TEST 4 Flashcards
fatty acid degradation properties
- Occurs in mitochondria
- Produces FADH 2 and NADH
- Produces acetyl CoA
fatty acid synthesis properties
- Occurs in cytoplasm
- Uses NADPH
- Uses acetyl CoA
triglyceride degradation
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
lipids are stored as what
mostly as tryglycerides
what does lipase do
oxidizes H20 to 02, adds hydrogen to equation
converts triglycerides to glycerol and fatty acids
liver cell degradation of triglycerols
glycolysis and gluconeogenesis
all other tissues of degradation of triglycerols
fatty acid oxidation, enters TCA cycle
transport of fatty acids into mitochondria
requires 2 ATP & carnitine
hydrolysis of PPi drives reaction of fatty acid to acyl adenylate to acyl CoA
B oxidation of fatty acids to produce acetyl CoA steps
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)
Step 1 of B Oxidation
oxidiation of Acyl Coa by FAD+
Step 2 of B Oxidation
Hydration
Step 3 of B Oxidation
Oxidation by NAD+
Step 4 of B Oxidation
Thiolysis of CoA to Acetyl CoA
How many carbons get removed per step in B Oxidation
2 carbons are removed per step
How many FADH2 and NADH2 are created per round B Oxidation
1 NADH
1 FADH2
How many FADH and NADH2 are created from a C16 saturated fatty acid?
7 NADH
7 FADH2
8 acetyl CoA
how to change unsaturated to saturated fatty acid
-isomerase shifts position of double bond
-no production of FADH 2 during
first round of β-oxidation if unsaturated
what occurs with a odd chain of fatty acids?
-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
ketone bodies
another source of fuel derived from fats
ketone bodies can be formed how
can be formed from acetyl CoA
properties of ketone bodies
-doesnt generate as much ATP
-water soluble easily transported
-can be used as fuel for brain as last resort
fatty acid synthesis transport from mitochondria to cytoplasm
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
acetyl CoA to malonyl CoA
step 2 of how fatty acid chains are created
requires ATP and CO2
attaches CO2 to acetyl CoA
fatty acid synthesis steps
- Condensation – Loss of CO2
- Reduction using NADPH – turns NADPH into NADP+
- Dehydration – loses H20
- Reduction using NADPH – turns NADPH into NADP+
each round of fatty acid synthesis adds how many carbons
2 carbons are added to the chain at a time
longest fatty acid synthase chain
16 carbon chains any longer requires special enzymes to add onto it
how many malonyl CoA are produced per acyl CoA
1 acyl CoA per 1 malonyl CoA
elongases
different enzymes that can add 2 carbon units to create chains longer than 16 carbons
desaturases
can introduce double bonds into fatty acids using
NAD(P)H and O2
mammals cannot introduce double bonds beyond carbon number 9
what cosubstrate that is not used the in overall reaction is require to make malonyl CoA
CO2
sources of amino acids
proteins from diet
degredation of defective or unneeded cellular proteins
What degrades proteins into individual amino acids
-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
how are proteins/amino acids stored
they are not stored, only utilized when needed and when availiable
amino acid utilizations
can be used as building blocks for new proteins
degraded - used for nitrogen
Amino acid degradation stpes
1) removal of nitrogen
2) Carbon skeletons
of 20 amino acids funneled
into 7 molecules
most all amino acids can be converted to what
alpha ketoglutarate which gets converteed to glutamate
can be interconverted and reversed as needed
deamination of glutamate
forms NH4 ammonia
regenerates alpha ketoglutarate
can be used to make amino acids to create urea (piss)
urea users
terrestrial vertebrates / sharks
uricotelic animals / uric acid users
birds / reptiles
Carbamoyl Phosphate Synthetase functions
creates carbanoyl phosphate which is used to create urea
uses 2 ATP
NH4 to NH3
carbon comes from HCO3 - hydrates CO2
where does the nitrogens from urea come from?
NH4 - ammonia
aspartate
urea cycle locations
mostly in cytosol
partly in mitochondrial matrix
Ketogenic Amino Acids
- 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
Glucogenic Amino Acids
- 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
phenylketonuria
-deficiency of phenylalanine hydroxylase
-leads to accumulation of phenylalanine because it cannot be converted to tyrosine
- therapy: low phenylalanine diet
ubiquitin
is a protein that signals for protein degradation by a proteosome
Aminotransferases contain which cofactor?
PLP
The nitrogens in urea generated from the
urea cycle come from
NH4+ and aspartate
A given amino acid is found to be metabolized to
yield acetoacetyl-CoA. What can be said about
this amino acid?
It is ketogenic
nitrogenase enzyme action and protein composition
-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
ways in which nitrogen is fixed
lightning
biochemically - nitrogenase
artifically - haber bosch
nitrogen assimlation
alpha ketoglutarate to glutamate which adds a nitrogen
glutamate to glutamine
glutamate to glutamine
adds side chain reaction
glutamine synthesis
after which nitrogen is then incorporated by aminotransferases
alpha ketoglutarate to glutamate
adds nitrogen
glutamate dehydrogenase
carbons are provided to amino acid synthesis how
provided by intermediates of glycolytic pathway TCA cycle and pentose phosphate pathway
amino acid synthesis in microbes vs humans
microbes - all 20 basic amino acids
humans - 9 amino acids can not be synthesized that are essential
tetrahydrofolate
carrier of activated one carbon units
essential for syntehesis of many amino acids and nucleotides
derived from vitamin B9
What does beta in beta oxidation mean
Beta refers to the 3rd carbon from the carbonyl group (which includes the carbon in the carbonyl group)
DNA characteristics
- semi conservative
- requires activated precursors
- initiation begins at origin of replication
- replication is bidirectional
- 5’ to 3’ direction
DNA polymerase
- 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
Meselson and Stahl experiement
found semi conservative replication
added radioactive nitrogen to both DNA strand
cut open new daughter cells
found it to be semi conservative
consensus sequence
order of repeated residues found in different positions
DNAB
joins and uses helicase activaity to start unwinding the double helix
OriC
4 copies of a sequence that are preferred binding sites for DnaA
DNA-A
origin recognition protein-replication factor
primase
makes primer
leading stand
continuous
lagging strand
discontinous
helicase
uses ATP
unwinds DNA
primosome
multisubunit complex of DNA replication
DNA ligase
seals nicks in DNA backbone where primers were
topoisomerase
unwinds the negative and positive supercoils ahead of the replication fork
Processivity
-a measure of the ability of an enzyme to catalyze consecutive reactions without releasing its substrate
exonuclease
removes mismatched nucleotides from the 3’ END of DNA by hydrolysis
many use 3’ to 5’
DNA pol w exonuclease activity
DNA Pol 1
DNA pol 1
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
DNA pol 3
main DNA polymerase
highly processive
extremely fast
DNA pol 2
only able to proof-read / repair
more processive than DNA pol 1 less than DNA pol 3
slow
DNA damage types
errors in replication
reactive oxygen species
radiation
deamination
alkylating agents
what mutation is most detrimental
genes encoding for proteins that repair DNA
genes encoding the cell cycle
types of DNA damage
- Missing base
- Altered bases
- Wrong base
- Deletions/Insertions
- Strand Breakage
- Cross-Linked Strands
what does an alkylating agent do?
in alkylating agent is usually a tri oxide ring, it can interact with bases so it doesnt allow for correct copying
thymine dimers
caused by UV light
fixed by photolyase, using light
puts two thymines on each DNA strand bonded together
deamination
removal of nitrogen from
cytosine can convert to uracil
template strand is tagged how?
it is methylated to distinguish itself from the new DNA
mismatch repair
energetically costly, needed to maintain integrity of DNA
mRNA
messenger RNA
gets translated into a protein
3-5% of cellular RNA
tRNA
transfer RNA
takes amino acid to ribosomes for translation
15% of cellular RNA
rRNA
ribosomal RNA
uses mRNA and tRNA to create proteins
80% of cellular RNA
snRA
small nuclear RNA
component of spliceosome - helps destroy invasive RNA sequences
RNA characteristics
single stranded
uracil instead of thyamine
has secondary structure
less stable than DNA
requirements to create RNA from RNA polymerase
activated precursors - UTP ATP GTP CTP
template strand
alpha subunit of RNA pol
helps to find promoter sequence (site where transcription
begins)
- finds TATA box / pribnow
-not all promoter sequences do their job equally as well
strong promoter
- Promoter sequence corresponds closely to consensus sequence
- Transcribed frequently
weak promoter
- Multiple substitutions at consensus sequence
- Transcribed less frequently
sigma 70
standard promoter
sigma 54
nitrogen starvation promoter
sigma 32
heat shock promoter
sigma definition
- promoter sequence
- helps find site where transcription begins
- participates in initiation of RNA synthesis and disassociates
initiation of transcription
no primer required
unwinds 17bp segment of DNA
elongation of transcription
has transcription bubble
loss of sigma unit allows for tight binding of RNA pol to DNA template
continues til termination sequence
transcription bubble
17 bp long unwinding of DNA allowing for transcription in 5 -> 3 direction
termination of transcription
controlled as tightly as initiation
2 types
- factor independent termination
- factor dependent termination
factor independent termination
rich GC region creates hairpin loop of RNA
factor dependent termination
-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
repressors
bind to DNA and prevent transcription of a gene
can be modified by ligand binding (corepressors and inducers)
negative regulation
activators
bind to DNA and promote transcription of a gene
can be modified by ligand binding (corepressors and inducers)
positive regulation
regulatory proteins of transcriptions
activators and repressors
proteins that bind to specific sequences on DNA and either
promote or repress transcription
repressor with inducer
the repressor is bound the DNA and stops transcription
once inducer is bound the repressor unbinds to the DNA and allows transcription
repressor with corepressor
the repressor is not bound to DNA, allows for transcription
once corepressor is bound to the repressor, they bind to DNA and stop transcription
activator with inducer
activator is not bound to DNA, gene is not transcribed
once inducer binds with activator, they bind to DNA and allow for transcription
activator with corepressor
activator is bound to DNA, gene is transcribed
once corepressor binds with activator, they unbind to DNA and stop transcription
The sigma subunit of RNA Polymerase
recognizes what on DNA?
the pattern of nucleotides at position -10
Factor independent transcription termination
involves _______.
formation of stem-loop structures in the transcript
What type of molecule can bind to a repressor to
prevent the repressor from binding to DNA, and
subsequently allowing transcription of the gene?
inducer
what RNA type is most abundant in the cell
rRNA
transcription in prokaryotes
- 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
transcription in eukaryotes
- 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
processing RNA in prokaryotes
one mNA strand can have several different types of RNA in it
ribonucleases cut them each out
processing RNA in eukaryotes
- 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 )
introns
non coding RNA regions
exons
coding RNA regions
5’ cap
contributes to stability
protects 5’ tail from degredation
usually in eukaryotes mRNA
poly A tail
generated by poly A polymerase
adds 250 A residues
enhances translation efficiency
contributes to mRNA half life
What removes introns
- 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
specificity of removal of introns is what
extremely high
if one nucleotide off its a frameshift mutation
mutations involving the splicing of introns account for how much of genetic diseases
15%
group 1 introns
catalytic RNA
self splicing introns
needs a guanosine or guanine to initiation splicing of intron
Alternative splicing
Different combinations of
exons in the same gene may
be spliced into mature
mRNA producing distinct
forms of a protein
translation cell energy use
90% of cell energy use
start codon
AUG which codes for methionine
cricks adaptor hypothesis
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
tRNA composition
attaches to amino acid on 3’ end
anticodon loop, where amino acid attaches
single stranded
accurate translation requires
correct amino acid attached to proper tRNA
correct pairing between anticodon on tRNA and the codon on mRNA
attachment of amino acid to tRNA
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
prokaryotic ribosomes subunits
50S and 30S = 70S
these numbers are based on mass and density
3 steps of protein synthesis
1initiation
2 elongation
3 termination
read 5-3’
created N to C terminus
shine delgarno sequence
centered -10 from initiator codon
pairs w 16S RNA
starting codon is usually AUG / methionine
APE site
A - (aminoacyl) binding site
P - (peptidyl) attachment site- this is where the growing amino acid chain grows
E - exit site
IF 1 2 4
initiation factor
requires 1 GTP
EF tu
elongation factors
requires GTP for activity
energy required for amino acid being added to chain per step
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
tRNA movements in ribosome
A site - tRNA moves to P site
P site - tRNA moves to exit site
E site - tRNA exits ribosome
elongation requires which elongation factor
EF- G translocase
requires GTP
termination of translation
stop codon are recognized by release factor,
breaks linage between tRNA and peptide chain
differences in translation in prokaryotes and eukaryotes
ribosomes in prokaryotes 50S + 30S = 70s
ribosome in eukaryotes 60S + 40S = 80S
separated by nucleus and cytoplasm in eukaryotes
post translational modification of proteins
can occur post or co translationally
he first step in the degradation of amino acids is the transfer of the ______ to α-ketoglutarate by a(n) ______.
Group of answer choices
transfer of amino group to alpha ketoglutarate by an aminotransferase
The error rate in the selection efficiency (tendency to choose the correct nucleotide initially) of DNA polymerase is approximately ________
10^4-10^5
purines
GA
2 rings
pyraminidines
TC
1 ring
TC
pyramindines
GA
purines
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 ________.
cori cycle
