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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
Q

zwitterion form

A

molecule has a separate pos and neg charge

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26
Q

isoelectric point

A

pH at which a particular molecule carries no net charge

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27
Q

protein structures

A
  • 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
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28
Q

simple proteins vs conjugated proteins

A

simple: contain only AA (albumin, keratin)

conjugated: simple protein + non-protein part; prosthetic groups include:
- glycoprotein (carb)
- lipoprotein (fat)
- hemoproteins (heme molecule)

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29
Q

protein functions

A
  • catalysis: enzymes
  • structure: collagen, elastin
  • movement: actin, myosin
  • defense: fibrin, thrombin, Ig
  • regulation: insulin, glucagon, GH
  • transport: hemoglobin, lipoproteins, Na+/K+ ATP ase
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30
Q

oxidoreductases

A

catalyzes the transfer of electrons from one molecule to another

  • dehydrogenase
  • hydroxylase
  • oxidase
  • oxygenase
  • peroxidase
  • reductase
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31
Q

oxygenases

A

incorporate oxygen into organic substrates

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32
Q

peroxidases

A

reduction of hydrogen peroxide and hydroperoxides

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33
Q

reductases

A

catalyze reduction

34
Q

dehydrogenases

A

oxidize substrates by transferring one or more hydride ions

35
Q

oxidases

A

oxygen as the hydrogen or electron accepter

36
Q

hydroxylases

A

add hydroxyl group to substrates

37
Q

transferases

A

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
Q

hydrolases

A

use water to break chemical bond

39
Q

phosphatase

A

removes phosphate group from a protein

40
Q

lyases

A

breaks bond by means other than hydrolysis

  • aldolase
  • decarboxylase (removes COOH groups from acidic substrates)
  • thiolase
  • dehydrase
  • synthase
41
Q

ligases

A

join 2 sep molecules together

  • carboxylase
  • synthetase
42
Q

endogenous/endergonic rxn

A

-energy required for rxn to proceed
- non-spontaneous
- +delta G

43
Q

exogenous/exergonic rxn

A
  • energy release by rxn
  • spontaneous, favorable
  • neg delta G
44
Q

what is michaelis-menten equation used for

A

regulation of enzymes via substrate/product concentration

45
Q

vmax

A

max rate of rxn - the point where all active sites are bound to substrate (enzyme is saturated)

46
Q

purine degradation forms what?

A

uric acid

47
Q

purine degradation waste products

A

ammonium

48
Q

important enzyme involved in purine degradation and its cofactor

A

xanthine oxidase

Mn (molybdenum)

49
Q

what are purines and pyrimidines

A

nitrogenous bases found in nucleic acids (DNA and RNA)

purine: two ring structure
pyrimidines: one ring structure

50
Q

major purines and what they bind with and other involvements

A

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
Q

carbamoyl phosphate synthetase I (CPSI)

path
source of N
location
activator
inihibitor

A

path: urea cycle
source of N: NH4+
location: mitochondria
activator: N-acetylglutamate
inhibitor: none

52
Q

carbamoyl phosphate synthetase II (CPSII)

path
source of N
location
activator
inihibitor

A

path: pyrimidine biosynthesis
source of N: glutamine
location: cytosol
activator: PRPP
inihibitor: UTP

53
Q

what can serve as an analogue of uracil or thymine in DNA synthesis

A

5 fluorouracil

54
Q

products of pyrimidine degradation

A

malonate, methylmalonate

55
Q

waste product of pyrimidine degradation

A

ammonia

56
Q

what is required to break down thymine in pyrimidine degradation

A

NADPH

57
Q

location of DNA replication

A

nucleus of eukaryotic cells

58
Q

location of transcription to RNA

A

nucleus of eukaryotes
cytoplasm of prokaryotes

59
Q

location of translation

A

ribosomes in cytoplasm

60
Q

where does transamination of protein breakdown occur? what enzymes perform this?

A

cytosol

  • alanine- and aspartate- aminotransferase
  • transaminases use vit B6 in form of PLP
61
Q

what AA do not participate in transamination

A

lysine
threonine

62
Q

oxidative deamination rxn

A

glutamate > a-ketoglutarate via glutamate dehydrogenase (needs NAD or NADP)

release NH3 as ammonium

63
Q

oxidative deamination upregulation

A

GDP, ADP, low energy states

64
Q

oxidative deamination down regulation

A

GTP, ATP, high energy states

65
Q

urea cycle location

A

mitochondria and cytosol of liver cells

66
Q

rate limiting step of urea cycle

A

CPSI
- upregulated by NAG
- stim by arginine

67
Q

most common def of urea cycle

A

ornithine transcarbamoylase enzyme def

68
Q

hemoglobin

A

globular protein with heme prosthetic group that carry oxygen

69
Q

hemoglobin vs myoglobin

A

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
Q

hemoglobin structure conformations

A
  • deoxy-HGB: taut, low affinity for oxygen
  • oxy-HGB > relaxed, high affinity for oxygen
71
Q

what AA is present at the active site of hemoglobin chain folding?

what AA sub takes place with sickle cell anemia?

A

normally glutamic acid

replaced with valine in sickle cell

72
Q

types of HGB/Hb most to least common and their chain compo

A

HbA - a2b2
HbA1C - a2b2glucose
HbA2 - a2g2
HbF - a2y2

73
Q

iron forms and their binding properties

A
  • Fe2+ (ferrous): binds oxygen, CO (carboxyhemoglobin)
  • Fe3+ (ferric): binds CN- (methemoglobin), does NOT bind oxygen
74
Q

left shift in graph meaning

graph comparing PP oxygen to saturation with oxygen

A

increased affinity for oxygen

  • H+ reduced (high pH)
  • CO2 reduced
  • 2,3-BPG reduced
75
Q

right shift in graph meaning

graph comparing PP oxygen to saturation with oxygen

A

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
Q

how does oxygen leave hemoglobin?

A

HALDANE EFFECT

in lungs..
- oxygenation of Hgb promotes dissociation of H+ from Hgb
- shifts equilibrium toward CO2 formation
- CO2 released from RBC

77
Q

heme synthesis sources

A

all nitrogen from glycine
all carbon from glycine and succinate

78
Q

heme synthesis starts with

A

succinyl coA + glycine

79
Q

what path could be indicated by increase in..

  • total bilirubin
  • direct/conjugated bilirubin
  • indirect/unconjugated bilirubin
A

-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
Q

liver detox pathway

A

xenobiotic/waste metabolite > phase I (hydroxylate)> primary metabolite > phase 2(conjugate) > secondary metabolite, suitable for excrretion

81
Q

phase I liver detox reactions

A

reduction
oxidation
hydroxylation
hydrolysis

82
Q

phase II liver detox reactions

A

conjugation
sulfation
methylation
glucuronidation

NPLEX I 2024 (23 decks)

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