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biochem Flashcards

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1
Q

what are enzymes

A

biological catalysts that kinetically increase the rate if a reaction without being consumed

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2
Q

what does the catalyst not affect?

A
  • – gibbs energy
  • – reactants
  • – products
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3
Q

hydrolase def

A

hydrolyzes chemical bonds (includes ATPases— breaks down ATP into ADP and into a phosphate group– , proteases, and others)

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4
Q

*isomerase def

A

rearranges bonds within a molecule to form of an isomer

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5
Q

kinase def

A

adding phosphate groups from a high energy carrier to other groups

ex: growth hormone, platelets, insulin

due to having a cascade

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6
Q

what causes denaturation of amino acids?

A
  1. high temp
  2. presence of high metals
  3. acidosis / alkalinosis
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7
Q

chymotrypsin

A

is the enzyme that selects for the aromatic amino acids: phenylalanine, tryptophan, and tyrosine at the carboxyl part

bulky belongs to longer part

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8
Q

trypsin

A

is the enzyme that selects for the basic amino acids: lysine and arginine at the carboxyl part

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9
Q

what causes protein building to become favorable

A

ATP coupling

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10
Q

difference of in vivo and in vitro being spontaneous

A

the cells in body are naturally more favorable bc it has ATP on the sidelines waiting to participate with atp coupling

however in vitro is a lab setting so it introduces an enzyme to an unfavorable reaction to take place and speed up rxn (kinetic)

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11
Q

why are enzymes more globular shaped than anything else

A

its easier for them to work bc they resemble a protein with a globular shape that has the active site better available for the substrate (reactant ) to bind to

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12
Q

to stabilize a charge do u need a similar charge or an opp charge?

A

u need an opp charge to stabiliz bc the same charge will just make it more reactive

lysisne will stabilize glutamate

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13
Q

do enzymes act or produce the transition state

A

produce

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14
Q

can a certain reactant or product be favorable at all times?

A

no bc it depends on the given time and what it has more of it … chetlatier principle always comes into play

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15
Q

what configurations are found in animals

A

L for AA (think of aLLLlanine) and D for sugars

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16
Q

recognition pocket

A

part of the enzymes structure near the active site that attracts certain aa residues to come along

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17
Q

why does a protein denature

A

the temp is too high and the protein starts to lose affinity for the substrate and the globular structure breaks

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18
Q

cofactors vs coenzymes

A

Cofactors serve the same purpose as coenzymes, as they regulate, control, and adjust how fast these chemical reactions would respond and take effect in our body. The big difference is that coenzymes are organic substances, while cofactors are inorganic

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19
Q

cofactors vs coenzymes ex

A

cofactors can be vitamins

coenzymes can nad and fad bc main function is to accept and store electrons within proteins.

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20
Q

saturation

A

even if u add more substartes there aren’t enough enzymes to bind to each one so the vmax will reach a horizontal slope and not increase

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21
Q

tense vs relaxed cooperativity

A

tense means u are not cooperative and can remain inactive not helping others to join whereas relaxed is active and will cause more to join

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22
Q

investment part of glycolysis

A

use 2 atp to make 2 PGAL (3 carbons attached to a phosphate group)

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23
Q

in glycolysis, each pgal produces 3 things

A

2 atp
pyruvate
NADH

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24
Q

structure of pyruvate

A

3 carbon molecule

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25
Q

how can aa make glucose

A

through oaa (oxaloacetate)

hpw is OAA made from pyruvate? pyruvate carboxylase which adds another carbon to make 4 that oaa should have

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26
Q

if there is too much amp then …

A

not enough atp so gluconeogen will be halted bc that requires a lot of atp

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27
Q

what is a slow regulator and may takes hour to days

A

anything that halts transcription

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28
Q

is atp consumed or produced for the pentose pathway

A

no

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29
Q

chylomicron

A

type of lipoptoeins (carries triglycerides and cholesterol) found in the small intestine once bile emulsifies fats into smaller particles

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30
Q

lacteal

A

lymphatic capillary that have larger pores that can carry the chylomicrons to different parts of the body especially to thoracic ducts

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31
Q

ischemia

A

restricted blood flow which can lead to decreased amount of o2

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32
Q

what happens when there isn’t enough glucose being made

A

there will be less pyruvate being made (glycolytic pathway) which in turn will cause less pyruvate to be moved to ether lactate (fermentation) or to krebbs …

so less pyruvate as well

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33
Q

main enzyme involved in leactic acid fermentation of pyruvate to lactate is

A

lactate degyhrogenase (LDH)

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34
Q

why is there an increase in ammonia when the body undergoes muscle fatigue

A

it is looking for its next fuel which will come from breaking down amino acids which will have byproduct of urea

35
Q

embolism

A

blood clot or air bubble

36
Q

edema

A

excessive fluid

37
Q

ischemia

A

reduced blood flow

38
Q

when does glycogenesis occur and what hormone stimulates it

A

mostly in the liver or muscles during the fed state and insulin helps it because it wants to put glucose into the cells

39
Q

alpha sugar vs beta sugar

A

beta has oh groups on same side whereas the alpha has the oh groups on opp sides like diff axial positions (one is up and the other one is down)

40
Q

the first carbon of the carbohydrate

A

is the reducing end and can take off the H so that the O can form a glycosidic linkage

41
Q

most important starting material for glycogenesis

A

udp - glucose (which to make is an endergonic reaction) but can be coupled by phosphatase energy

42
Q

glycogenin

A

has a specific tyrosine that attracts the udp-glucose

has autoglyocsylation

43
Q

autoglycosylation

A

when it comes to glycosidic linkages, no specific enzymes are needed

44
Q

basic process for glycogenesis

A

use the phosphatases for energy to get have udp as a byproduct and make aoutoglycosylation linkages with glucose to glycosidic bonds to have END PRODUCT OF GLYCOGEN

45
Q

two enzymes involved in glycogenesis

A

glycogen synthetase:
makes the line of 1-> 4 bonds
can also add once the branching enzyme makes the first branch

branching enzyme :
-break the 1 -> 4 bond to make branches that are part of the 1 -> 6 bonds

46
Q

why does glycogenlysis occur

A

the blood glucose is low

fasting state

47
Q

hormones in charge of glycogenlysis?

A

glucagon
epinephrine
neriephrine
growth hormone

48
Q

glycogen phosphorylase involved with glycogenlysis?

A

glycogen phosrylase cuts the glucose bond and adds phosphate group to individ glucose but cannot go to the glucose that are close to the 1-6 bond and has to wait for the debranching

49
Q

debranching enzyme involved in glycogenlysis

A

debranches the 1-6 glucose bond and transfers 3 glucose molecules to the 1 4 bond

50
Q

which hormones use gcpr pathway

A

glucagon
N.E.
epineph.

51
Q

anterograde vs retrograde

A

ante is fwd

retro is reverse

52
Q

protein kinase a

A

made from camp and can inhibit glycogenesis and promote glycogenolysis to get fatty acids

53
Q

where does gluconeogenesis occurs

A

liver and kidneys (proximal convoluted tubule)

54
Q

pyruvate carboxylase

A

adds co2 of pyruvate to make OAA

55
Q

special about malate from krebbs

A

PUSHED OUT OF MATRIX , converted back into OAA , then PEP (step b4 making pyruvate in glycolysis)

enxyme that makes the oaa into pep is pepck (phosphor enol pyruvate carboxy kinase)

pep is 3 carbons

56
Q

fructo bis phosphatase

A

rds for gluconeogenesis that make fructo 6 phosphate

57
Q

relationship btwen smooth er and glucose6 phosphatase

A

enzyme (glucose 6 phosphatase) take off phosphate off of glucose so it can leave and enter blood

58
Q

when glycerol has a phosphate what happens

A

it turns into DHAP of glycolysis

59
Q

when it comes to disulfide bonds and agents, tell me what is going on

A

OPP OF WHAT U THINK
reducing agents are the ones that are reduced so they are breaking the disulfide bonds by putting h

oxidizing agents are the op they are building the disulfide bonds

usually has to do with cysteine amino acid

60
Q

when it comes to beta oxidation, how many fadh2 and nadh are made from a 14 carbon going to acetyl coA (2 carbons)

A

14/2 - 1 = 6 for each coenzyme

61
Q

when it comes to atomic atoms that are closed shells and half shelled, would s or d sublevel be more stable?

A

closed d sublevel

62
Q

which hormone is responsible for fatty acid synthesis

A

insulin because to promote the synthesis, there needs to be high blood glucose and a fed state

63
Q

why would too much atp cause fatty acid synthesis

A

because if u have too much atp u don’t want to keep breaking down products. u will start the neg feedback and now do synthesis

64
Q

what does citrate lyase do

A

changes citrate back into OAA and aceyl COA

then OAA turns into malate and then malate turns into pyruvate by producing NDAPH

65
Q

acaetyl co A carboxylase

A

carries biotin(coenzyme) and adds in another carbon in the form of co2 onto the acetyl coA to make the acetyl coA (2 carbons) into malonyl coA (3 carbons)

keep in mind that the coA of the malonate will then be transferered by tranactylase to a fatty acid

66
Q

types of regulation for acetyl coA carboxylase

A

citrate which will promote

long fatty acids with coA that will inhibit because they are coming from oxidation

insulin will promote

cortisol, glucagon, epi/norepi will inhibit

67
Q

active and inactive form of acetylco A carboxylase

A

dimers is inactive form and the polymerization (when the dimers are all in a group) will be the active form

68
Q

fatty acid oxidation vs synthesis

A

oxidation breaks down the fatty acids

69
Q

what is the role that protein kinase A have on acetylk co A carboxylase

A

it phosphorylates the ACC which causes it to back into the dimer inactive form which will then need a phosphatase to remove the phosphate if it ever planned to become active again

70
Q

carnitine acytle transporter I vs II

keep in mind that these are actually 16 fatty acids called palmitoil

A

I brings the fatty acids into mitochrondria for oxidation while the II is already in mitochrondria

if I is inhibited it cant bring fatty acids into the mitcondria so the fatty acids will just go on to synthesis

71
Q

acetyl I transacetylase

A

taking up actyl coA and turning it into acetate and move the acetate group onto the cystine group

72
Q

overall steps for fatty acid synthesis

A

Location: cytosol of cell
1-Citrate leaves mitochondrial matrix, crosses double membrane layers, to cytosol
2-Citrate converted to acetyl CoA + OAA via enzyme citrate lyase
3-Acetyl CoA (2C) gets converted to malonyl CoA (3C) via enzyme ACC (acetyl CoA carboxylase)
4-Malonyl CoA gets lengthened 2 C at a time via enzyme fatty acid synthase
5-Regulation: high insulin triggers fatty acid synthesis
6-Fatty acid + glycerol = triglycerides (stored in adipocyte cells)

ACC is the rate-limiting step. It also needs NADPH (which we get from PPP). Malonyl-CoA from FA synthesis inhibits beta oxidation by inhibiting carnitine acyltransferase I (@ outer mitochondrial membrane), part of the transport system that lets activated FA back into the mitochondria. (thus FA synth and beta ox are antagonistic pathways like glycolysis and gluconeo)

73
Q

hydride

A

one h proton with 2 electrons

74
Q

why are free fatty acids not sent off to rbc or blood brain barrier

A

FFA enter blood and are transported by albumin to other cells (mostly liver and muscle). They don’t get transported to RBCs or the brain because RBCs don’t have mitochondria, and FFA can’t pass the blood-brain barrier.

75
Q

What is the basic order of events in the digestion and mobilization of dietary fats?

A

Dietary fats are insoluble in aqueous solution, and cannot be absorbed by the intestinal mucosa.
Hint #2
2 / 5
Bile is secreted from the gallbladder to emulsify dietary fat particles to form finely dispersed, soluble micelles.
Hint #3
3 / 5
The formation of micelles allows for intestinal lipases to degrade the dietary particles so that they may be absorbed and used to form TAGs.
Hint #4
4 / 5
The triacylglycerols are incorporated with cholesterol and apolipoproteins within the intestinal mucosa.
Hint #5
5 / 5

The correct order is: emulsified by bile→ degradation by lipases→ absorption and conversion into triacylglycerols→ incorporation into chylomicrons.

76
Q

upregulate vs downregulate activity usually done by transcription factors

A

upregulate is good and will promote the activity

downregulate is bad bc it will decrease the activity

upreg incr # of receptors so more sensitivity
downred decr # of receptors so less sensitivity and can be a problem like insulin reg in type 2 diabetes

77
Q

replication vs transcription

A

replication really has to do only with the dna strand.. transcription has to do with regulating activity effects

78
Q

methionine vs cysteine

A

Disulfide bonds in proteins are formed between the thiol groups of cysteine residues by the process of oxidative folding. The other sulfur-containing amino acid, methionine, cannot form disulfide bonds.

79
Q

refractory period

A

due to the hyperpolarization that occurs after the action potential due to the K+ voltage gated channel allow too much K+ to exit the cell during depolarization.

80
Q

relationship btwn depolarization, action pot, and potassium

A

no relationship bc needs sodium

81
Q

folding of proteins happen in what organelle

A

rer

82
Q

diff btwn locations of the protron gradient and etc

A

etc is across inner membrame and protron gradient is inside the inner

83
Q

acetyl coA structure

A

two carbons and S-CoA

two carbons are the methyl group and the carbonyl

MCAT PREP (14 decks)

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