactions between two charges via

A

the dielectric constant of 80

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27
Q

water divides the interactions between to charges by

A

80

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28
Q

excess salt further diminishes (screens) interactions between charges as found by debye and huckel meaning that

A

it goes exponentially to zero with ionic strength

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29
Q

right handed form of DNA

A

A and B

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30
Q

left handed form of DNA

A

z

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31
Q

diameter of A form

A

26 A

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32
Q

diameter of B form

A

20A

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33
Q

diameter of z form

A

18A

34
Q

base pairs per helical turn for A form

A

11

35
Q

base pairs per helical turn for B form

A

10.5

36
Q

base pairs per helical turn for Z form

A

12

37
Q

base tilt normal to the helix axis for A form

A

20 degrees

38
Q

base tilt normal to the helical axis for B and Z form

A

6-7 degrees

39
Q

sugar pucker conformation for A form

A

C-3’ endo
north

40
Q

sugar pucker conformation for B form

A

c-2’ endo
south

41
Q

sugar pucker conformation for Z form

A

C-2’ endo for pyrimidines
C-3’ endo for purines

42
Q

DNA changes shape with respect to

A

salt concentration

43
Q

at zero salt DNA

A

does not form a dimer

44
Q

DNA shape with increasing salt concentration

A

single
B
A
Z

45
Q

there are many base pairing possibilities due to

A

the number of hydrogen bonding groups

46
Q

triple helices

A

major groove binding
base triple specific
high salt requirement

47
Q

quadruplex

A

g-quartets
loops of 3-4 bases
binds ions specifically in the core

48
Q

if you add poly- a and poly - t to a solution,

A

TAT will form a triple helix
A will go in solution (more soluble)

49
Q

triplets of bases are reasonably

A

stable

50
Q

common base triplets

A

TAT
CGC

51
Q

in a quadruplex, how many hydrogen bonds does each base have

A

4 h bonds per base

52
Q

the center of a quadruplex is full of

A

oxygens and lone pairs

53
Q

what ion goes in the middle of a quadruplex

A

K+
more stable than Na+

54
Q

g tetrads can form in

A

any G-rich sequence

55
Q

how to break a g tetrad

A

12M LiCl and boiling

56
Q

many RNAs are inherently

A

single stranded

57
Q

most RNAs fold up forming

A

secondary and tertiary structures

58
Q

how do RNAs fold

A

each strands find complementary sections, often times short sections where complementary holds

59
Q

structures in RNA

A

stems
loops
bulges
try on MFOLD

60
Q

mRNA carries the code from DNA to the

A

synthesis machinery

61
Q

before mRNA can be read

A

it must be processed into a mature form by removing the introns

62
Q

the genetic code has some redundancies in

A

the third slot of the codon

63
Q

some species are specific in their codons requiring

A

codon optimization

64
Q

domains in rRNA are more structurally varied than in

A

proteins

65
Q

robosomal subunits

A

30S (lower)
50S (upper)

66
Q

what ribosomal subunit holds the mRNA

A

30S

67
Q

what subunit catalyses the peptide bond formation

A

50S

68
Q

translocation and successive binding of tRNA are

A

GTP dependent

69
Q

three sites of tRNA binding

A

APE

70
Q

as the peptide is made it can either coil into an alpha helix or

A

await pickup by a chaperonin (beta sheets)

71
Q

what signals the end of protein synthesis

A

release factor

72
Q

release of the ribosome subunits allows for

A

ribosome recycling and energy conservation

73
Q

what do helicases do

A

twist and untwist DNA

74
Q

twisting a duplex can change

A

local and large scale structure

75
Q

twist equation

A

L=T+W
linking number = twist + writhe

76
Q

what is twisting equilibrium

A

how an open transcription bubble is in equilibrium with the various shapes

77
Q

twisting can lead to

A

strand separation

78
Q

what can mechanically separate strands of DNA

A

gyrase
topoisomerase
helicase

79
Q

what transcribed mRNA

A

RNA polymerase

80
Q

the RNA DNA hybrid is known as

A

RNA-DNA double helix D-loop

81
Q

DNA synthesis goes in a

A

5’ to 3’ direction

82
Q

enzymes involved in the replication process

A

helicase
DNA binding protein
dnaB
primase
DNA polymerase
DNA ligase

GSBS Biochem (10 decks)

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