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102 Cards in this Set

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Urea Cycle: function
RLE:
Activator:
Inhibitor:
removes toxic NH4+
RLE: CPS 1
Activator: N-acetylglutamate
Inhibitor: None
what is the only pathway that never turns off?
urea cycle
urea cycle: where is the major location
where is it excreted?
why does liver failure lead to death?
90% in Liver:
• Excreted in-GI tract
• Liver failure leads to death due to GABA connection
where does the other 10% of the urea cycle
what does this leads to and why?
what enzyme does it have and what does it splits off?
10% in Kidney Collecting Duct:
• Leads to increased BUN (dying cells lead to ⇧BUN)
• Has glutaminase, which splits off ammonia
what the components of the urea cycle?
"Ordinarily Careless Crappers Are Also Frivolous About Urination"
Ornithine
Carbamoyl phosphate
Citrulline
• Asp
• Arginosuccinate
• Fumarate
• Arg
• Urea
which compund in the urea cycle goes in from mitochondria?
Carbamoyl phosphate
where does fumarate go?
Fumarate => out to malate => kreb cycle
where does urea go?
out to the kidneys to be excreted
Glu + NADH ⇨ αKG + NH4+ NAD
what enzyme does it use?
what does it liberate?
• Uses glutamate Dehydrogenase
• Liberates amonia for Urea Cycle
NH4+ + CO2 + 2ATP ~> Carbomyl Phosphate
enzyme/rate limiting enzyme:
Allosteric activator:
• Carbamyl phosphate synthetase (CPS1)
• Rate limiting enzyme
• Allosteric activator: N-acetylglutamate
Carbamyl Phosphate ~> Citrulline
enzyme:
Ornithine transcarbamylase
Citrulline + Asp ~> Arginosuccinate
enzyme
aa and where is it from?
• Arginosuccinate synthetase
• Asp (from Mallate-Aspartate shuttle)
Arginosuccinate ~> Arginine + Fumarate
arginosuccinate Lyase
Arginine~> Urea+ Ornithine
what does this reaction do?
Urea gets rid of Nitrogen waste and C02
Hepatorenal Syndrome: pathogenesis
Gln -> Glu + NADH -> αKG + NH4+
Liver failure occurs first "hepato---"
High ammonia suppresses glutaminase in kidneys, leading to renal failure
• No way to get rid of ammonia, leading to coma and death
Hepatorenal Syndrome: tx
Kidney can still be transplanted, as long as it gets away from the high amonnia
Urea Cycle Defects:
how to choose where is the defect
what happens when there is an increase in NH4 levels?
• Increase in blood NH4+ levels -> ⇧GABA -> ⇧serum pH
• when trying to detect which enzyme is the defect, pick the earlier enzyme in the list. If orotic Acid mentioned
chose the later enzyme in the list.
fatty Acid Synthesis:
3 Functions:
fuel, padding, insulation
AcetylCoA⇨A(enzyme)⇨FA
Activator:
Inhibitors: (2)
RLE:
A: AcCoA carboxylase
Activator: Citrate
Inhibitors: palmitic acid, Malonyl CoA
RLE: Acetyl CoA carboxylase
Acetyl CoA Carboxylase:
RLE
cofactor
what does it make?
• Rate limiting enzyme for fatty acid synthesis
• Acetyl CoA -> Malonyl CoA
• Biotin is cofactor
Acetyl CoA Carboxylase:
need what for energy
activator
inhibitors
Needs ATP
Activator: Citrate
Inhibitor: Malonyl CoA and Palmitic Acid
Citrate -> Acetyl CoA + OAA:
enzyme
energy
• ciitrate lyase
• uses ATP
Fatty Acid Synthase:
describe
how many enzyme does it have?
• Largest quarternary enzyme in biochemistry
• Seven enzymes
Fatty Acid Rules:
maximum carbons
DB:
saturated
unsaturated
• C16 = max limit "Palmitic Acid"
• Double bonds must be 3 Carbons apart (Ex: C4-C3)
• No double bonds after C:10 (Ex: C10 okay b/c it is C10=C11)
• Saturated (w/ H) -> no double bonds
• Unsaturated -> it-has double-bonds
calculate How many ATP used
number of C-1
How many rounds?
how many ATP?
(1/2C)-1
2ATPs per round
How many NAPDH used for the fatty acid process?
(1/2C-1)X 2
what are the 2 Essential Fatty Acids:
which one is used to make arachadonic acid?
• Linolinic
• Linoleic (used to make arachadonic acid)
Only source is from diet; body can not make these
Cholesterol function (3)
membrane component
precursor of bile acids
hormones => droplets
AcetylCoA Mevalonate⇨A⇨ mevalonate ⇨ cholesterol
enzyme and inhibitor
HMG CoA reductase
Inhibitor: Dietary cholesterol
Phospholipids: function
Function: components of membranes and lipoproteins
how are phospholipids made?
Glycerol -> (Liver: Glycerol kinase) -> Gly-3P<=(Gly-3P dehydro) <~DHAP

the Gly-3P->phosphatidic acid and then make both triglycerides and phospholipids
what are 5 the different types of phospholipids?
Lecithin
Cephalin
phosphatidyl isositol
Phosphatidyl Serine
Cardiolipin
Lecithin
phosphatidyl Choline (emulsify fat with bile, also part of surfactant)
Cephalin
phosphatidyl Ethanolamine
Cardiolipin
Anti-cardiolipin Ab => recurrent abortions-, clotting then bleeding
Sphingolipids: function and name them and how are they made?
Function: component of membranes/neuronal tissue => bilayer vesicles
Sphingosine -> Ceramide -> Sphingomyelin+ Cerebrosides,Gangliosides
• Sphingosine
• Cerebroside
• Ganglioside
Sphingosine
palmitoylCoA + serine
Cerebroside
ceramide + UDP sugar
Ganglioside
a "gang" of cerebrosides
Tay-Sachs
hexosaminidase A deficiency=> blindness, incoordination, dementia
Sandhoffs
hexosaminidase A/B deficiency
Gaucher's
glucocerebrosidase deficiency.=> wrinkled tissue MP
"wrinkled grouch"
Neimann-Pick
enzyme deficiency
bodies
sphingomyelinase deficiency => zebra bodies (demyelination)
Fabry's
mode of inheritance
enzyme
presentation
(XL): α galactosidase-def =>corneal clouding, attacks baby's kidneys
Krabbe's
enzyme deficiency
bodies
galactocerebrosidase deficiency=> globoid bodies
Metachromatic Leukodystrophy
arylsulfatase deficiency => childhood MS
Hurler's
mode of inheritance
enzyme deficiency
better/worse form
(AR):L-iduronidase deficiency, worse form
Hunter's
mode of inheritance
enzyme defieciency
(XL):α L-iduronidase deficiency
"X marks the hunter's target"
Cherry-red macula
tay Sachs,Neimann-pick (hepatosplenomegaly)
Gargoyle-face
Gaucher's, Hurler's
"hurl when you see a gouchy gargoyle face"
2 X-linked diseases
fabry's, hunter's
function of nucleotides
Fxn: Carriers (Ex: UDP), Energy (Ex: ATP), 2nd messengers (Ex: cAMP)
Purine synthesis and degradation
when is the salvage pathway used? and denovo pathway?
Low PRPP => salvage pathway (uses Gly, take bases from dying cells)
High PRPP => de novo synthesis (uses Ribose-5P in rapid growth periods)
Gly, Ribose-5P⇨A(enzyme)⇨AMP/GMP⇨B(enzyme)⇨uric acid
A: HGPRT, PRPP
B: xanthine oxidase
what drug inhibits xanthine oxidase?
allopurinol
Lesch-Nyhan
type of disease
deficiency
what does this lead to? (3)
purine disease
(HGPRT deficiency) => gout, neuropathy, self-mutilation
Gout
type of disease
pathogenesis and what causes crystals to form?
what does this lead to?
Purine Disease:
(excess uric acid, dehydration causes crystals)
=> podagra
SCID:
type of disease
enzyme deficiency
what does this lead to?
Purine Disease: (adenosine deaminase deficiency) = > decreases rapidly dividing cells by inhibiting ribonucleotide reductase
what is this reaction and name the enzymes
Gln⇨A⇨Asp transcarbamylase,
Orotic acid⇨B⇨UMP⇨C02 + Urea
Pyrimidine synthesis and degradation
A: Asp transcarbamylase, CPS-II
B: THF
white diaper crystals
type of disease
Pyrimidine Diseases:
excess orotic acid
Types of RNA:
rRNA
mRNA
tRNA
rRNA - most abundant, comes from nucleolus
mRNA- most variable, largest "Big mama"
tRNA- smallest (AUG= start codon, UAA, UAG, UGA =stop codons)
SnRNPs
Types of DNA:
A:
B:
Z:
base
Types of DNA:
A: R hand helix, 10 bp per turn
B: R hand helix, 11 bp per turn -we have this
Z: L hand helix 12 bp per turn - prokaryotes have this, more compact
Base- closest to neighbor 4 doors down (3.6 bases per turn)
big picture of DNA synthesis and replication, read in what direction?
DNA synthesis -> Replication (make 2nd strand) -> Transcription (make DNA babies)
Replicate: 5' -> 3' (RNA Pol replicates it with "U")
Read: 3' -> 5'
DNA synthesis
G0 stage:
what cells stays on this stage?
what cells do not?
do nothing (cardiac, neurons= permanent cells)
(liver, kidney can be bribed to leave)
DNA synthesis
G1 stage:
make all proteins for DNA synthesis
DNA synthesis
S phase: (2)
do synthesis (and make centrioles)
DNA synthesis
G2 phase:
make all proteins for mitosis
M: and its 5 phases
>>do mitosis
Interphase
Prophase
Metaphase
Anaphase
Telophase
Interphase
intermission
Prophase
nuclear membrane dissolves; chromosomes clump, then pair up
Metaphase
line up in the middle
Anaphase
what may happen in this phase?
pull apart, non-disjunction may occur
Telophase
cell tears in two
Histones: function, H1, H2a, H2b, H3, H4
wrap around DNA
H1 -> linker protein
H2a, H2b, H3, H4 -> nucleosome
what is the only virus that inhibits proofreading?
HIV
Heterochromatin
tightly coiled
Euchromatin
loose (10nm fibers)
DNA Replication: Prokatyotes
DNA-A:
SSB:
Helicase:
Primase:
DNA Replication: Prokatyotes
DNA-A: uses ATP to denature polyA tail
SSB: stabilizes 2 single strands
Helicase: uses ATP to break bonds
Primase: RNA Pol lays down 8-10 nucleotides
DNA Replication: Prokatyotes
DNA Pol III:
DNA Pol I:
DNA ligase:
DNA Pol III: 5' -> 3' polymerase, has 3' -> 5' exonuclease
DNA Pol I: DNA Pol III fxn plus 5' ~> 3' exonuclease
DNA ligase: makes final bond
DNA Replication: Prokatyotes
topoisomerase function and its two types and function
Topisomerase: removes supercoils
• Topo I cuts one strand, spins around once, removes one supercoil
• Topo II can insert a negative supercoil
DNA Replication: Eukaryotes
α=
β=
y =
δ=
ε =
(multiple replication forks and are bidirectional)
α= primase
β= DNA Pol I
y = mitochondrial DNA only "Gamma = The Geek"
δ= DNA Pol III leading strand
Heterochromatin = tightly coiled
Euchromatin = loose (10nm fibers)
ε = DNA Pol III lagging strand
Methyl Donors:
Biotin
THF
SAM
Biotin - for carboxylation
THF - for nucleotides
SAM - for all other rxns
monocistronic
Euks are monocistronic:
1 mRNA -> 1 protein
polycistronic
Proks are polycistronic:
1 mRNA -> many proteins
lab test:
Southen blot
Northen blot
"SNoW
"DRoP"
Southern blot: DNA
Northern blot: RNA
DNA Transcription: components
replicates 1 gene
Zinc Fingers
RNA Pol
Core enzyme
Holoenzyme
Promoter
Enhancer
Initiator
Repressor
Post-Transcription Modification:
1) splice away introns, smoosh exons together
2) add 3' polyA tail -> sticks to polyU "Shine Delgano sequence" on 30S
3) add 5' guanosine cap
4) transport to cytoplasm
5) methylate guanosine
6) ready for translation
Protein Translation:
#GTP
30S
50S
takes 4 GTP per amino acid
• tRNA 3' end: CCA-aa, uses 2 GTP to activate
• 30S subunit made = > initiation factors released (IF:)
• 5OS subunit made => creates A, P sites
Protein Translation II
how are the aa incoporated?
AUG -> falls into P site => Met (Euks) or fMet (Proks)
• Elongation factors released (EF:) - brings tRNA over, uses 1 GTP
• Peptidyl transferase - makes peptide bond
• Translocation- costs another GTP
Silent mutation
same aa
Point mutation
change 1 base
transition
its a type of point mutation
1 purine to another purine
transversion
change families from purine to pyrimidine "converted"
point mutation
Frameshift:
onset of diseaes
insert or delete 1-2 bases => early onset diseases,
Missense:
onset of disease
mistake =>late onset diseases
Nonsense:
onset of diseases
stop codon (UAA, UGA, UAG) => early onset diseases
how do we duplicate DNA in the lab?
PCR = most specific test
1) add a ton of primers
2) wash off excess
3) add heat-stable DNA
polymerase
4) denature
Label thymidine - DNA
Label cytosine- RNA
Pyrimidines
how are cystine and thymidine made for uracil
C,U,T "CUT the py''
U -> (CH3) -> T
U -> (NH3) -> C
Purines:
A,G
Higher Tm:
C-G (more bonds)
Guanine vs Guanosine
= Base
= Base + Sugar