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BMS 300 > Proteins and DNA > Flashcards

Proteins and DNA Flashcards

1
Q

Where does DNA –> RNA occur

A

nucleus

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2
Q

what is it called for DNA to be converted to RNA

A

transcription

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3
Q

where does RNA convert to protein

A

cytoplasm

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4
Q

what is it called for RNA to be converted to protein

A

translation

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5
Q

what is the primary structure of proteins composed of

A

amino acids

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6
Q

how are amino acids in primary structures held together

A

peptide bonds

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7
Q

what kind of bonds are peptide bonds

A

covalent

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8
Q

what is the chain of amino acids called

A

polypeptide chain

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9
Q

how do secondary structure proteins come about

A

polypeptide chains fold into sheets

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10
Q

what are secondary structures due to

A

H-bonds

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11
Q

what makes the backbone of a protein

A

primary structure proteins

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12
Q

what are the 2 types of secondary structure proteins

A

A helix and B sheets

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13
Q

what is a shape characteristic of alpha helixes

A

corkscrew

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14
Q

what is a shape characteristic of beta sheets

A

parallel or antiparallel

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15
Q

where does C=O bind to N-H in alpha helixes

A

4 AA residues ahead

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16
Q

where does C=O bind to N-H in beta sheets

A

side by side sheets

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17
Q

which way do R groups point in beta sheets

A

in

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18
Q

which way do R groups point in alpha helixes

A

out

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19
Q

are tertiary structure proteins hydrophobic or hydrophilic

A

hydrophobic

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20
Q

what determines the shape of tertiary structure proteins

A

polar/nonpolar R groups

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21
Q

what 3 things determine protein shape

A

type of amino acid, order of amino acid, and bonds between amino acid

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22
Q

what are prion proteins

A

bad proteins

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23
Q

what is an amyloid

A

PRPsc enters protein and makes it defective

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24
Q

where is DNA located

A

in the nucleus

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25
Q

what kind of RNA leaves the nucleus

A

fully modified

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26
Q

is euchromatin or heterochromatin loose

A

euchromatin

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27
Q

is DNA accessible in euchromatin

A

yes

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28
Q

is DNA accessible in heterochromatin

A

no

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29
Q

what is a nucleotide

A

phosphate and sugar

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30
Q

what is a nucleoside

A

just sugar

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31
Q

what are the two types of nitrogen bases

A

purines and pyrimidines

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32
Q

what are the purines nitrogen bases

A

adenine and guanine (pure silver - Ag)

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33
Q

what are the pyrimidines nitrogen bases

A

cytosin, thymine, and uracil

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34
Q

what is the nitrogen base that is only found in RNA

A

uracil

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35
Q

what is pentose

A

a 5 carbon sugar (penthouse has 5 floors)

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36
Q

what does carbon 1 do

A

links bases

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37
Q

what does carbon 2 do

A

identifies sugar

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38
Q

what does carbon 3 and 5 do

A

phosphodiester bond

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39
Q

what is called when the hydrogen on carbon 2 contains a oxygen

A

ribose

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40
Q

what is it called when the hydrogen on carbon 2 doesn’t contain a oxygen

A

deoxyribose

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41
Q

what kind of bond is between carbon 3 and 5 on a pentose

A

phosphodiester bond

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42
Q

what is the 1st nucleotide on a pentose

A

OH on 3’ carbon

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43
Q

what is the 2nd nucleotide on a pentose

A

phosphate group of 5’ carbon

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44
Q

what does the OH on 3’ carbon bind to

A

phosphate group of 5’ carbon

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45
Q

what does the binding of OH to phosphate cause on a pentose

A

3rd phosphate of ATP is cut off to form backbone

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46
Q

what kind of bond are base pairs

A

H bonds

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47
Q

what is needed for base pairs to bond

A

optimal distance

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48
Q

how many copies of DNA does the nucleus contain

A

1

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49
Q

what does helicase do

A

breaks H bonds

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50
Q

what does primase do

A

create RNA primer

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51
Q

which way does polymerase read

A

3’-5’

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52
Q

what way does polymerase write

A

5’-3’

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53
Q

what is called when the polymerase writes the protein in segments

A

ozaki fragments

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54
Q

what happens to the ozaki fragments

A

they are ligated

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55
Q

what is ligation

A

to be put together

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56
Q

what is the base of the promoter region called

A

TATA box

57
Q

what does the TATA box recruit

A

transcription factors

58
Q

what do the transcription factors on the TATA box recruit

A

RNA polymerase

59
Q

what is another function of RNA polymerase

A

unwinds DNA

60
Q

what does U replace in RNA

A

T

61
Q

what does A pair with

A

T

62
Q

what does C pair with

A

G

63
Q

what is the type of RNA for polymerase 1

A

rRNA

64
Q

what is the type of RNA for polymerase 2

A

mRNA and snRNA

65
Q

what is the type of RNA for polymerase 3

A

rRNA, tRNA, and snRNA

66
Q

where on the pentose is RNA found

A

OH on 2’ carbon group

67
Q

is RNA or DNA more stable

A

DNA

68
Q

what is the main structure for RNA

A

single stranded but can fold

69
Q

what is the function of rRNA

A

core of ribosomes

70
Q

what is the function of mRNA

A

protein synthesis template

71
Q

what is the function of tRNA

A

carries AA to ribosomes for protein synthesis

72
Q

what is the function of snRNA

A

processes DNA and RNA

73
Q

what is 5’ capping

A

attaching a nucleotide on the 5’ end

74
Q

what is 3’ poly adenylation

A

adding a lot of A nucleotides to 3’ end

75
Q

what is splicing

A

removing the intron, exons join together

76
Q

which way is mRNA read

A

5’ - 3’

77
Q

what is the word for 3 bases

A

codon

78
Q

what is a codon

A

a specific amino acid

79
Q

what is the wobble

A

3rd base that differs/varies

80
Q

what is a point mutation

A

single base changed

81
Q

what is a frameshift mutation

A

all codons after mutation are different

82
Q

what is a missense mutation

A

changed base –> 1 changed codon

83
Q

what is a nonsense mutation

A

stop codon made

84
Q

what is a silent mutation

A

base change doesn’t result in anything

85
Q

what do ribosomes translate mRNA to

A

proteins

86
Q

what do rRNA bundles make

A

subunits

87
Q

what does the small subunit do

A

read mRNA

88
Q

what does the large subunit do

A

docking site for tRNA

89
Q

what is the order of the initiation sites

A

E P A (APE)

90
Q

where is tRNA found

A

ribosomes

91
Q

what does tRNA contain

A

anticodons

92
Q

what happens when tRNA binds to codon

A

it releases its amino acid

93
Q

what charges empty tRNA

A

tRNA synthetase

94
Q

in charging tRNA, what does ATP cleavage link together

A

amino acids and tRNA

95
Q

what does tRNA drop at the ribosome

A

amino acids

96
Q

what is elongation in translation initiation

A

addition of amino acid

97
Q

what happens when the subunit makes a stop codon in translation initiation

A

proteins releases and ribosomes dissociates from mRNA

98
Q

where are proteins with a signal sequence moved to

A

rough endoplasmic reticulum

99
Q

what does the ERAD do

A

degrades troubled proteins

100
Q

what causes ERAD to start

A

the cell recognizes misfolded protein

101
Q

what is added to protein in the ERAD process

A

ubiqudin

102
Q

where does ubiqudin cause the protein to move to

A

cytosol to cytoplasm

103
Q

what degrades the protein once it moves to the cytoplasm

A

proteasome

104
Q

what does unfolded protein response (UPR) stop

A

translation

105
Q

what do chaperons do

A

folds and unfolds protein

106
Q

what does UPR create more of in response to misfolded protein

A

chaperons

107
Q

where are chaperons found

A

endoplasmic reticulum

108
Q

what is the last resort for misfolded proteins

A

autophagy

109
Q

what is autophagy

A

cell death

110
Q

what does the Golgi apparatus sort

A

ER products

111
Q

how do vesicles enter the golgi

A

cis face or trans face

112
Q

what is cis face

A

part of golgi closest to nucleus

113
Q

what is trans face

A

part of golgi furthest to nucleus

114
Q

what part of the cell is the “road”

A

cytoskeleton

115
Q

what part of the cell is the “vehicle”

A

motor proteins

116
Q

where does the + end send stuff toward

A

membrane

117
Q

where does the - end send stuff toward

A

nucleus

118
Q

do microtubules carry stuff short or long distances

A

long distances

119
Q

does f-actin carry stuff short or long distances

A

short distances (this man is so f-ing short)

120
Q

which way does kinesin carry stuff

A

+ end

121
Q

which was does dynein carry stuff

A

minus end

122
Q

what is the way to remember what motor proteins carry stuff which direction

A

(+)K5 - D6

123
Q

what is endocytosis

A

moving things into cytoplasm

124
Q

what is phagocytosis

A

big particles get eaten

125
Q

what is pinocytosis

A

fluid gets drunk (Pino like the wine)

126
Q

where does COP2 carry stuff in receptor mediated endocytosis

A

ER –> golgi

127
Q

where does COP1 carry stuff in receptor mediated endocytosis

A

golgi –> ER (the L in golgi looks like a 1)

128
Q

where does clathrin carry stuff in receptor mediated endocytosis

A

to and from plasma membrane

129
Q

what separates vesicle and membrane in receptor mediated endocytosis

A

dynamin (dynamite causes stuff to break apart)

130
Q

what happens to the cage at the docking site in receptor mediated endocytosis

A

it sheds

131
Q

what happens when V-snare binds to T-snare

A

water is squeezed out

132
Q

what is V-snare

A

the vesicle

133
Q

what is T-snare

A

the target/membrane

134
Q

what are the V-snare(s)

A

VAMP

135
Q

what are the T-snare(s)

A

syntaxin and snap-25 (Taylor swift) (sin and snap)

136
Q

what is the calcium binding protein

A

synaptotagmin (tags the membrane because it’s on the vesicle)

137
Q

what activates the SNARE complex

A

calcium binding

138
Q

what is formed when V and T snares wind together

A

A helices

BMS 300 (14 decks)

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