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MCAT Biology > Biologically Important Molecules > Flashcards

Biologically Important Molecules Flashcards

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1
Q

basic amino acids

A

R (Arginine), K (Lysine), H (Histidine)

can ionically bond

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2
Q

hydrophobic/nonpolar amino acids

A

AVGWILF

A (Alanine), V (Valine), G (Glycine), W (Tryptophan), I (Isoleucine), L (Leucine), F (Phenylalanine)

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3
Q

polar amino acids

A

STQNYC

S (Serine), T (Threonine), Q (Glutamine), N (Asparagine), Y (Tyrosine), C (Cysteine)

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4
Q

sulfur containing amino acids

A

M (Methionine), C (Cysteine)

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5
Q

isoelectric point

A

pH at which molecule is uncharged (zwitterion)

average pKas of both functional groups

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6
Q

disulfide bonds, what kind of reaction makes them form

A

cysteine gets oxidized by removing Hs to become cystine

-SH SH- S-S

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7
Q

why proline is not in alpha helix

A

formation of peptide bond eliminates only hydrogen atom so there is no NH for backbone
it’s structure kinks the polypeptide chain

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8
Q

unique properties of alpha helix

A

secondary structure, alpha carboxyl oxygen hydrogen bonds to alpha amino proton of amino acid 3 residues away
used in transmembrane regions because polar NH and CO groups are contained inside helix, good for stabilizing in hydrophobic cell membrane

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9
Q

ways to regulate enzyme activity

A

covalent modification (kinase, phosphorylase, phosphatase)
proteolytic cleavage (zymogen cleavage by protease)
association with other polypeptides
allosteric regulation

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10
Q

Km of an enzyme

A

Km is amount of substrate required to reach 1/2Vmax

low Km means high affinity

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11
Q

positive cooperativity of enzyme

A

binding of one substrate to one subunit increases affinity of other subunit for substrate

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12
Q

noncompetitive inhibitor

A 
binds to allosteric site
Vmax diminishes (no matter how much substrate, inhibitor will not be displaced), does not change Km
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13
Q

competitive inhibitor

A

Vmax is not affected (amount of substrate can overcome inhibitor), Km increased

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14
Q

uncompetitive inhibitor

A 
binds to enzyme substrate complex
decreases vmax (limits amount of enzyme substrate complex available)
decrease Km (increases apparent affinity of enzyme for substrate that cant disassociate)
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15
Q

mixed type

A 
either binds to enzyme or enzyme substrate complex
Vmax decreases (either way allosteric)
Km varies (if attracted to free form, Km increases, if attracted to complex, Km decreases)
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16
Q

lineweaver burk plot
slope
y intercept
x intercept

A

slope: Km/Vmax
y intercept: 1/Vmax
x intercept: -1/Km

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17
Q

trend at which reaction rate increase

A

linearly until saturation level

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18
Q

shape of curve of positive cooperative binding

A

sigmoidal curve

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19
Q

trait of fructose

A

a ketone

hexose

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20
Q

trait of glucose

A

aldehyde at the end

hexose

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21
Q

trait of ribose

A

aldehyde at end

pentose

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22
Q

how do sugars link

A

glycosidic linkage

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23
Q

sucrose is made of

A

glucose + fructose

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24
Q

lactose is made of

A

galactose + glucose

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25
Q

maltose is made of

A

glucose x2

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26
Q

name of carb depending on where it is found

A

glycogen - animals
starch - glycogen in plants
cellulose - straight and fibrous

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27
Q

types of glycosidic linkages

A

alpha 1, 4 straight

alpha 1, 6 branching

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28
Q

carbohydrate formula

A

Cn(H2O)n

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29
Q

3 primary roles of lipids

A

triglycerides as adipose
phospholipids as membranes
cholesterol as steroids

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30
Q

triglycerol structure

A 
O
                      II
CH2 ---O -----C -------- R1
I
I
I                     O
I                      II
CH2 ---O -----C -------- R2
I
I
I                     O
I                      II
CH2 ---O -----C -------- R3
31
Q

triacylglycerol + NaOH —->

A 
CH2 ---OH
I
I
I                     
I                      
CH2 ---OH 
I
I
I                     
I                      
CH2 ---OH
\+
         O
         II
O-----C------R1 x3
glycerol + 3 fatty acids
32
Q

phospholipid structure

A

diacylglucerol phosphate

33
Q

sphingolipids, what it is similar to, what it is used in

A

similar to phospholipids but backbone is phingosine

only used in spingomyelin, important in myelin sheath

34
Q

wax structure

A

long chain fatts esterified to long chain alcohol

35
Q

4 fat soluble vitamins, similarity in structure

A

A, D, E, K

all have ring structures

36
Q

path of fat from chylomicron, where it goes, what are intermediates, what is produced at end

A

chylomicron carried via lymphatic system undergoes beta oxidation at outer mitochondrial membrane, which becomes fatty acetyl CoA (using 2 ATP) and transported into matrix where it undergoes repeated cleavage to release acetyl CoA, FADH2, NADH
acetyl CoA is sent to Krebs cycle

37
Q

if 12 carbon saturated fatty acid goes through fatty acid oxidation, you get

A

5 rounds of beta oxidation
5 FADH2, 5 NADH, 6 acetyl CoA
6 acetyl CoA in Krebs make 18 NADH, 6 FADH2, 6 GTP
total make 78 ATP

38
Q

ketogenesis, when it happens, where, what it makes

A

during periods of starvation, no glycogen or glucose
liver generates ketone bodies in mitochondrial matrix from acetyl CoA
makes acetone, acetoacetate, beta hydroxybutyrate, which can cross blood brain barrier and be converted to acetyle CoA at destination to enter Krebs cycle

39
Q

ketogenesis can happen even when not starving - when? why is that harmful?

A

when glucose cannot enter cell - type 1 diabetes without insulin
glucose cant enter without insulin and needs fatty acid oxidation to make actyl CoA
levels get too high and make acidic ketone bodies, leading to diabetic ketoacidosis

40
Q

fatty acid synthesis, where it happens, enzymes involved, energy carrier involved

A

takes place in cytoplasm (keeps enzymes separated from catabolism process)
acetyl CoA activated and carboxylated with CO2+ATP by acetyl CoA carboxylase to make malonyl CoA

fatty acid synthase’s domain acyl carrier protein binds acetyl Coa to malonyl CoA with use of NADPH

41
Q

how protein can be used for energy

A

amine - nitrogen containing compounds or urea

carbon skeleton - glucose (glucogenic amino acid) or acetyl CoA

42
Q

terpene based on isoprene units

A

hemiterpene: half a terpene, 1 isoprene unit
monoterpene: 2 isoprene units
sesquiterpene: 1.5 terpenes - 3 isoprene units
diterpene: 4 isoprene units

43
Q

form of phosphoric acid in body

A

most common is HPO42-, then HPO4-, then H2PO4-

44
Q

pyrophosphate, 3 reasons why they store so much energy

A

two orthophosphate via anhydride linkage
negative charges repel each other, orthophosphate has more resonance forms, orthophosphate has more favorable interactions with solvent water

45
Q

purines, structure

A

A, G

double ringed

46
Q

pyrimidine, structure

A

C, T

single ring

47
Q

right handed double helix is stabilized by

A

van der waals forces between bases and hydrophobic interactions

48
Q

snRNA

A

associate with proteins to form spliceosome

49
Q

miRNA & siRNA

A

post transcriptional regulation of gene expression

50
Q

PIWI interacting RNA

A

work with regulatory proteins to prevent transposons from mobilizing

51
Q

long ncRNA

A

control basal transcription by regulating initiation complex on promoter

52
Q

why is deoxyribose used in DNA instead of ribose

A

lack of 2’OH group stabilizes DNA

53
Q

hydrogen bonds between G-D

A

3

54
Q

hydrogen bonds between A-T

A

2

55
Q

heterochromatin condensing level

A

dark regions, denser, rich in repeats

56
Q

euchromatin condensing level

A

lighter region, higher transcription rate, high gene activity, loose packing

57
Q

deoxyribose vs deoxynucleoside vs deoxynucleotide

A

deoxyribose: pentose sugar without OH at 2’
deoxynucleoside: pentose sugar + base
deoxynucleotide: pentose sugar + base + phosphates

58
Q

how is DNA stored in eukaryotoes

A

chromatin -histone compleses

59
Q

efflux and influx

A

pumping out, pumping in

60
Q

primary, secondary, tertiary, and quarternary structure of protein

A

amino acid sequence
hydrogen bonds between NH & CO
tertiary: interactions between amino acid residues
quarternary: interactions between polypeptide units

61
Q

4 denaturing forces on proteins and which bonds they affect

A
  1. urea (H bonds, 2-3-4)
  2. pH (ionic bonds, 3-4)
  3. temperature (2-3-4)
  4. salt concentration (H bonds, 2-3-4)
62
Q

enantiomer of protein found in body

A

L, not D

63
Q

where does cholesterol for steroids come from

A

diet + liver, transported as lipoprotein

64
Q

deoxyribose vs deoxynucleoside vs deoxynucleotide

A

deoxyribose: pentose sugar without OH at 2’
deoxynucleoside: pentose sugar + base
deoxynucleotide: pentose sugar + base + 3 phosphates

65
Q

levels of DNA condensation

A

DNA gyrase creates supercoils
supercoils around 8 histones to make nucleosome
(with acetyl, uncoiled, without acetyl, coiled)
chromatin

66
Q

names of chromosome based on centromere location

A 
p over q
centromere slowly moving up (shorter and shorter p)
metacentric
submetacentric 
acrocentric
telocentric
67
Q

telomere - type of DNA, Hayflick limit

A

combination of single and double stranded DNA
prevents chromosome deterioration and fusion with neighboring chromosomes
hayflick limit: # of times cell can divide till telomere length stops cell divison

68
Q

intergenic region of DNA

A

noncoding DNA

69
Q

telomerase comprises of

A

RNA primer and reverse transcriptase

70
Q

hnRNA

A

precursor to mRNA

71
Q

good ligands have what chemical property

A

higher electron density at core

charged attachments will add to a center element’s electron density

72
Q

acidic amino acids

A

ED
aspartic acid, glutamic acid
can ionically bond

73
Q

hydrogen donating, hydrogen accepting, and both amino acids (hydrogen bonding)

A

LWR (lysine, tryptophan, arginine)
ED (aspartic acid, glutamic acid)
NQHSTY (asparagine, glutamine, histidine, serine, threonine, tyrosine)

74
Q

determining oxidation number of element in organic molecule

A

of bonds to more electronegative elements - # of bonds to less electronegative elements

MCAT Biology (10 decks)

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