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MCAT Biology > Biologically Important Molecules > Flashcards

Biologically Important Molecules Flashcards

(74 cards)

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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
maltose is made of
glucose x2
26
name of carb depending on where it is found
glycogen - animals starch - glycogen in plants cellulose - straight and fibrous
27
types of glycosidic linkages
alpha 1, 4 straight | alpha 1, 6 branching
28
carbohydrate formula
Cn(H2O)n
29
3 primary roles of lipids
triglycerides as adipose phospholipids as membranes cholesterol as steroids
30
triglycerol structure
``` 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
triacylglycerol + NaOH ---->
``` 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
phospholipid structure
diacylglucerol phosphate
33
sphingolipids, what it is similar to, what it is used in
similar to phospholipids but backbone is phingosine | only used in spingomyelin, important in myelin sheath
34
wax structure
long chain fatts esterified to long chain alcohol
35
4 fat soluble vitamins, similarity in structure
A, D, E, K | all have ring structures
36
path of fat from chylomicron, where it goes, what are intermediates, what is produced at end
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
if 12 carbon saturated fatty acid goes through fatty acid oxidation, you get
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
ketogenesis, when it happens, where, what it makes
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
ketogenesis can happen even when not starving - when? why is that harmful?
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
fatty acid synthesis, where it happens, enzymes involved, energy carrier involved
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
how protein can be used for energy
amine - nitrogen containing compounds or urea | carbon skeleton - glucose (glucogenic amino acid) or acetyl CoA
42
terpene based on isoprene units
hemiterpene: half a terpene, 1 isoprene unit monoterpene: 2 isoprene units sesquiterpene: 1.5 terpenes - 3 isoprene units diterpene: 4 isoprene units
43
form of phosphoric acid in body
most common is HPO42-, then HPO4-, then H2PO4-
44
pyrophosphate, 3 reasons why they store so much energy
two orthophosphate via anhydride linkage negative charges repel each other, orthophosphate has more resonance forms, orthophosphate has more favorable interactions with solvent water
45
purines, structure
A, G | double ringed
46
pyrimidine, structure
C, T | single ring
47
right handed double helix is stabilized by
van der waals forces between bases and hydrophobic interactions
48
snRNA
associate with proteins to form spliceosome
49
miRNA & siRNA
post transcriptional regulation of gene expression
50
PIWI interacting RNA
work with regulatory proteins to prevent transposons from mobilizing
51
long ncRNA
control basal transcription by regulating initiation complex on promoter
52
why is deoxyribose used in DNA instead of ribose
lack of 2'OH group stabilizes DNA
53
hydrogen bonds between G-D
3
54
hydrogen bonds between A-T
2
55
heterochromatin condensing level
dark regions, denser, rich in repeats
56
euchromatin condensing level
lighter region, higher transcription rate, high gene activity, loose packing
57
deoxyribose vs deoxynucleoside vs deoxynucleotide
deoxyribose: pentose sugar without OH at 2' deoxynucleoside: pentose sugar + base deoxynucleotide: pentose sugar + base + phosphates
58
how is DNA stored in eukaryotoes
chromatin -histone compleses
59
efflux and influx
pumping out, pumping in
60
primary, secondary, tertiary, and quarternary structure of protein
amino acid sequence hydrogen bonds between NH & CO tertiary: interactions between amino acid residues quarternary: interactions between polypeptide units
61
4 denaturing forces on proteins and which bonds they affect
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
enantiomer of protein found in body
L, not D
63
where does cholesterol for steroids come from
diet + liver, transported as lipoprotein
64
deoxyribose vs deoxynucleoside vs deoxynucleotide
deoxyribose: pentose sugar without OH at 2' deoxynucleoside: pentose sugar + base deoxynucleotide: pentose sugar + base + 3 phosphates
65
levels of DNA condensation
DNA gyrase creates supercoils supercoils around 8 histones to make nucleosome (with acetyl, uncoiled, without acetyl, coiled) chromatin
66
names of chromosome based on centromere location
``` p over q centromere slowly moving up (shorter and shorter p) metacentric submetacentric acrocentric telocentric ```
67
telomere - type of DNA, Hayflick limit
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
intergenic region of DNA
noncoding DNA
69
telomerase comprises of
RNA primer and reverse transcriptase
70
hnRNA
precursor to mRNA
71
good ligands have what chemical property
higher electron density at core | charged attachments will add to a center element's electron density
72
acidic amino acids
ED aspartic acid, glutamic acid can ionically bond
73
hydrogen donating, hydrogen accepting, and both amino acids (hydrogen bonding)
LWR (lysine, tryptophan, arginine) ED (aspartic acid, glutamic acid) NQHSTY (asparagine, glutamine, histidine, serine, threonine, tyrosine)
74
determining oxidation number of element in organic molecule
of bonds to more electronegative elements - # of bonds to less electronegative elements

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