Ppal99 Dissecting The Usmle 1,2,3 Amino Acids/fatty Acids/nucleotides

Front 1

Urea Cycle: function
RLE:
Activator:
Inhibitor:

Back 1

removes toxic NH4+
RLE: CPS 1
Activator: N-acetylglutamate
Inhibitor: None

Front 2

what is the only pathway that never turns off?

Back 2

urea cycle

Front 3

urea cycle: where is the major location
where is it excreted?
why does liver failure lead to death?

Back 3

90% in Liver:
• Excreted in-GI tract
• Liver failure leads to death due to GABA connection

Front 4

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?

Back 4

10% in Kidney Collecting Duct:
• Leads to increased BUN (dying cells lead to ⇧BUN)
• Has glutaminase, which splits off ammonia

Front 5

what the components of the urea cycle?

Back 5

"Ordinarily Careless Crappers Are Also Frivolous About Urination"
Ornithine
Carbamoyl phosphate
Citrulline
• Asp
• Arginosuccinate
• Fumarate
• Arg
• Urea

Front 6

which compund in the urea cycle goes in from mitochondria?

Back 6

Carbamoyl phosphate

Front 7

where does fumarate go?

Back 7

Fumarate => out to malate => kreb cycle

Front 8

where does urea go?

Back 8

out to the kidneys to be excreted

Front 9

Glu + NADH ⇨ αKG + NH4+ NAD
what enzyme does it use?
what does it liberate?

Back 9

• Uses glutamate Dehydrogenase
• Liberates amonia for Urea Cycle

Front 10

NH4+ + CO2 + 2ATP ~> Carbomyl Phosphate
enzyme/rate limiting enzyme:
Allosteric activator:

Back 10

• Carbamyl phosphate synthetase (CPS1)
• Rate limiting enzyme
• Allosteric activator: N-acetylglutamate

Front 11

Carbamyl Phosphate ~> Citrulline
enzyme:

Back 11

Ornithine transcarbamylase

Front 12

Citrulline + Asp ~> Arginosuccinate
enzyme
aa and where is it from?

Back 12

• Arginosuccinate synthetase
• Asp (from Mallate-Aspartate shuttle)

Front 13

Arginosuccinate ~> Arginine + Fumarate

Back 13

arginosuccinate Lyase

Front 14

Arginine~> Urea+ Ornithine
what does this reaction do?

Back 14

Urea gets rid of Nitrogen waste and C02

Front 15

Hepatorenal Syndrome: pathogenesis

Back 15

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

Front 16

Hepatorenal Syndrome: tx

Back 16

Kidney can still be transplanted, as long as it gets away from the high amonnia

Front 17

Urea Cycle Defects:
how to choose where is the defect
what happens when there is an increase in NH4 levels?

Back 17

• 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.

Front 18

fatty Acid Synthesis:
3 Functions:

Back 18

fuel, padding, insulation

Front 19

AcetylCoA⇨A(enzyme)⇨FA
Activator:
Inhibitors: (2)
RLE:

Back 19

A: AcCoA carboxylase
Activator: Citrate
Inhibitors: palmitic acid, Malonyl CoA
RLE: Acetyl CoA carboxylase

Front 20

Acetyl CoA Carboxylase:
RLE
cofactor
what does it make?

Back 20

• Rate limiting enzyme for fatty acid synthesis
• Acetyl CoA -> Malonyl CoA
• Biotin is cofactor

Front 21

Acetyl CoA Carboxylase:
need what for energy
activator
inhibitors

Back 21

Needs ATP
Activator: Citrate
Inhibitor: Malonyl CoA and Palmitic Acid

Front 22

Citrate -> Acetyl CoA + OAA:
enzyme
energy

Back 22

• ciitrate lyase
• uses ATP

Front 23

Fatty Acid Synthase:
describe
how many enzyme does it have?

Back 23

• Largest quarternary enzyme in biochemistry
• Seven enzymes

Front 24

Fatty Acid Rules:
maximum carbons
DB:
saturated
unsaturated

Back 24

• 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

Front 25

calculate How many ATP used

Back 25

number of C-1

Front 26

How many rounds?
how many ATP?

Back 26

(1/2C)-1
2ATPs per round

Front 27

How many NAPDH used for the fatty acid process?

Back 27

(1/2C-1)X 2

Front 28

what are the 2 Essential Fatty Acids:
which one is used to make arachadonic acid?

Back 28

• Linolinic
• Linoleic (used to make arachadonic acid)
Only source is from diet; body can not make these

Front 29

Cholesterol function (3)

Back 29

membrane component
precursor of bile acids
hormones => droplets

Front 30

AcetylCoA Mevalonate⇨A⇨ mevalonate ⇨ cholesterol
enzyme and inhibitor

Back 30

HMG CoA reductase
Inhibitor: Dietary cholesterol

Front 31

Phospholipids: function

Back 31

Function: components of membranes and lipoproteins

Front 32

how are phospholipids made?

Back 32

Glycerol -> (Liver: Glycerol kinase) -> Gly-3P<=(Gly-3P dehydro) <~DHAP

the Gly-3P->phosphatidic acid and then make both triglycerides and phospholipids

Front 33

what are 5 the different types of phospholipids?

Back 33

Lecithin
Cephalin
phosphatidyl isositol
Phosphatidyl Serine
Cardiolipin

Front 34

Lecithin

Back 34

phosphatidyl Choline (emulsify fat with bile, also part of surfactant)

Front 35

Cephalin

Back 35

phosphatidyl Ethanolamine

Front 36

Cardiolipin

Back 36

Anti-cardiolipin Ab => recurrent abortions-, clotting then bleeding

Front 37

Sphingolipids: function and name them and how are they made?

Back 37

Function: component of membranes/neuronal tissue => bilayer vesicles
Sphingosine -> Ceramide -> Sphingomyelin+ Cerebrosides,Gangliosides
• Sphingosine
• Cerebroside
• Ganglioside

Front 38

Sphingosine

Back 38

palmitoylCoA + serine

Front 39

Cerebroside

Back 39

ceramide + UDP sugar

Front 40

Ganglioside

Back 40

a "gang" of cerebrosides

Front 41

Tay-Sachs

Back 41

hexosaminidase A deficiency=> blindness, incoordination, dementia

Front 42

Sandhoffs

Back 42

hexosaminidase A/B deficiency

Front 43

Gaucher's

Back 43

glucocerebrosidase deficiency.=> wrinkled tissue MP
"wrinkled grouch"

Front 44

Neimann-Pick
enzyme deficiency
bodies

Back 44

sphingomyelinase deficiency => zebra bodies (demyelination)

Front 45

Fabry's
mode of inheritance
enzyme
presentation

Back 45

(XL): α galactosidase-def =>corneal clouding, attacks baby's kidneys

Front 46

Krabbe's
enzyme deficiency
bodies

Back 46

galactocerebrosidase deficiency=> globoid bodies

Front 47

Metachromatic Leukodystrophy

Back 47

arylsulfatase deficiency => childhood MS

Front 48

Hurler's
mode of inheritance
enzyme deficiency
better/worse form

Back 48

(AR):L-iduronidase deficiency, worse form

Front 49

Hunter's
mode of inheritance
enzyme defieciency

Back 49

(XL):α L-iduronidase deficiency
"X marks the hunter's target"

Front 50

Cherry-red macula

Back 50

tay Sachs,Neimann-pick (hepatosplenomegaly)

Front 51

Gargoyle-face

Back 51

Gaucher's, Hurler's
"hurl when you see a gouchy gargoyle face"

Front 52

2 X-linked diseases

Back 52

fabry's, hunter's

Front 53

function of nucleotides

Back 53

Fxn: Carriers (Ex: UDP), Energy (Ex: ATP), 2nd messengers (Ex: cAMP)

Front 54

Purine synthesis and degradation
when is the salvage pathway used? and denovo pathway?

Back 54

Low PRPP => salvage pathway (uses Gly, take bases from dying cells)
High PRPP => de novo synthesis (uses Ribose-5P in rapid growth periods)

Front 55

Gly, Ribose-5P⇨A(enzyme)⇨AMP/GMP⇨B(enzyme)⇨uric acid

Back 55

A: HGPRT, PRPP
B: xanthine oxidase

Front 56

what drug inhibits xanthine oxidase?

Back 56

allopurinol

Front 57

Lesch-Nyhan
type of disease
deficiency
what does this lead to? (3)

Back 57

purine disease
(HGPRT deficiency) => gout, neuropathy, self-mutilation

Front 58

Gout
type of disease
pathogenesis and what causes crystals to form?
what does this lead to?

Back 58

Purine Disease:
(excess uric acid, dehydration causes crystals)
=> podagra

Front 59

SCID:
type of disease
enzyme deficiency
what does this lead to?

Back 59

Purine Disease: (adenosine deaminase deficiency) = > decreases rapidly dividing cells by inhibiting ribonucleotide reductase

Front 60

what is this reaction and name the enzymes
Gln⇨A⇨Asp transcarbamylase,
Orotic acid⇨B⇨UMP⇨C02 + Urea

Back 60

Pyrimidine synthesis and degradation
A: Asp transcarbamylase, CPS-II
B: THF

Front 61

white diaper crystals
type of disease

Back 61

Pyrimidine Diseases:
excess orotic acid

Front 62

Types of RNA:
rRNA
mRNA
tRNA

Back 62

rRNA - most abundant, comes from nucleolus
mRNA- most variable, largest "Big mama"
tRNA- smallest (AUG= start codon, UAA, UAG, UGA =stop codons)
SnRNPs

Front 63

Types of DNA:
A:
B:
Z:
base

Back 63

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)

Front 64

big picture of DNA synthesis and replication, read in what direction?

Back 64

DNA synthesis -> Replication (make 2nd strand) -> Transcription (make DNA babies)
Replicate: 5' -> 3' (RNA Pol replicates it with "U")
Read: 3' -> 5'

Front 65

DNA synthesis
G0 stage:
what cells stays on this stage?
what cells do not?

Back 65

do nothing (cardiac, neurons= permanent cells)
(liver, kidney can be bribed to leave)

Front 66

DNA synthesis
G1 stage:

Back 66

make all proteins for DNA synthesis

Front 67

DNA synthesis
S phase: (2)

Back 67

do synthesis (and make centrioles)

Front 68

DNA synthesis
G2 phase:

Back 68

make all proteins for mitosis

Front 69

M: and its 5 phases

Back 69

>>do mitosis
Interphase
Prophase
Metaphase
Anaphase
Telophase

Front 70

Interphase

Back 70

intermission

Front 71

Prophase

Back 71

nuclear membrane dissolves; chromosomes clump, then pair up

Front 72

Metaphase

Back 72

line up in the middle

Front 73

Anaphase
what may happen in this phase?

Back 73

pull apart, non-disjunction may occur

Front 74

Telophase

Back 74

cell tears in two

Front 75

Histones: function, H1, H2a, H2b, H3, H4

Back 75

wrap around DNA
H1 -> linker protein
H2a, H2b, H3, H4 -> nucleosome

Front 76

what is the only virus that inhibits proofreading?

Back 76

HIV

Front 77

Heterochromatin

Back 77

tightly coiled

Front 78

Euchromatin

Back 78

loose (10nm fibers)

Front 79

DNA Replication: Prokatyotes
DNA-A:
SSB:
Helicase:
Primase:

Back 79

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

Front 80

DNA Replication: Prokatyotes
DNA Pol III:
DNA Pol I:
DNA ligase:

Back 80

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

Front 81

DNA Replication: Prokatyotes
topoisomerase function and its two types and function

Back 81

Topisomerase: removes supercoils
• Topo I cuts one strand, spins around once, removes one supercoil
• Topo II can insert a negative supercoil

Front 82

DNA Replication: Eukaryotes
α=
β=
y =
δ=
ε =

Back 82

(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

Front 83

Methyl Donors:
Biotin
THF
SAM

Back 83

Biotin - for carboxylation
THF - for nucleotides
SAM - for all other rxns

Front 84

monocistronic

Back 84

Euks are monocistronic:
1 mRNA -> 1 protein

Front 85

polycistronic

Back 85

Proks are polycistronic:
1 mRNA -> many proteins

Front 86

lab test:
Southen blot
Northen blot

Back 86

"SNoW
"DRoP"
Southern blot: DNA
Northern blot: RNA

Front 87

DNA Transcription: components

Back 87

replicates 1 gene
Zinc Fingers
RNA Pol
Core enzyme
Holoenzyme
Promoter
Enhancer
Initiator
Repressor

Front 88

Post-Transcription Modification:

Back 88

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

Front 89

Protein Translation:
#GTP
30S
50S

Back 89

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

Front 90

Protein Translation II
how are the aa incoporated?

Back 90

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

Front 91

Silent mutation

Back 91

same aa

Front 92

Point mutation

Back 92

change 1 base

Front 93

transition

Back 93

its a type of point mutation
1 purine to another purine

Front 94

transversion

Back 94

change families from purine to pyrimidine "converted"
point mutation

Front 95

Frameshift:
onset of diseaes

Back 95

insert or delete 1-2 bases => early onset diseases,

Front 96

Missense:
onset of disease

Back 96

mistake =>late onset diseases

Front 97

Nonsense:
onset of diseases

Back 97

stop codon (UAA, UGA, UAG) => early onset diseases

Front 98

how do we duplicate DNA in the lab?

Back 98

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

Front 99

Pyrimidines
how are cystine and thymidine made for uracil

Back 99

C,U,T "CUT the py''
U -> (CH3) -> T
U -> (NH3) -> C

Front 100

Purines:

Back 100

A,G

Front 101

Higher Tm:

Back 101

C-G (more bonds)

Front 102

Guanine vs Guanosine

Back 102

= Base
= Base + Sugar