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BIOCHEM > TEST 4 > Flashcards

TEST 4 Flashcards

1
Q

fatty acid degradation properties

A
  • Occurs in mitochondria
  • Produces FADH 2 and NADH
  • Produces acetyl CoA
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2
Q

fatty acid synthesis properties

A
  • Occurs in cytoplasm
  • Uses NADPH
  • Uses acetyl CoA
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3
Q

triglyceride degradation

A

1) hydrolysis of tryglycerides to get fatty acids
2) activation and transport of fatty acids into mitochondria
3) Beta oxidation of fatty acids to produce acyl CoA

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4
Q

lipids are stored as what

A

mostly as tryglycerides

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5
Q

what does lipase do

A

oxidizes H20 to 02, adds hydrogen to equation
converts triglycerides to glycerol and fatty acids

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6
Q

liver cell degradation of triglycerols

A

glycolysis and gluconeogenesis

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7
Q

all other tissues of degradation of triglycerols

A

fatty acid oxidation, enters TCA cycle

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8
Q

transport of fatty acids into mitochondria

A

requires 2 ATP & carnitine
hydrolysis of PPi drives reaction of fatty acid to acyl adenylate to acyl CoA

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9
Q

B oxidation of fatty acids to produce acetyl CoA steps

A

1) oxidation of Acyl CoA by FAD+, FAD+ gets reduced
2) Hydration (addition of H20 to CoA molecule)
3) oxidiation of CoA molecule by NAD+, NAD+ gets reduced
4) Thiolysis of CoA (cleaving of molecule CoA group from molecule to make Acetyl CoA)

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10
Q

Step 1 of B Oxidation

A

oxidiation of Acyl Coa by FAD+

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11
Q

Step 2 of B Oxidation

A

Hydration

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12
Q

Step 3 of B Oxidation

A

Oxidation by NAD+

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13
Q

Step 4 of B Oxidation

A

Thiolysis of CoA to Acetyl CoA

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14
Q

How many carbons get removed per step in B Oxidation

A

2 carbons are removed per step

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15
Q

How many FADH2 and NADH2 are created per round B Oxidation

A

1 NADH
1 FADH2

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16
Q

How many FADH and NADH2 are created from a C16 saturated fatty acid?

A

7 NADH
7 FADH2
8 acetyl CoA

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17
Q

how to change unsaturated to saturated fatty acid

A

-isomerase shifts position of double bond
-no production of FADH 2 during
first round of β-oxidation if unsaturated

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18
Q

what occurs with a odd chain of fatty acids?

A

-final round of B oxidation produces acetyl CoA as normal,
-once it hits the end, it creates 3 carbon propionyl CoA which is then turned into Succinyl CoA for use in TCA cycle

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19
Q

ketone bodies

A

another source of fuel derived from fats

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20
Q

ketone bodies can be formed how

A

can be formed from acetyl CoA

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21
Q

properties of ketone bodies

A

-doesnt generate as much ATP
-water soluble easily transported
-can be used as fuel for brain as last resort

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22
Q

fatty acid synthesis transport from mitochondria to cytoplasm

A

1) Acetyl-CoA transferred from
mitochondria to cytoplasm.

2) Acetyl-CoA activated to malonyl CoA.

3) Reaction intermediates attached to thiol
groups on fatty acid synthase

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23
Q

acetyl CoA to malonyl CoA

A

step 2 of how fatty acid chains are created

requires ATP and CO2
attaches CO2 to acetyl CoA

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24
Q

fatty acid synthesis steps

A
  1. Condensation – Loss of CO2
  2. Reduction using NADPH – turns NADPH into NADP+
  3. Dehydration – loses H20
  4. Reduction using NADPH – turns NADPH into NADP+
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25
Q

each round of fatty acid synthesis adds how many carbons

A

2 carbons are added to the chain at a time

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26
Q

longest fatty acid synthase chain

A

16 carbon chains any longer requires special enzymes to add onto it

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27
Q

how many malonyl CoA are produced per acyl CoA

A

1 acyl CoA per 1 malonyl CoA

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28
Q

elongases

A

different enzymes that can add 2 carbon units to create chains longer than 16 carbons

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29
Q

desaturases

A

can introduce double bonds into fatty acids using
NAD(P)H and O2

mammals cannot introduce double bonds beyond carbon number 9

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30
Q

what cosubstrate that is not used the in overall reaction is require to make malonyl CoA

A

CO2

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31
Q

sources of amino acids

A

proteins from diet
degredation of defective or unneeded cellular proteins

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32
Q

What degrades proteins into individual amino acids

A

-availability of H2O and H+ helps denaturation of proteins through hydrolysis

proteases- variety of enzymes that break peptide bonds

Proteasomes- proteins tagged for destruction by peptide ubiquitin

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33
Q

how are proteins/amino acids stored

A

they are not stored, only utilized when needed and when availiable

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34
Q

amino acid utilizations

A

can be used as building blocks for new proteins
degraded - used for nitrogen

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35
Q

Amino acid degradation stpes

A

1) removal of nitrogen
2) Carbon skeletons
of 20 amino acids funneled
into 7 molecules

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36
Q

most all amino acids can be converted to what

A

alpha ketoglutarate which gets converteed to glutamate
can be interconverted and reversed as needed

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37
Q

deamination of glutamate

A

forms NH4 ammonia
regenerates alpha ketoglutarate
can be used to make amino acids to create urea (piss)

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38
Q

urea users

A

terrestrial vertebrates / sharks

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39
Q

uricotelic animals / uric acid users

A

birds / reptiles

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40
Q

Carbamoyl Phosphate Synthetase functions

A

creates carbanoyl phosphate which is used to create urea
uses 2 ATP
NH4 to NH3
carbon comes from HCO3 - hydrates CO2

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41
Q

where does the nitrogens from urea come from?

A

NH4 - ammonia
aspartate

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42
Q

urea cycle locations

A

mostly in cytosol
partly in mitochondrial matrix

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43
Q

Ketogenic Amino Acids

A
  • can be degraded to acetyl CoA or
    acetoacetyl CoA
  • can give rise to ketone
    bodies or fatty acids, but
    CANNOT be used to
    synthesize glucose
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44
Q

Glucogenic Amino Acids

A
  • can be degraded to pyruvate, ⍺-
    ketoglutarate, succinyl CoA,
    fumarate, oxaloacetate
  • these are later intermediates in the
    TCA cycle

-can be converted into
phosphoenolpyruvate and
eventually glucose

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45
Q

phenylketonuria

A

-deficiency of phenylalanine hydroxylase

-leads to accumulation of phenylalanine because it cannot be converted to tyrosine
- therapy: low phenylalanine diet

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46
Q

ubiquitin

A

is a protein that signals for protein degradation by a proteosome

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47
Q

Aminotransferases contain which cofactor?

A

PLP

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48
Q

The nitrogens in urea generated from the
urea cycle come from

A

NH4+ and aspartate

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49
Q

A given amino acid is found to be metabolized to
yield acetoacetyl-CoA. What can be said about
this amino acid?

A

It is ketogenic

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50
Q

nitrogenase enzyme action and protein composition

A

-catalyzes the conversion of N2 to 2NH 3
-requires 16 ATP
-nitrogenase is a combination of the nitrogenase protein (MoFe protein) and reductase protein (Fe protein)

  • the reductase oxidizes ATP to ADP for use in the nitrogenase
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51
Q

ways in which nitrogen is fixed

A

lightning
biochemically - nitrogenase
artifically - haber bosch

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52
Q

nitrogen assimlation

A

alpha ketoglutarate to glutamate which adds a nitrogen
glutamate to glutamine

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53
Q

glutamate to glutamine

A

adds side chain reaction
glutamine synthesis

after which nitrogen is then incorporated by aminotransferases

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54
Q

alpha ketoglutarate to glutamate

A

adds nitrogen
glutamate dehydrogenase

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55
Q

carbons are provided to amino acid synthesis how

A

provided by intermediates of glycolytic pathway TCA cycle and pentose phosphate pathway

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56
Q

amino acid synthesis in microbes vs humans

A

microbes - all 20 basic amino acids
humans - 9 amino acids can not be synthesized that are essential

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57
Q

tetrahydrofolate

A

carrier of activated one carbon units
essential for syntehesis of many amino acids and nucleotides
derived from vitamin B9

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58
Q

What does beta in beta oxidation mean

A

Beta refers to the 3rd carbon from the carbonyl group (which includes the carbon in the carbonyl group)

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59
Q

DNA characteristics

A
  • semi conservative
  • requires activated precursors
  • initiation begins at origin of replication
  • replication is bidirectional
  • 5’ to 3’ direction
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60
Q

DNA polymerase

A
  • requires a primer that has a free 3’-OH group
  • needs activated nucleotides - dATP, dCTP, dGTP, dTTP
  • creates phosphodiester linkages joining units to the DNA backbone
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61
Q

Meselson and Stahl experiement

A

found semi conservative replication
added radioactive nitrogen to both DNA strand
cut open new daughter cells
found it to be semi conservative

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62
Q

consensus sequence

A

order of repeated residues found in different positions

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63
Q

DNAB

A

joins and uses helicase activaity to start unwinding the double helix

64
Q

OriC

A

4 copies of a sequence that are preferred binding sites for DnaA

65
Q

DNA-A

A

origin recognition protein-replication factor

66
Q

primase

A

makes primer

67
Q

leading stand

A

continuous

68
Q

lagging strand

A

discontinous

69
Q

helicase

A

uses ATP
unwinds DNA

70
Q

primosome

A

multisubunit complex of DNA replication

71
Q

DNA ligase

A

seals nicks in DNA backbone where primers were

72
Q

topoisomerase

A

unwinds the negative and positive supercoils ahead of the replication fork

73
Q

Processivity

A

-a measure of the ability of an enzyme to catalyze consecutive reactions without releasing its substrate

74
Q

exonuclease

A

removes mismatched nucleotides from the 3’ END of DNA by hydrolysis
many use 3’ to 5’

75
Q

DNA pol w exonuclease activity

A

DNA Pol 1

76
Q

DNA pol 1

A

exonuclease activity is used to degrade primer add new DNA
main job is the previous function

largest DNA pol enzymes
not very processive
very slow

77
Q

DNA pol 3

A

main DNA polymerase
highly processive
extremely fast

78
Q

DNA pol 2

A

only able to proof-read / repair
more processive than DNA pol 1 less than DNA pol 3
slow

79
Q

DNA damage types

A

errors in replication
reactive oxygen species
radiation
deamination
alkylating agents

80
Q

what mutation is most detrimental

A

genes encoding for proteins that repair DNA
genes encoding the cell cycle

81
Q

types of DNA damage

A
  • Missing base
  • Altered bases
  • Wrong base
  • Deletions/Insertions
  • Strand Breakage
  • Cross-Linked Strands
82
Q

what does an alkylating agent do?

A

in alkylating agent is usually a tri oxide ring, it can interact with bases so it doesnt allow for correct copying

83
Q

thymine dimers

A

caused by UV light
fixed by photolyase, using light

puts two thymines on each DNA strand bonded together

84
Q

deamination

A

removal of nitrogen from
cytosine can convert to uracil

85
Q

template strand is tagged how?

A

it is methylated to distinguish itself from the new DNA

86
Q

mismatch repair

A

energetically costly, needed to maintain integrity of DNA

87
Q

mRNA

A

messenger RNA
gets translated into a protein

3-5% of cellular RNA

88
Q

tRNA

A

transfer RNA
takes amino acid to ribosomes for translation

15% of cellular RNA

89
Q

rRNA

A

ribosomal RNA
uses mRNA and tRNA to create proteins

80% of cellular RNA

90
Q

snRA

A

small nuclear RNA
component of spliceosome - helps destroy invasive RNA sequences

91
Q

RNA characteristics

A

single stranded
uracil instead of thyamine
has secondary structure
less stable than DNA

92
Q

requirements to create RNA from RNA polymerase

A

activated precursors - UTP ATP GTP CTP
template strand

93
Q

alpha subunit of RNA pol

A

helps to find promoter sequence (site where transcription
begins)

  • finds TATA box / pribnow
    -not all promoter sequences do their job equally as well
94
Q

strong promoter

A
  • Promoter sequence corresponds closely to consensus sequence
  • Transcribed frequently
95
Q

weak promoter

A
  • Multiple substitutions at consensus sequence
  • Transcribed less frequently
96
Q

sigma 70

A

standard promoter

97
Q

sigma 54

A

nitrogen starvation promoter

98
Q

sigma 32

A

heat shock promoter

99
Q

sigma definition

A
  • promoter sequence
  • helps find site where transcription begins
  • participates in initiation of RNA synthesis and disassociates
100
Q

initiation of transcription

A

no primer required
unwinds 17bp segment of DNA

101
Q

elongation of transcription

A

has transcription bubble
loss of sigma unit allows for tight binding of RNA pol to DNA template
continues til termination sequence

102
Q

transcription bubble

A

17 bp long unwinding of DNA allowing for transcription in 5 -> 3 direction

103
Q

termination of transcription

A

controlled as tightly as initiation
2 types
- factor independent termination
- factor dependent termination

104
Q

factor independent termination

A

rich GC region creates hairpin loop of RNA

105
Q

factor dependent termination

A

-Rho protein binds to RNA and slides up the strand towards the RNA pol

-Rho protein has ATPase that pulls the transcript off the RNA pol

-RNA pol hits the termination sequence and waits for Rho to disassemble the complex

106
Q

repressors

A

bind to DNA and prevent transcription of a gene
can be modified by ligand binding (corepressors and inducers)

negative regulation

107
Q

activators

A

bind to DNA and promote transcription of a gene
can be modified by ligand binding (corepressors and inducers)

positive regulation

108
Q

regulatory proteins of transcriptions

A

activators and repressors

proteins that bind to specific sequences on DNA and either
promote or repress transcription

109
Q

repressor with inducer

A

the repressor is bound the DNA and stops transcription

once inducer is bound the repressor unbinds to the DNA and allows transcription

110
Q

repressor with corepressor

A

the repressor is not bound to DNA, allows for transcription

once corepressor is bound to the repressor, they bind to DNA and stop transcription

111
Q

activator with inducer

A

activator is not bound to DNA, gene is not transcribed

once inducer binds with activator, they bind to DNA and allow for transcription

112
Q

activator with corepressor

A

activator is bound to DNA, gene is transcribed

once corepressor binds with activator, they unbind to DNA and stop transcription

113
Q

The sigma subunit of RNA Polymerase
recognizes what on DNA?

A

the pattern of nucleotides at position -10

114
Q

Factor independent transcription termination
involves _______.

A

formation of stem-loop structures in the transcript

115
Q

What type of molecule can bind to a repressor to
prevent the repressor from binding to DNA, and
subsequently allowing transcription of the gene?

A

inducer

116
Q

what RNA type is most abundant in the cell

A

rRNA

117
Q

transcription in prokaryotes

A
  • transcription and translation both take place in cytoplasm
  • mRNA seldom processed
  • transcription and translation occur at the same time
  • tRNA and rRNA undergo processing (cleavage, termini processing)
  • often polycistronic- multiple genes on a single transcript
118
Q

transcription in eukaryotes

A
  • transcription (nucleus) and translation (cytoplasm) spatially and temporally separate
  • virtually all initial products of transcription undergo further processing and modification
  • multiple RNA Polymerases; transcription more highly regulated
  • often monocistronic
119
Q

processing RNA in prokaryotes

A

one mNA strand can have several different types of RNA in it
ribonucleases cut them each out

120
Q

processing RNA in eukaryotes

A
  • nucleotides cleaved from 5’ end and removal of introns
  • nucleotide addition ( CCA added to 3’ end )
  • Addition of a 5’ cap ( Contributes to the stability of mRNA protects 5’ end from degradation )
  • addition of PolyA tail ( Contributes to the stability of mRNA, enhances translation efficiency, contributes to mRNA half-
    life )
121
Q

introns

A

non coding RNA regions

122
Q

exons

A

coding RNA regions

123
Q

5’ cap

A

contributes to stability
protects 5’ tail from degredation

usually in eukaryotes mRNA

124
Q

poly A tail

A

generated by poly A polymerase
adds 250 A residues

enhances translation efficiency
contributes to mRNA half life

125
Q

What removes introns

A
  • spliceosomes: group of snRNAs and
    more than 300 proteins
  • snRNPs: snRNA molecules and their
    associated proteins
  • initiated by attack from 2’ OH from
    adenine contained within the intron
126
Q

specificity of removal of introns is what

A

extremely high
if one nucleotide off its a frameshift mutation

127
Q

mutations involving the splicing of introns account for how much of genetic diseases

A

15%

128
Q

group 1 introns

A

catalytic RNA
self splicing introns

needs a guanosine or guanine to initiation splicing of intron

129
Q

Alternative splicing

A

Different combinations of
exons in the same gene may
be spliced into mature
mRNA producing distinct
forms of a protein

130
Q

translation cell energy use

A

90% of cell energy use

131
Q

start codon

A

AUG which codes for methionine

132
Q

cricks adaptor hypothesis

A

amino acids cant recognize codons
an adaptor molecule is require for translation
tRNA serves as adaptor molecule between codon and amino acid
requires at least 1 tRNA for each amino acid

133
Q

tRNA composition

A

attaches to amino acid on 3’ end
anticodon loop, where amino acid attaches
single stranded

134
Q

accurate translation requires

A

correct amino acid attached to proper tRNA
correct pairing between anticodon on tRNA and the codon on mRNA

135
Q

attachment of amino acid to tRNA

A

1) activation of amino acid to form aminoacyladenylate

2) transfer of aminoacyl group to a particular tRNA

both of these steps are done by aminoacyl-tRNA synthetases
requires 2 ATP

binds 3’ end and carboxyl group

136
Q

prokaryotic ribosomes subunits

A

50S and 30S = 70S
these numbers are based on mass and density

137
Q

3 steps of protein synthesis

A

1initiation
2 elongation
3 termination

read 5-3’
created N to C terminus

138
Q

shine delgarno sequence

A

centered -10 from initiator codon
pairs w 16S RNA
starting codon is usually AUG / methionine

139
Q

APE site

A

A - (aminoacyl) binding site
P - (peptidyl) attachment site- this is where the growing amino acid chain grows
E - exit site

140
Q

IF 1 2 4

A

initiation factor
requires 1 GTP

141
Q

EF tu

A

elongation factors
requires GTP for activity

142
Q

energy required for amino acid being added to chain per step

A

2 ATP - required to attach amino acid to RNA
1 ATP- require to bring tRNA to ribosome by EF
1 ATP - required to add tRNA to ribosome

4 total ATP

143
Q

tRNA movements in ribosome

A

A site - tRNA moves to P site
P site - tRNA moves to exit site
E site - tRNA exits ribosome

144
Q

elongation requires which elongation factor

A

EF- G translocase
requires GTP

145
Q

termination of translation

A

stop codon are recognized by release factor,
breaks linage between tRNA and peptide chain

146
Q

differences in translation in prokaryotes and eukaryotes

A

ribosomes in prokaryotes 50S + 30S = 70s
ribosome in eukaryotes 60S + 40S = 80S

separated by nucleus and cytoplasm in eukaryotes

147
Q

post translational modification of proteins

A

can occur post or co translationally

148
Q

he first step in the degradation of amino acids is the transfer of the ______ to α-ketoglutarate by a(n) ______.
Group of answer choices

A

transfer of amino group to alpha ketoglutarate by an aminotransferase

149
Q

The error rate in the selection efficiency (tendency to choose the correct nucleotide initially) of DNA polymerase is approximately ________

A

10^4-10^5

150
Q

purines

A

GA
2 rings

151
Q

pyraminidines

A

TC
1 ring

152
Q

TC

A

pyramindines

153
Q

GA

A

purines

154
Q

Lactate can be transported from muscle tissue to the liver where the reactions of gluconeogenesis can convert it back into glucose to then be transported back to the muscle in order to generate ATP via the reactions of glycolysis. This process is called the ________.

A

cori cycle

155
Q
A

BIOCHEM (8 decks)

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