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MCB 3010 > EXAM 2 > Flashcards

EXAM 2 Flashcards

1
Q

formula of carb

A

Cn(H2O)n

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2
Q

how are carbs produced

A

from Co2 and H2O via photosynthesis

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3
Q

small carb

A

glyceraldehyde (90 g/mol)

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4
Q

large carb

A

amylopectin (200million g/mol)

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5
Q

functions of carbs

A

energy source and storage

structural component of cell walls and exoskeletons

informational molecules in cell-cell signaling

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6
Q

configuration of a monosaccharide is based on the OH on the

A

penultimate carbon

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7
Q

epimer

A

diastereomers that differ only in configuration of 1 carbon

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8
Q

D-fructose

A

ketose of glucose at C2

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9
Q

D-galactose

A

C4 epimer of glucose

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10
Q

D-mannose

A

C2 epimer of glucose

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11
Q

most common monosaccharides

A

hexoses
D-glucose
D-fructose

pentose
D-ribose

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12
Q

aldose + mild oxidizing agent =

A

aldonic acids

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13
Q

aldoses are

A

reducing sugars

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14
Q

naturally occurring ketoses almost always carry the keto group on

A

carbon 2

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15
Q

aldehyde and ketone carbons are

A

electrophilic

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16
Q

reactions of aldehyde/ketone and alcohol oxygens allow monosaccharides to form

A

ketones

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17
Q

when 2 monosaccharides are bound together

A

acetals and ketals form

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18
Q

monosaccharides with sufficiently long chains can cyclicize spontaneously… leads to

A

pyranose or furanose

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19
Q

pyranose

A

6 carbons

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20
Q

furanose

A

5 carbons

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21
Q

how do cells prevent formation of fructopyranose?

A

glucose and fructose are phosphorylated at C6

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22
Q

how does carbon 6 point for a D isomer

A

up

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23
Q

how does hydroxyl on animeric carbon point

A

right is down

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24
Q

animeric carbon

A

new chiral carbon in haworth perspective formula

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25
Q

fructofuranose has ____ not in the ring

A

C1 and C6

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26
Q

in glucose chair conformations

A

all OH groups are equatorial except C1, the anomeric carbon in alpha form

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27
Q

ribose in nucleotides is usually

A

phosphorylated at C5

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28
Q

lactose connection

A

B1-4

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29
Q

lactose molecules

A

B galactose + B glucose

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30
Q

sucrose connection

A

a1, 2B

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31
Q

sucrose molecules

A

B fructose + a glucose

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32
Q

maltose molecules

A

2 glucose

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33
Q

what connects two monosaccharides into disaccharides?

A

glycosidic bond

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34
Q

what is produced by most mammals but not us

A

galactose - a-1,3 - galactose

can acquire allergy by bite of lone star tick or chemo from mice

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35
Q

polysaccharides

A

natural carbohydrates, usually found as polymers for storage

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36
Q

polysaccharides can be

A

linear
branched

homopolysacc
heteropolysacc

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37
Q

how are polysaccharides made?

A

no template – made based on concentrations of monosaccharides

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38
Q

polysaccharides molecular weight

A

not defined

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39
Q

glycogen

A

branched homo-disccharide of glucose

MW reaches several millions

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40
Q

glycogen structure

A

glucose monomers form a1-4 chains

branch points with a1-6 linkages every 8-12 residues

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41
Q

glycogen function

A

main storage polysaccharide in animals

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42
Q

starch

A

mixture of 2 homopolysaccharides of glucose
main storage polysaccharide in plants

amylose
amylopectin

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43
Q

amylose

A

starch; long unbranched polymer of a1-4 linked residues

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44
Q

amylopectin

A

starch; branched (like glycogen) branch points with a1-6 linkages every 24-30 residues

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45
Q

cellulose

A

unbranched homopolysaccharide of glucose
tough, water insoluble
most abundant polysacch, found in plant cell walls

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46
Q

cellulose structure

A

glucose monomers form b1-4 linked chains

hydrogen bonds form between adjacent monomers

additional H bonds between other cellulose chains

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47
Q

cellulose metabolism

A

difficult to digest
cellulase allows fungi, bacteria, protozoa to use wood as glucose

ruminants and termites live symbiotically with microorganisms that secrete cellulase

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48
Q

why is cellulose difficult to digest?

A

fibrous structure and water insolubility –> not many enzymes hydrolyze b1-4 linkages

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49
Q

chitin

A

major building block in exoskeleton of arthropods
cell walls in some fungi

tough, flexible, water insoluble (more than cellulose)

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50
Q

chitin structure

A

identical to cellulose but monomer is N-acetylglucosamine

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51
Q

tertiary structure of polysaccharides is determined by

A

weak interactions

regions of rigid structures

steric hinderance

limited bonds that can rotate

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52
Q

tertiary structure of starch ang lycogen

A

form tightly coiled helix

stabilized by H bonds

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53
Q

tertiary structure of cellulose

A

extended structure with H bonding between chains

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54
Q

glycoproteins

A

proteins with oligosaccharides attached

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55
Q

glycoprotein structure

A

anomeric carbon binds to the serine or threonine residues (O linked) or the asparagine (N linked)

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56
Q

how many proteins in mammals are glycosylated?

A

1/2

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57
Q

how does adding oligosaccharides to proteins affect the protein?

A

increases solubility

can target proteins for certain cellular locations
can change protein structure

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58
Q

Nucleotide functions

A

building blocks

energy for metabolism (ATP)
enzyme cofactors (NAD+)
signal transduction (cAMP)
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59
Q

nucleic acid functions

A

storage of genetic info (DNA)
transmission of genetic info (mRNA)
processing of genetic info (ribozymes)
protein synthesis (tRNA, rRNA)

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60
Q

Nucleoside structure

A

no phosphate

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61
Q

phosphate group

A

negatively charged
on 5’ carbon of pentose ring
(sometimes other positions)

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62
Q

nucleic acids are built using

A

5’-triphosphates (ATP, GTP)

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63
Q

nucleic acid structure

A

one phosphate group per nucleotide molecule

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64
Q

nucleotide structure

A

can be 5’diphosphate, 5’-triphosphate

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65
Q

C2’ Endo

A

C2 carbon off plane, 5’ carbon on the same plane

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66
Q

C3’ Endo

A

C3’ carbon off of plane, 5’ carbon on same plane

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67
Q

nitrogenous bases

A

derivatives of pyramidine or purine
nitrogen containing heteroaromatic molecules
planar or almost planar

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68
Q

pyrimidine bases

A 
1 ring
cytosine
thymine
uracil
all good G bond donors and acceptors
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69
Q

purine bases

A

2 rings
adenine
guanine
good H bond donor and receptors

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70
Q

B-N-glycosidic bond

A

anomeric carbon in b conformation
N1 in pyrimidines
N9 in purines

difficult to hydrolyze

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71
Q

UV abs at 250-270

A

used to determine concentration of a solution of nucleic acids

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72
Q

conformation of N glycosidic bond

A

can rotate with N-C1 (chi)

0* = syn
180 * = anti

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73
Q

purine conformation

A

syn, anti

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74
Q

pyrimidine conformation

A

anti only because interactions of sugar ring and =O

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75
Q

B dna conformation

A

anti conformation

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76
Q

minor nucleosides in DNA

A

5 methylcytidine

N6 methyladenosine

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77
Q

5 methylcytidine

A

eukaryotes and some bacteria

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78
Q

N6 menthyladenosine

A

bacteria not eukaryotes

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79
Q

epigenetic marker

A

phenotype change without change in DNA

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80
Q

prokaryotic epigenetic markers

A

mark own DNA so only foreign DNA is degraded

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81
Q

eukaryotic epigenetic markers

A

marks which genes should be active

methylated = not transcribed

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82
Q

nucleotide functions

A

energy source

coenzymes

regulatory molecules

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83
Q

nucleotide functions: energy source

A

3 PO4 provides energy by cleaving

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84
Q

nucleotide functions: coenzymes

A

Coenzyme A –> nucleotide makes up part of it, not prosthetic group

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85
Q

nucleotide functions: regulatory molecules

A

cAMP, cGMP = signaling molecules part of signal transduction and amplification

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86
Q

oligonucleotides

A

phosphodiester bonds link nucleotides covalently
PO4 from C5’ onto C3 oh of another

negatively charged backbone

linear polymers

directionality

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87
Q

DNA backbone

A

fairly stable

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88
Q

RNA backbone

A

less stable

OH at C2’ can bind to PO4, breaking covalent bond at C5’ of next nucltodie

cyclic PO4 between C2’ and C3’

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89
Q

H bonding in oligonucleotides in RNA

A

G pairs with U for structure formation or codon/anticodon wobble

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90
Q

base stacking in oligonucleotides

A 
holds helix together
noncovalent interactions (hydrophobic, van der waals)
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91
Q

franklin and wilkins

A

cross in x ray crystalography = helix

diamonds = sugar po4 backbone on outside

calculated helical parameters

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92
Q

watson and crick

A

missing layer in cross = major and minor groove
H bonding AT/CG
double helix

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93
Q

Forms of DNA

A

A
B
Z

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94
Q

A DNA

A

wider, c3’ endo (more like RNA)

all anti

Franklin found it in dehydrated DNA

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95
Q

B DNA

A

C2’ endo

all anti

Watson and crick

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96
Q

Z DNA

A

left handed helix

pyrimidines: c2’ endo, anti
purines: c3’ endo, syn

may be formed during transcription

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97
Q

DNA denaturation

A

separates 2 strands of DNA
covalent bonds remain in tact, genetic code remains in tact

UV ABS INCREASES due to loss of interactions between bases

high temp or change in pH

reversible, can bind other molecules

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98
Q

Factors affecting Tm

A

base composition

DNA length

ionic strength

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99
Q

Tm

A

midpoint of melting

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100
Q

Factors affecting Tm: base composition

A

more CG = increases Tm

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101
Q

Factors affecting Tm: DNA length

A

longer DNA increases Tm

more interactions = stronger base stacking

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102
Q

Factors affecting Tm: Ionic strength

A

high salt increases Tm

salt binds PO4 backbone, decreases repelling and creates stronger interactions

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103
Q

DNA Mutagenesis

A

spontaneous mutagenesis

oxidative and chemical mutagenesis

radiation induced mutagenesis

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104
Q

DNA mutagenesis: spontaneous

A

deamination

depurination

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105
Q

DNA mutagenesis: spontaneous deamination

A

amino group converted to carbonyl

good to have thymine in DNA because uracil is detected as a problem (C–> U 100/day in mammalian cell)

slow reactions

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106
Q

DNA mutagenesis: spontaneous depurination

A

N glycosidic bond is hydrolyzed

10K purines lost a day

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107
Q

DNA mutagenesis: oxidative mutagenesis

A

hydroxylation of guanine

often in mitochondrial DNA because lots of oxidative phosphorylation takes place

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108
Q

DNA mutagenesis: chemical alkylation

A

methylation of guanine

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109
Q

DNA mutagenesis: radiation induced mutagenesis

A

UV light

ionizing radiation (X rays, gamma rays)

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110
Q

DNA mutagenesis: UV light

A

dimerization of pyrimidines

main mechanism for skin cancer

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111
Q

DNA mutagenesis: ionizing radiation

A

x rays
gamma rays

ring opens, strand breaks

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112
Q

accumulation of mutations leads to

A

aging and cancer

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113
Q

segments of DNA are arranged either within a ______ or between two _____

A

within a chromotome or between two DNA molecules giving offpsring novel DNA

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114
Q

DNA metabolism consists of

A

a set of tightly regulated processes that achieve these tasks

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115
Q

DNases

A

nucleases that cleave DNA (enzymes)

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116
Q

exonucleases

A

cleave a bond that removes a nucleotide from the end of DNA; can keep cleaving

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117
Q

endonucleases

A

cleaves a bond within a DNA sequence, between nucleotides, cleaves once and makes nick

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118
Q

3 fundamental rules of replication

A

semi conservative

begins at an origin and proceeds bidirectionally

synthesis of new DNA occurs in 5’ to 3’ direction and is semi-discontinuous

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119
Q

MESELSON-STAHL

A

cells grown on heavy medium with N15; found one band

cells on N14 medium divided once; one band on higher position

cells divided again in N14; two bands, one with N14DNA, one hybrid

semiconservative**

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120
Q

leading strand

A

made continuously as replication fork advances

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121
Q

lagging strand

A

made discontinuously away from replication fork in short pieces that are later joined together

okazaki fragments

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122
Q

DNA polymerases

A

synthesizes DNA, requires a primer

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123
Q

primer

A

short strand of NT complementary to template; provides required 3’OH to begin the DNA polymerase catalyzed reaction

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124
Q

substrates in strand synthesis

A

nucleoside triphosphates

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125
Q

how many phosphates removed during catalysis as one unit?

A

2; pyrophosphate

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126
Q

what is attached to growing DNA strand?

A

dNMP

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127
Q

what attacks the a-phosphate on incoming trinucleotide?

A

nucleophilic 3’OH on growing strand

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128
Q

Mg2+ purpose

A

makes 3’O on growing strand more powerful nucleophile by stabilizing it –> allows it to attack a-PO4

orients the components, making b and y PO4 better LG

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129
Q

how is Mg2+ in catalytic site of DNA polymerase?

A

interactions with aspartate groups

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130
Q

errors in E.Coli base pairing

A

1/10^9

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131
Q

ways to limit incorrect base pairing

A

base pair geometry at insertion site

errors during synthesis are corrected by 3’-5’ exonuclease activity

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132
Q

base pair geometry

A

geometry limits incorrect base pairing bc doesnt fit in catalytic site

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133
Q

DNA polymerase has ___ and __

A

primary active site

secondary active site

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134
Q

primary active site in DNA polymerase

A

synthesis; polymerase

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135
Q

secondary active site in DNA polymerase

A

exonuclease activity

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136
Q

3’ to 5’ exonuclease activity

A

proofreads synthesis for mismatched repair

translocation of enzyme to next position is inhibited until the enzyme can remove the incorrect nucleotide just added

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137
Q

DNA polymerase I (E.Coli)

A

abundant, not ideal for replication

600 nt/min (slower than replication fork)

low processivity

for primer replacement

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138
Q

DNA polymerase III (E.Coli)

A

principle replication polymerase

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139
Q

DNA polymerases II, IV, V

A

DNA repair

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140
Q

DNA Polymerase I 5’to3’ exonuclease

A

in addition to 3’to5’

activity has a distinct domain

works ahead of polymerase activity – hydrolyzes nucleotides off chain in its path before adding new nucleotides with polymerase activity

nick translation

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141
Q

nick translation

A

DNA pol I

movement of strand break along with enzyme resynthesis

combined 5’ to 3’ exonuclease activity and polymerase activity

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142
Q

DNA polymerase III

A

10 types of subunits

two core polymerases made of a, e, theta subunits

clamp loader complex

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143
Q

clamp loader complex

A

DNA pol III

links core polymerases

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144
Q

core polymerases in DNA pol III

A

each interact with a dimer of beta subunits that increase the processivity of complex

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145
Q

sliding clamp

A

B subunits on DNA pol III form this; prevents dissociation

polymerase holds clamp, clamp holds DNA

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146
Q

processivitiy of DNA pol III

A

> 500k bp

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147
Q

a subunit of core DNA polymerase on DNA Pol III

A

polymerization

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148
Q

e subunit of core DNA poly on DNA pol III

A

3’-5’ proofreading exonuclease

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149
Q

theta subunit of DNA poly

A

stabilization of e subunit

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150
Q

DNA replication in E.COli

A

replisome

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151
Q

replisome

A

over 20 proteins required for replication in E.Coli

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152
Q

replisome proteins

A

helicase

topoisomerase

DNA binding proteins

primase

DNA ligase

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153
Q

helicase

A

cannot separate strands; continue separating strands, unwinds DNA with ATP

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154
Q

topoisomerase

A

relieves stress caused by unwinding; releases strain in front of forks by cutting DNA, relieves twist, then joins them again

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155
Q

DNA binding proteins

A

stabilizes separated strands

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156
Q

primase

A

enzyme that makes RNA primers 5-15 bases long; provides 3’OH

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157
Q

DNA ligase

A

seals nicks in backbone

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158
Q

Initiation of prokaryotes

A

begins at origin: oriC

highly conserved sequence elements

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159
Q

origin in prokaryotes

A

oriC

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160
Q

oriC

A

origin; 245 bp

5 repeats of a sequence that forms binding site for DnaA

A-T rich DUE

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161
Q

DnaA

A

initiator protein; first protein that binds origin

prokaryotes

162
Q

DUE

A

DNA unwinding element; A-T rich

strands pop open and strands separate

with binding sites for DnaA and other proteins

163
Q

prepriming complex

A

goal after opening helix in prokaryotes

164
Q

DnaA

A

recognizes ori sequence, opens duplex at specific sites in origin

p

165
Q

DnaB

A

helicase; unwinds DNA

166
Q

DnaG

A

primase; synthesizes RNA primers

167
Q

SSBP

A

binds single stranded DNA

168
Q

DNA gyrase

A

DNA topoisomerase II

relieves torsional strain

169
Q

DnaA proteins binding at oriC

A

ATPases

8 DnaAs bind

DNA wraps around 8 protein complex forming a positive supercoil

strain leads to denaturation of DNA in nearby DNA unwinding element, overcomes base stacking

170
Q

Elongation in prokaryotes

A

DNA polymerase III adds beta clamp at primer and core polymerase binds to b clamp

adds deoxynucleotides in 5’ to 3’ direction

lagging strand, leading strand synthesis – SAME DNA POLY

171
Q

lagging strand synthesis

A

okazaki fragments

DNA polIII adds NT in short segments, ends when hits previous primer

172
Q

connecting okazaki fragments

A

core poly of DNA polIII dissociates from one b clamp, binds to a new one

DNA pol I
DNA ligase

173
Q

DNA pol I with okazaki fragments

A

associates with b clamp, and nick translates

5’to3’ exonuclease to remove primer
polymerase to replace primer with DNA (and on leading strand)

174
Q

DNA ligase

A

makes bond between a 3’OH and a 5’PO4

175
Q

DNA ligase mechanism

A

removes AMP from ATP or NAD+

attach AMP on lysine on ligase (itself)

attaches AMP onto 5’PO4 on strand

3’OH attacks 5’PO4, AMP is displaced

176
Q

Termination in prokaryotes

A

replication forks meet within a region of Ter sequences

177
Q

Ter sequences

A

Ter sites found near each other but in groups oriented in opposite directions near tus proteins

create a site that replication forks cannot leave

178
Q

Tus proteins

A

terminus utilization sequence

binds ter sites (not all are bound by tus)

catches the fastest fork and waits for catch up

179
Q

yeast have X defined origins

A

400

180
Q

why do eukaryotes have more origins?

A

more chromosomes

181
Q

origin recognition complex (ORC)

A

in eukaryotes; loads a helicase onto DNA

hexamer of mini-chromosome maintenance proteins

similar to DnaA

182
Q

eukaryotic replication

A

slower

50 nt/sec (250 in E.Coli)

compensated by origins every 30-300 kb

183
Q

termination occurs in eukaryotes when

A

replication forks converge

184
Q

DNA polymerase alpha primase complex

A

in eukaryotic replication

all removed after replication is over

makes primers with RNA, then 10nt DNA

separates subunits for primase and polymerase activities

no 3’-5’ proofreading

185
Q

DNA polymerase delta

A

synthesizes lagging strand

3’-5’ proofreading

binds to PCNA protein

186
Q

PCNA

A

proliferating cell nuclear antigen

acts like a beta clamp to increase processivity in DNA polymerase delta

187
Q

DNA polymerase e

A

synthesizes leading strand

3’ to 5’ proofreading

binds to PCNA to increase processivity

188
Q

messenger RNA

A

encodes the aa sequences of all polypeptides found in cell

189
Q

transfer RNA

A

match specific aa to triplet codons of mRNA during protein synthesis

190
Q

ribosomal RNA

A

constituents of ribosomes along with proteins

191
Q

ribonucleic acids

A

act as genomic material in viruses

192
Q

transcription

A

ribonucleic acids are synthesized in cells using DNA as a template

tightly regulated in order to control the concentration of RNA and save energy

193
Q

many RNA molecules can

A

fold into structures with functions

194
Q

most RNAs are processed after synthesis

A

elimination of introns, joining of exons
poly-adenylation
capping

195
Q

Transcription in E.Coli: RNA polymerase

A

catalyzes synthesis in 5’to3’ direction

doesnt need primer

first nucleotide retains all 3 phosphates on 5’ end

NTPs are used to add NMPs to the 3’ end of growing strand

196
Q

RNA polymerase in E.Coli

A

binds promoter

opens up and unwinds DNA (unwound duplex forms a bubble 17bp long)

topoisomerase releases strain

growing end of new RNA temporarily base pairs with DNA template for 8 bp

197
Q

RNA polymerase is a multisubunit

A

holoenzyme

5 core subunits a2bb’w and sigma as a sixth

no 3’to5’ exonuclease; high error rate, does proofread though

198
Q

sigma subunit on RNA polymerase

A

directs enzyme to the promoter

diff subunits bind diff promoters

199
Q

promoters in E.Coli

A

sequences in DNA where RNA polymerase binds with sigma subunit

200
Q

two promoter consensus sequences in E.Coli

A

TATA sequences

-10 (TATAAT) and -35 (TTGACA) for sigma subunit binding

201
Q

UP element

A

AT rich upstream promoter element

between -40 and -60 binds the alpha subunit

promote strand separation

202
Q

AT rich upstream promoter elements promote strand separation

A

sequences govern efficacy of RNA poly binding, affecting gene expression binding

not every promoter has this; differences impact how good the polymerase binds

203
Q

sigma 70

A

housekeeping, many molecules present at a time

204
Q

sigma 32

A

heat shock genes

205
Q

holoenzyme ratio

A

how much RNA polymerase binds to that sigma subunit

206
Q

DNA footprinting

A

a way to find the binding site on DNA for a DNA binding protein

DNA bound by a protein will be protected from chemical cleavage at its binding site

207
Q

DNA footprinting steps

A
  1. isolate DNA fragment with binding site
  2. radiolabel DNA and split sample into two tubes
  3. add binding protein to DNA in one tube
  4. protein will bind to sequence
  5. treat both tubes with chemical or enzymatic agent to cleave DNA into many pieces
  6. separate fragments by gel electrophoresis

if protein binds, multiple bands will be missing in the lane for that sample –> where RNA poly bound to DNA

208
Q

transcription initiation: RNA polymerase

A

uses the sigma subunit to separate the DNA strands without helicase or primers

209
Q

closed complex

A

RNA polymerase binds to promoter with sigma subunit, creating closed complex because DNA is not unwound

210
Q

open complex

A

region of DNA from -10 to 2 is separated

211
Q

sigma subunit holds the RNA to the promoter and

A

must dissociate to allow elongation

212
Q

transcription elongation

A

not as efficient as DNA polymerase

RNA polymerase adds NMPs; can stall or backtrack

213
Q

RNA polymerase proofreading

A

moves backwards which separates the 3’ end of RNA

RNA probably cleaved in catalytic site of RNA polymerase and resynthesized

GreA and GreB

214
Q

GreA and GreB

A

elongation factor binding to RNA polymerase increases efficiency of RNA poly proofreading

215
Q

two types of termination in prokaryotes

A

rho-independent termination in E.Coli

rho-dependent termination in E.coli

216
Q

Rho-independent termination in E.Coli

A

intrinsic

self complementary regions in mRNA transcript form a hairpin 15-20 nt before 3’ end

makes RNA poly pause

RNA dissociates from DNA due to poly-U region

217
Q

why does the RNA dissociate from DNA at the poly-U region?

A

A-U binding is weak

218
Q

rho-dependent termination in E.Coli

A

rho-helicase binds to Rut site on RNA

proceeds 5’to3’ until it reaches paused RNA poly

uses helicase activity to release RNA from DNA

219
Q

rut site

A

rho utilization element on mRNA

220
Q

regulation of transcription

A

regulate affinity of RNA poly for a promoter

alter promoter sequence

activator proteins make RNA poly more likely to bind

repressor proteins make RNA poly less likely to bind

221
Q

Eukaryotic RNA polymerases

A

RNA pol I
RNA pol II
RNA pol III
RNA pol IV

222
Q

Eukaryotic RNA pol I

A

synthesizes pre-reibosomal RNA

precursor for rRNAs

223
Q

Eukaryotic RNA pol II

A

responsible for synthesis of mRNA

very fast (500-1k nt/sec)

can recognize thousands of promoters

224
Q

Eukaryotic RNA pol III

A

makes tRNAs and some small RNA products

225
Q

Eukaryotic RNA polymerase IV

A

some plants, synthesizes siRNA

226
Q

Eukaryotic mRNA transcription: binding at promoter

A

relies on protein-protein contacts, with highly conserved tfs

227
Q

RNA polymerase II in eukaryotic transcription

A

large complex of 12 subunits

largest subunit has a carboxy-terminal domain (CTD)

228
Q

CTD

A

contains highly conserved repeats which are phosphorylated and dephosphorylated to control transcription

eukaryotic

229
Q

Eukaryotic initiation of transcription

A

TATA binding protein (TBP) binds to the promoter

230
Q

TATA binding protein is similar to

A

sigma subunit in prokaryotes

231
Q

TFIIH functions

A

helicase activity

kinase activity

232
Q

TFIIH helicase activity

A

unwinds DNA at promoter

233
Q

TFIIH kinase activity

A

other kinases phosphorylate the CTD of RNA pol II

changes conformation and enables RNA pol II to transcribe

234
Q

Elongation factors in Eukaryotes

A

bound to RNA pol II

enhance processivitiy

allow correction of incorrect base addition

coordinate post-transcriptional modification

235
Q

RNA pol II is dephosphorylated for termination

A

once the RNA is out of RNA pol II, protein complex that cleaves bind to the CTD, cleave RNA and add a poly-A-tail before polymerase finishes making mRNA

doesn’t matter where termination occurs

236
Q

Rna pol phosophorylated =

A

transcription

237
Q

Rna pol dephos

A

termination

238
Q

5’ cap

A

7-methylguanosine

links to the 5’ end of mRNA

239
Q

7’methylguanosine links to 5’ end of mRNA via

A

5’,5’-triphosphate link

may include additional methylations at 2’OH group sof next two nucleotides

240
Q

functions of 5’cap

A

protects RNA from exonucleases

forms a binding side for ribosome

added during transcription by complex of 4 enzymes

241
Q

how is 5’ cap added to mRNA during transcription?

A

4 enzymes attached to CTD of RNA pol II

as mRNA exits polymerase, cap is put on

242
Q

introns

A

segments not part of DNA

50-20k nt

243
Q

classes of introns

A

group 1 and 2 (selfsplicing)

spliceosomal introns

tRNA introns

244
Q

group 1 and 2 introns

A

self-splicing

ribozymes that cleave themselves or another RNA

3D structure integral to function

MM kinetics

no additional proteins or ATP

245
Q

genomes of group 1 and 2 introns

A

nuclear, mito, chloro

246
Q

group 1 and 2 introns differ in

A

splicing mechanism

247
Q

spliceosomal introns

A

spliced by spliceosomes

most common introns

frequent in protein-coding regions of eukaryotic genomes

248
Q

spliceosomes

A

complexes with RNA and proteins

associates with the CTD of RNA pol II, splices as RNA is made

249
Q

tRNA introns

A

spliced by protein based enzymes

primary transcript cleaved by endonuclease

exons joined by ATP ligase

250
Q

poly A tail

A

RNA pol II synthesizes the mRAN past cleavage site

protein complex binds mRNA at cleavage site

endonuclease recognizes site, cleaves RNA 10-30nt downstream from AAUAA

added by polyadenylate polymerase

subject to exonuclease activity

251
Q

polyadenylate polymerase

A

synthesizes 80-250 nt of adenine without a template onto 3’OH at end of mRNA with AAUAA site

252
Q

how to get diff mature transcripts from gene?

A

RNA processing

location determines expression

253
Q

average RNA half life

A

3 hours

10 turnovers/cell generation

254
Q

bacterial cells half lives

A

shorter (1.5 min)

255
Q

ribonucleases

A

degrade mRNA

256
Q

endoribonuclease

A

clips RNA into segments

257
Q

exoribonuclease

A

breaks down fragments generated by endoribonuclease or degrades whole RNA strand at either end

5’ cap must be removed in eukaryotes via decapping enzymes before 5’-3’ exoribonuclease activity

258
Q

why is protein synthesis controlled?

A

it is energy demanding

uses 90% of chemical energy in the cell

259
Q

how many proteins does protein synthesis require?

A

> 300 biomolecules in eukaryotes

260
Q

proteins are synthesized within

A

ribosomes attached to cytosolic face of ER

261
Q

amino acids are activated for synthesis by

A

attachment to tRNA

262
Q

how are AA attached to tRNA?

A

aminoacyl-tRNA synthetases

263
Q

tRNA acts as an ____ to translate mRNA into protein

A

adapter

264
Q

first codon

A

establishes reading frame

265
Q

degenerate code

A

61 out of 64 codons code for 20 amino acids

266
Q

initiation codon

A

AUG

267
Q

termination codons

A

3 out of 64; UAA UGA UAG

268
Q

genetic code in mitochondria

A

contain DNA to make a few proteins but with a slightly different code

encode their own tRNAs and use 22 instead of 32

269
Q

silent mutations

A

diff NT in DNA or mRNA but same AA in protein

270
Q

conservative substitution

A

in some cases where mutation in the first base of a codon encodes an AA with similar characteristics

GUU – valine
AUU – isoleucine
CUU – leucine

271
Q

how does the codon in mRNA base pair with the anticodon on tRNA?

A

hydrogen bonding, antiparallel

272
Q

wobble base pair

A

third base of a codon of mRNA can form non-canonical base pairs with complement in tRNA

G can bind U

273
Q

inosinate (I)

A

can bind A C U non canoncially

274
Q

how many tRNAs properly translate 61 codons?

A

32

275
Q

are there tRNAs for stop codons?

A

no

276
Q

5 stages of p synthesis

A

activation of AA

initiation of translation

elongation

termination and ribosome recycling

folding and post translational processing

277
Q

5 stages of p synthesis:

activation of AA

A

by binding to tRNA

end result: tRNA is aminoacylated

278
Q

5 stages of p synthesis:

initiation of translation

A

mRNA and first aminoacylated tRNA bind to ribosome

279
Q

5 stages of p synthesis:

elongation

A

cycles of aminoacyl-tRNA binding and peptide bond formation until stop codon

280
Q

5 stages of p synthesis:

termination and ribosome recycling

A

stop codon enters ribosome, protein leaves ribosome, ribosome and mRNA recycled

281
Q

5 stages of p synthesis:

folding and post translational processing

A

catalyzed by a variety of enzymes

282
Q

tRNA features

A

73-93 nt in both bact and euk

2D: cloverleaf
3D: twisted L

G at 5’ end
CCA at 3’ end

283
Q

aminoacyl-tRNA synthetase

A

binds a specific amino acid to its matching tRNA

20 in each cell, for each AA

specific for AA and tRNA

284
Q

second genetic code

A

matching each AA with the correct tRNA

285
Q

how is the AA linked to the tRNA?

A

through the carboxyl group of AA to the 3’ O of the last nucleotide on the 3’ end of tRNA

286
Q

synthesis of aminoacylated tRNAs steps

A
  1. creation of aminoacyl intermediate
  2. transfer of aminoacyl to tRNA

all in catalytic site of aminoacyl tRNA synthetase

287
Q

synthesis of aminoacylated tRNAs steps:

creation of intermediate

A

aminoacyl-tRNA synthetases esterify 20 AA to corresponding tRNAs

carboxyl of AA attacks alpha PO4 of ATP, creating intermediate

pyrophosphate is cleaved and becomes product

288
Q

what drives the creation of aminoacyl intermediate?

A

two phosphoanhydride bond cleavages

breaking bond between AMP and pyrophosphate
AND
energy from breaking bond from two inorganic phosphates

289
Q

synthesis of aminoacylated tRNAs steps:

transfer of aminoacyl to tRNA

A

2’OH or 3’OH of tRNA attacks the carbonyl carbon of the amino acyladenylate intermediate

creates ester bond between AA to the 3’O of the tRNA

290
Q

what if the 2’OH attacks the carbonyl carbon of the aminoacyladenylate intermediate?

A

3’O attacks the carbon to transfer the AA

291
Q

ribosome makes up ___ weight in bacteria

A

25%

292
Q

ribosome structure

A

65% rRNA, 35% protein

2 subunits bound together

293
Q

rRNA

A

forms the core of ribosome, does catalysis of peptide formation

294
Q

does protein catalyze peptide bond formation?

A

NO, rRNA does

295
Q

ribosome subunits bacteria

A

50s and 30s = 70s

296
Q

ribosome subunits eukaryotes

A

60s and 40s = 80s

297
Q

why is there a large subunit of ribosomes?

A

heavier; bigger, sediments down in centrifugation

298
Q

rRNA secondary structure

A

three single stranded rRNAs of E.Coli have specific 3D structure with intrachain base pairs

shape of rRNAs is highly conserved (bacteria, archea, eukaryotes)

299
Q

first codon is

A

AUG

300
Q

all organisms have ____ tRNAs for Met

A

2

1 for initiating tRNA and one for an internal tRNA

301
Q

bacteria Met

A

N-formylmethionine; fMet

initiation tRNA: tRNAfmet

interior met: normal tRNAmet

302
Q

eukaruotes Met

A

protein begins with Met BUT a special initiating tRNA is used

303
Q

bacteria initiation of translation requires

A

small 30S ribosomal subunit

mRNA

fmet-tRNA (initiating tRNA)

initiation factors

GTP

large 50S ribosomal subunit (for end of initiation)

304
Q

initiating factors required for bacterial translation

A

IF1
IF2
IF3

305
Q

prokaryotic initiation

A

can start during transcription

306
Q

prokaryotic initiation:

steps

A

30S subunit bound by IF3, IF1

mRNA binds small subunit

initiating 5’AUG codon is guided to correct position in robosome via shine-dalgarno sequence

IF2 helps tRNA fmet bind in P site

IF3 departs

large subunit binds

initiation complex is completed

IF2 hydrolyzes GTP to GDP

IF1 and IF2 dissociate

307
Q

what directs 5’AUG initiating codon to correct ribosomal position?

A

shine-dalgarno sequence

308
Q

shine-dalgarno sequence

A

region in mRNA that is complementary to a sequence in rRNA

16s rRNA

309
Q

IF3

A

keeps 30s subunit and 50s apart

310
Q

IF1

A

blocks the A site to prevent tRNA binding accidentally

311
Q

IF2

A

bound to GTP, binds small subunit at P site

helps formulmethionine-tRNAfmet bind in the P site to initiating AUG

312
Q

initiating complex in prokaryotes

A

all subunits bound

313
Q

at the end of initiation

A

complete ribosome with mRNA bound and the initiating tRNA in the p site

314
Q

initiation of translation in eukaryotes

A

elF2 ginds met-tRNAmet and brings it to P site of small (40S) subunit

elF4F binds mRNA and helps it bind to small subunit

small subunit moves along mRNA until AUG is in the P site

then binds initiating methionine tRNA

initiating factors leave, 60s subunit binds

315
Q

elF1A

A

IF1

blocks A site to prevent tRNA binding accidentally

316
Q

elF1

A

IF3

keeps small and large subunit separate

317
Q

elF4F

A

orients mRNA by binding of 5’cap to rRNA

SD sequence similarity

318
Q

elongation in prokaryotes

A

next aminoacyl tRNA binds to EF-Tu

one AAtRNA in A site, one in P site

N-formylmethionine or growing peptide is transfered from tRNA in P site to AA in A site

peptide bond formation catalyzed by 23S rRNA

deacetylated tRNA in P site

ribosome translocation

319
Q

EF-Tu

A

elongation factor Tu

docks amino-acyl tRNA EF Tu GTP at A site of 70S initiation complex

hydrolyzes GTP, leaves

recycled

320
Q

how does EF-Tu recycle

A

interactions with EF-Ts by loss of GDP and binding of GTP

321
Q

23S rRNA

A

catalyzes peptide bond formation in prokaryotes

322
Q

elongation in prokaryotes:

ribosome translocation

A

ribosome moves one codon toward the 3’ end of mRNA

uses energy from hydrolysis of GTP on EF-G

uncharged tRNA now in E site and can leave ribosome

growing peptide chain on tRNA in p site

A site open for new AA tRNA

323
Q

EF-G

A

binds at A site, hydrolyzes GTP, leaves, recycles

324
Q

eukaryotic elongation factors

A

eEF1alpha
eEF1by
eEF2

325
Q

eEF1alpha

A

EF-Tu

binds to aminoacyl tRNA and docks at the A site of large subunit; hydrolyzes GTP and is recycled

326
Q

eEF1by

A

EF-Ts

interacts with eEF1alpha and recycles it

327
Q

eEF2

A

EF-G

hydrolyzes GTP in A site for translocation, leaves

328
Q

termination in prokaryotes

A

elongation continues until a stop codon reaches the A site

UAA, UAG, or UGA on mRNA triggers action of termination factors

329
Q

Termination factors prokaryotes

A

RF1/RF2

RF3

330
Q

RF1/RF2

A

hydrolyzes terminal peptide-tRNA bond to release peptide from tRNA

each one binds different stop codons

331
Q

RF3

A

releases RF1 or RF2 from the ribosome

332
Q

ribosome recycling

A

binding of ribosomal recycling factor (RRF) and EF-G and hydrolysis of GTP

333
Q

binding of ribosomal recycling factor (RRF) and EF-G and hydrolysis of GTP causes…

A

exit of tRNAs
dissociation of large subunit from small subunit
release of mRNA

IF3 binds again to small subunit to prevent reassociation of ribosomal subunits

334
Q

termination in Eukaryotes

A

eRF1

ABCE1

335
Q

eRF1

A

RF1/RF2

recognizes all 3 stop codons and releases peptide from tRNA via hydrolysis

336
Q

ABCE1

A

ATP-binding cassette subfamily E member 1

interacts with eRF1 and separates the subunits of ribosome

requires ATP hydrolysis, part of recycling

337
Q

protein synthesis features

A

large energy cost

can be rapid when accomplished on polysome

in bacteria, tightly coupled to transcription

338
Q

large energy cost of protein synthesis

A

1 ATP to put AA on tRNA with aminoacyl-tRNA synthetases

2 GTP/amino acid (one for EF-G ribosome translocation, one for EF-Tu for AA-tRNA bind to A site)

1 GTP for initiation (IF2 hydrolyzes after helping initiating tRNA bind in P site)

1 GTP for termination (recycling of EF-G after translocation)

339
Q

polysome

A

clusters of ribosomes

340
Q

posttranslational modifications

A

removal of formyl group on first residue or removal of Met and other N term residues

acetylation of N term residue

removal of signal sequences or other regions

attach. carbs

modify AAs with additional COO-, CH3, or OH

addition of isoprenyl groups or other lipids (anchoring in membranes)

adding cofactors

forming disulfide links

proteolysis of proproteins

341
Q

signal sequences

A

direct proteins from site of synthesis; at or near N terminus

342
Q

as peptide emerges from the ribosome, signal sequence is bound by a

A

signal recognition particle (SRP)

made of RNA and proteins

343
Q

SRP binds GTP and

A

inhibits translation of protein

344
Q

SRP / peptide / ribosome / RNA complex goes to ER

A

SRP helps bind outside of the ER, dissociates with GTP hydrolysis

protein translation finishes

stays in the ER membrane or translated through

signal peptide is cleaved, modification takes place

345
Q

transport vesicles

A

take proteins from ER to golgi if protein is destined for another organelle or for secretion

346
Q

proteins for mito and chloroplasts bind ________ in cytosol and are delivered to ___________ on the organelle

A

chaperone proteins; receptors on the exterior of the organelle

347
Q

proteins destined for the nucleus have

A

a nuclear localization sequence (NLS)

348
Q

NLS

A

not cleaved after protein is targeted because the nuclear envelope can break down during mitosis and proteins will need to reenter the nucleus

349
Q

how does NLS go to nucleus?

A

binds importin alpha and beta and RanGTPase

complex docks at a nuclear pore and is imported

350
Q

half life of metabolism regulatory proteins that respond to rapidly changing needs

A

short lived

351
Q

biological functions of lipids

A

energy storage

insulation

water repellant

buoyancy control and acoustics in marine animals

membrane structure

signaling molecules

pigments

antioxidants

352
Q

biological functions of lipids:

energy storage

A

composed of. reduced compounds for available energy

hydrophobicity allows lots of packing bc of no water

353
Q

biological functions of lipids:

insulation

A

low thermal conductivity

high heat capacity

mechanical protection

354
Q

biological functions of lipids:

water repellent

A

hydrophobicity keeps surface of organism dry

no wetting
no evaporation

355
Q

biological functions of lipids:

signaling molecules

A

paracrine (local)

steroid (body wide)

growth factors

Vitamins A and D (hormone precursors)

356
Q

biological functions of lipids:

pigments

A

tomatoes, carrots, pumpkins, birds, leaves

357
Q

classification of lipids

A

do not contain fatty acids

do contain fatty acids

358
Q

lipids that do contain fatty acids

A

storage lipids (neutral)

membrane lipids (polar)

359
Q

fatty acids

A

carboxyllic acids with hydrocarbon chains with 4-36 carbons

most 12-24

even number of carbons

360
Q

most natural fatty acids are

A

unbranched

361
Q

levels of saturation in fatty acids: mono

A

one c=c bond

362
Q

conformation of fatty acids

A

saturated chains tend to adopt extended conformations

double bonds in natural unsaturated fatty acids are in cis conformation which kinks the chain

363
Q

essential nutrients

A

things we cannot synthesize
omega 3
omega 6 fatty acids

364
Q

as the chain length increases, solubility

A

decreases because there are more hydrophobic interactions

365
Q

as the chain length increases, the melting point

A

increases because there are more interactions which require more energy to melt

366
Q

as the number of double bonds increases, the melting point

A

decreases because they are packed less tightly and have less interactions

367
Q

saturated double bonds pack in a. _______ and have a _____ Tm

A

more orderly way and have a higher Tm

368
Q

unsaturated fatty acids with cis c=c pack ______orderly due to kink

A

less;

less thermal energy to disrupt disordered packing, lower Tm

369
Q

how do trans fatty acids form?

A

partial hydrogenation of unsaturated fatty acids

done to increase stability at high temperature of oils used in cooking or longer shelf life

370
Q

trans fatty acids

A

allows a fatty acid to adapt an extended conformation like a saturated fatty acid

371
Q

triacylglycerols

A

storage lipid

three fatty acids form ester linkages with three hydroxyl groups of glycerol

majority of FA in biological systems in this form

primary storage form of lipids in organisms

372
Q

solid triacylglycerols

A

fats

373
Q

liquid triacylglycerols

A

oils

374
Q

properties of triacylglycerols

A

less soluble in water than fatty acids due to lack of charged carboxyl group

less dense than water, fats and oils float

375
Q

advantage of fats over polysaccharides

A

carry more energy per carbon because they are more reduced sugars

carry less water per gram because are non polar and pack tightly

376
Q

short term energy needs

A

glucose and glycogen, storage for carbs, quick delivery

377
Q

long term energy needs

A

fats, good storage, slow delivery

378
Q

waxes

A

esters of long chain sat or unsat fatty acids with long chain alcohols

379
Q

wax properties

A

insoluble, high melting points

380
Q

functions of waxes

A

protection and pliability for hair and skin in verts

waterproofing of feathers

protection from evaporation in plants

used by people in lotions and ointments etc

381
Q

structural lipids in membranes

A

polar head groups and nonpolar tails (typically fatty acids)

382
Q

diversification of membrane lipids comes from

A

different backbone
different fatty acids
addition of head groups

383
Q

what determines the surface properties of membranes?

A

properties of. head groups

384
Q

glycerophospholipids

A

type of lipid in membranes

primary constituents of cell membranes

two FA form ester linkages with first and second hydroxyl groups of L-glycerol-3-phosphate

head group on phosphate group

unsat FA on C2

385
Q

phosphatidylcholine

A

most common glycerophospholipid

major component of most cell membranes (euk)

not in prokaryotes, cant be synthesized

386
Q

sphingolipids

A

second type of lipids in membranes

backbone is sphingosine (long chain amino alcohol)

FA joined to sphingosine via amide linkage

head group on sphingosine via glycosidic or phosphodiester linkage

387
Q

where are sugar-containing glycosphingolipids often found?

A

outer face of plasma membrane

388
Q

blood groups are determined by

A

type of sugars located on the head groups in glycosphingolipids

389
Q

the structure of the sugar in head group of glycosphingolipid is determined by expression of specific

A

glycosyltransferases

390
Q

no glycosyltransferases?

A

o antigen

391
Q

glycosyltransferase for N-acetyl galactosamine?

A

A antigen

392
Q

glycosyltransferase for galactose?

A

b antigen

393
Q

sterols

A

cholesterol = most common

steroid nucleus of 4 rings, almost planar

hydroxyl group/polar head in A ring

various nonpolar side chains

394
Q

physiological role of sterols (cholesterol)

A

present in the membranes of. most eukaryotic cells

modulate fluidity and permeability

thicken membranes

395
Q

bacteria lack

A

sterols

396
Q

how do mammals obtain cholesterol?

A

from food or synthesize in liver

397
Q

cholesterol is transported to tissues in

A

lipoproteins

398
Q

lipoproteins

A

transports choelsterol

combination of lipids and proteins

categorized by density

399
Q

small particles have

A

high density

400
Q

large particles have

A

low density

401
Q

low-density lipoproteins

A

tend to deposit and clog arteries

402
Q

physiological role of sterols (hormones)

A

hormones are derivatives of sterols

MCB 3010 (12 decks)

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