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NPLEX I 2024 > Biochem (Genetic + Molecular) > Flashcards

Biochem (Genetic + Molecular) Flashcards

1
Q

chemical makeup of the body

A

92% sulfur
8% - calcium, potassium, chloride, sodium, magnesium, trace minerals

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2
Q

why is carbon so special?

A
  • atomic number 6 (6 protons+, 6 electrons-)
  • 2 are in inner shell (cant bind)
  • 4 in outer shell - can form 4 stable covalent bonds
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3
Q

strong bonds

A

covalent
- sharing of electrons
- no electron transfer
- ex: C-C bonds (very stable, nonpolar, difficult to cleave)

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4
Q

weak bonds

A
  • vander waals: transient dipoles of atoms/molecules
  • hydrophobic: self association with other non-polar compounds
  • hydrogen: R-OH, electroneg, partial pos and neg charges
  • ionic: full + or - charges, complete transfer of electrons from one atom to another, ex: NaCl
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5
Q

nucleophilic substituion rxn

A

A: + B–X > A–B + X:

A = nucleophile
B = electrophile
X = leaving group

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6
Q

isomerization rxn

A

intramolecular shift of atoms or groups

Ex: Ch3 group moving from one spot to another

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7
Q

elimination rxn

A

double bond is formed when atoms are removed

ex: removinng H and OH group and forming new molecule plus water (double bond in new molecule since two side chains were removed)

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8
Q

hydrolysis rxn

A

cleavage of covalent bond by wayer

molecule + water > two new molecules

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9
Q

oxidation-reduction (redox) rxn def

A

transfer of electrons from one molecule to another (they can occur at the same time!)

oxidizing agent gets reduced
reducing agent gets oxidized

OILRIG

oxidaiton = loss of electrons, loss of hydrogen, gain of oxygen, gain of double bond

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10
Q

oxidation-reduction (redox) rxn requirements and example

A

every shift in oxidation state (either direction) needs:
- enzyme (BLANK dehydrogenase)
- cofactor (NAD/NADH, NADP/NADPH, FAD/FADH)

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11
Q

most important side chains

A
  • Carbon oxygen groups
  • carbon sulfur groups
  • carbon nitrogen groups
  • esters and amides
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12
Q

acid
alcohol
aldehyde/keton
alkene
alkane

rank most reduced to most oxidized

A

(most reduced) alkane > alkene > alcohol - aldehyde/keton > acid (most oxidized)

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13
Q

acids vs bases

A

acids = proton (H+) donors

bases = proton acceptors

pH = - log (H+]

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14
Q

what happens to acid in water?

A

strong acid - dissociates completely in water (Ex: HCL > H+ + Cl-)

weak acid - dissociates at a rate determined by equilibrium constnat (Ka)
- ex: -COOH > H+ + COO-

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15
Q

when does pKa = pH

A

when
- the acid (HA) has donated half of its H+
- the acid (HA) is 1/2 deprotonated
- [HA] = [A-]

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16
Q

acids in normal blood

A

all weak
- carbonic acid (CO2 from TCA)
- lactic acid (anaerobic glycolysis)
- pyruvic acid (glycolysis)
- citric acid (TCA and citrus fruit)
- acetoacetic acid (fatty acid oxidation into ketone bodies)
- B-hydroxybutric acid (FA oxidation into ketone bodies)
- acetic acid (ethanol metabolism)

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17
Q

can acids act as buffers?

A

acids can act as buffers within 1 point (+/-) of pKg

ex: bicarb buffer system

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18
Q

essential amino acids

A

NEED TO CONSUME FROM DIET - FOUND IN COMPLETE PROTEINS

PVT TIM HaLL
- phenylalanine
- valine
- tryptophan
- threonine
- isoleucine
- methionine
- histidine
- lysine
- leucine

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19
Q

nonpolar AAs

A

glycine
alanine
proline
valine
leucine
isoleucine
methionine
tryptophan
phenylalanine
cysteine

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20
Q

aromatic amino acid

A

phenylalanine
tyrosine
tryptophan

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21
Q

polar, uncharged AAs

A

asparagine
glutamine
serine
threonine

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22
Q

sulfur containing amino acids

A

methionine
cysteine

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23
Q

polar, charged AAs

A

neg (acidic)
- aspartate
- glutamate

pos (basic)
- arginine
- lysine
- histidine

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24
Q

what AA is the best buffer for physiologic pH?

A

histidine

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25
zwitterion form
molecule has a separate pos and neg charge
26
isoelectric point
pH at which a particular molecule carries no net charge
27
protein structures
- primary (planar): covalent/peptide bonds between AAs - secondary (a-helices and B-sheets): hydrogen bonds bw C=O and N-H - tertiary: H bonds, electrostatic, vander waals, covalent/disulfide bonds between R groups - quarternary: same as tertiary, bw protein subunits
28
simple proteins vs conjugated proteins
simple: contain only AA (albumin, keratin) conjugated: simple protein + non-protein part; prosthetic groups include: - glycoprotein (carb) - lipoprotein (fat) - hemoproteins (heme molecule)
29
protein functions
- catalysis: enzymes - structure: collagen, elastin - movement: actin, myosin - defense: fibrin, thrombin, Ig - regulation: insulin, glucagon, GH - transport: hemoglobin, lipoproteins, Na+/K+ ATP ase
30
oxidoreductases
catalyzes the transfer of electrons from one molecule to another - dehydrogenase - hydroxylase - oxidase - oxygenase - peroxidase - reductase
31
oxygenases
incorporate oxygen into organic substrates
32
peroxidases
reduction of hydrogen peroxide and hydroperoxides
33
reductases
catalyze reduction
34
dehydrogenases
oxidize substrates by transferring one or more hydride ions
35
oxidases
oxygen as the hydrogen or electron accepter
36
hydroxylases
add hydroxyl group to substrates
37
transferases
catalyze transfer of speciifc functional group from one molecule to another - kinases (transfer phosphate) - transaminase (amino gropu from a-AA > a-keto acid) - synthase (joint 2 molecules while ATP hydrolysis occurs)
38
hydrolases
use water to break chemical bond
39
phosphatase
removes phosphate group from a protein
40
lyases
breaks bond by means other than hydrolysis - aldolase - decarboxylase (removes COOH groups from acidic substrates) - thiolase - dehydrase - synthase
41
ligases
join 2 sep molecules together - carboxylase - synthetase
42
endogenous/endergonic rxn
-energy required for rxn to proceed - non-spontaneous - +delta G
43
exogenous/exergonic rxn
- energy release by rxn - spontaneous, favorable - neg delta G
44
what is michaelis-menten equation used for
regulation of enzymes via substrate/product concentration
45
vmax
max rate of rxn - the point where all active sites are bound to substrate (enzyme is saturated)
46
purine degradation forms what?
uric acid
47
purine degradation waste products
ammonium
48
important enzyme involved in purine degradation and its cofactor
xanthine oxidase Mn (molybdenum)
49
what are purines and pyrimidines
nitrogenous bases found in nucleic acids (DNA and RNA) purine: two ring structure pyrimidines: one ring structure
50
major purines and what they bind with and other involvements
Adenine: H bonds with thymine in DNA, uracil in RNA (part of ATP, AMP, cAMP) Guanine: H bonding with cytosine in DNA and RNA (part of GTP)
51
carbamoyl phosphate synthetase I (CPSI) path source of N location activator inihibitor
path: urea cycle source of N: NH4+ location: mitochondria activator: N-acetylglutamate inhibitor: none
52
carbamoyl phosphate synthetase II (CPSII) path source of N location activator inihibitor
path: pyrimidine biosynthesis source of N: glutamine location: cytosol activator: PRPP inihibitor: UTP
53
what can serve as an analogue of uracil or thymine in DNA synthesis
5 fluorouracil
54
products of pyrimidine degradation
malonate, methylmalonate
55
waste product of pyrimidine degradation
ammonia
56
what is required to break down thymine in pyrimidine degradation
NADPH
57
location of DNA replication
nucleus of eukaryotic cells
58
location of transcription to RNA
nucleus of eukaryotes cytoplasm of prokaryotes
59
location of translation
ribosomes in cytoplasm
60
where does transamination of protein breakdown occur? what enzymes perform this?
cytosol - alanine- and aspartate- aminotransferase - transaminases use vit B6 in form of PLP
61
what AA do not participate in transamination
lysine threonine
62
oxidative deamination rxn
glutamate > a-ketoglutarate via glutamate dehydrogenase (needs NAD or NADP) release NH3 as ammonium
63
oxidative deamination upregulation
GDP, ADP, low energy states
64
oxidative deamination down regulation
GTP, ATP, high energy states
65
urea cycle location
mitochondria and cytosol of liver cells
66
rate limiting step of urea cycle
CPSI - upregulated by NAG - stim by arginine
67
most common def of urea cycle
ornithine transcarbamoylase enzyme def
68
hemoglobin
globular protein with heme prosthetic group that carry oxygen
69
hemoglobin vs myoglobin
hemoglobin - carries 4 oxygen molecules in blood streatm - two a chains, two b chains myoglobin - carries 1 oxygen molecule intracellularly - single a chain - high affinity for oxygen
70
hemoglobin structure conformations
- deoxy-HGB: taut, low affinity for oxygen - oxy-HGB > relaxed, high affinity for oxygen
71
what AA is present at the active site of hemoglobin chain folding? what AA sub takes place with sickle cell anemia?
normally glutamic acid replaced with valine in sickle cell
72
types of HGB/Hb most to least common and their chain compo
HbA - a2b2 HbA1C - a2b2glucose HbA2 - a2g2 HbF - a2y2
73
iron forms and their binding properties
- Fe2+ (ferrous): binds oxygen, CO (carboxyhemoglobin) - Fe3+ (ferric): binds CN- (methemoglobin), does NOT bind oxygen
74
left shift in graph meaning | graph comparing PP oxygen to saturation with oxygen
increased affinity for oxygen - H+ reduced (high pH) - CO2 reduced - 2,3-BPG reduced
75
right shift in graph meaning | graph comparing PP oxygen to saturation with oxygen
decreased affinity for oxygen (all three stabilize taut form) - inc H+ (low pH) - bohr effect; H binds several ionizable groups on Hgb - elevated CO2: co2 directly inc H, and binds directly to uncharegd AA on Hgb > carbamate ion - elevated 2,3-BPG: neg charge binds pos charged pocket between B units
76
how does oxygen leave hemoglobin?
HALDANE EFFECT in lungs.. - oxygenation of Hgb promotes dissociation of H+ from Hgb - shifts equilibrium toward CO2 formation - CO2 released from RBC
77
heme synthesis sources
all nitrogen from glycine all carbon from glycine and succinate
78
heme synthesis starts with
succinyl coA + glycine
79
what path could be indicated by increase in.. - total bilirubin - direct/conjugated bilirubin - indirect/unconjugated bilirubin
-**total**: liver dz, bile duct obstruction, hemolytic anemia - **direct**: bile exretion (bile duct obstruction, liver cell damage, dubin-johnson/rotor) - **indirect**: giberts syndrome (benign), hemolysis (sickle cell, thalassemia), newborn jaundice
80
liver detox pathway
xenobiotic/waste metabolite > phase I (hydroxylate)> primary metabolite > phase 2(conjugate) > secondary metabolite, suitable for excrretion
81
phase I liver detox reactions
reduction oxidation hydroxylation hydrolysis
82
phase II liver detox reactions
conjugation sulfation methylation glucuronidation

NPLEX I 2024 (23 decks)

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