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Biology - MCAT > Class One > Flashcards

Class One Flashcards

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1
Q

forms of energy in chemistry (x2)

A

kinetic and potential

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2
Q

kinetic energy

A

movement of molecules

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3
Q

potential energy

A

energy stored in chemical bonds

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4
Q

first law of thermodynamics

A

energy of the universe is constant

e.g. when energy of a system decreases, energy of surroundings has to increase

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5
Q

second law of thermodynamics

A

entropy of the universe tends to increase (spon. reactions increase disorder)

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6
Q

what does a negative change in entropy mean

A

lost entropy = disorder has decreased

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7
Q

Gibbs free energy equation

A
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8
Q

enthalpy equation

A

delta H = delta E + (P x delta V)

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9
Q

free energy relationship with enthalpy and entropy

A

free energy increases with increased enthalpy + decreases with increased entropy

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10
Q

which reaction is more favourable: decreased or increased delta G

A

decreased (means that there is high entropy)

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11
Q

spon. reactions: neg or pos delta G

A

negative

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12
Q

exergonic reactions

A

reactions with neg delta G: energy exits the system

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13
Q

endergonic reactions

A

reactions with pos delta G: only occur if energy is added

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14
Q

exothermic reactions

A

reactions with neg delta H (enthalpy) → release heart

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15
Q

endothermic reactions

A

reactions with pos delta H → require an input of heat

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16
Q

Gibbs free energy and equilibrium equation

A
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17
Q

what is K

A

ratio of products to reactants during equilibrium

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18
Q

difference between lnK and lnQ in Gibbs free energy equation

A

lnK is used when equilibrium has been reached

lnQ is used at any point of time

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19
Q

removal of reactant/product & its effect on Q and Keq

A

causes a change in Q but not Keq

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20
Q

delta G = 0

A

reaction is at equilibrium

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21
Q

spontaneous reaction & delta G

A

spon. reactions have a neg delta G

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22
Q

spontaneity and reaction rates

A

a spon reaction means it is energetically favourable but says nothing about the rate of reaction

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23
Q

what is activation energy

A

the energy required to produce the transition state (very unstable)

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24
Q

what is a catalyst

A

something that lowers the Ea without changing the delta G

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25
Q

how does a catalyst work

A

lowers Ea by stabilizing the transition state → makes it less thermodynamically unfavourable

*never consumed in a reaction

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26
Q

photosynthesis definition

A

process in which plants store energy from the sun in the bond energy of carbohydrates

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27
Q

photoautotrophs

A

something that uses energy from light to make their own food

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28
Q

chemoheterotrophs

A

something that uses the energy if chemicals produced by other living things (e.g. plants & animals)

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29
Q

oxidation reactions

A

gain of oxygens atoms

loss of hydrogen atoms

loss of electrons

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30
Q

reduction reactions

A

loss of oxygen atoms

gain of hydrogen atoms

gain of electrons

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31
Q

redox pair

A

when one atom gets reduced, another must be oxidized

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32
Q

catabolism

A

process of breaking down molecules

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33
Q

anabolism

A

building up metabolism

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34
Q

are anabolic reactions usually reductive or oxidative

A

reductive

e.g. fatty acid are generated by the successive reductions of a carbon chain

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35
Q

Bronsted-Lowry acids and bases

A

acids are proton donors (H+)

bases are proton acceptors

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36
Q

Lewis acids and bases

A

acids are electron pair acceptors

bases are electron pair donors

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37
Q

Lewis acid/base reactions usually occur due to the formation of…

A

coordinate covalent bonds

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38
Q

biological example of a coordinate covalent bond

A

oxygen binding to the iron atom in a heme group

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39
Q

conjugate base

A

remaining structure after a B-L acid donates an H+

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40
Q

conjugate acid

A

reminding structure after a B-L base bonds with H+

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41
Q

difference between a B-L acid & its conjugate base

A

base is missing an H+

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42
Q

difference between a B-L base and its conjugate acid

A

acid has an extra H+

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43
Q

strength of an acid formula

A

conc. of products over reactants

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44
Q

what is Ka

A

the acid-ionization constant of an acid

aka the equilibrium expression for an acid-dissociation reaction

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45
Q

strength of a base formula

A

conc. of products over reactions

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46
Q

polyprotic

A

a substance that has more than one proton to donate

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47
Q

amphoteric substance

A

something that can act as an acid or base

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48
Q

what is always amphoteric

A

conjugate use of a weak polyprotic acid

(can either donate or accept another proton)

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49
Q

why is HCO3- a weaker acid than H2CO3

A

every time a polyprotic acid donates a proton, the resulting compound will be a weaker acid than the one before

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50
Q

pH of an acid formula

A

pH = -log[H+]

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51
Q

pOH of a base fomula

A

pOH = -log[OH-]

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52
Q

pH and pOH relationship

A

pH + pOH = 14

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53
Q

pKa and pKb

A

pKa = -logKa

pKb = -logKb

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54
Q

pKa/pKb and strength

A

the lower the pKx, the stronger the acid/base

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55
Q

what is a buffer

A

a solution that resists changing pH when a small amount of acid/base is added

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56
Q

most important buffer system in blood plasma

A

bicarbonate buffer system

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57
Q

bicarbonate buffer system

A

H2CO3 → H+ + HCO3-

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58
Q

how is carbonic acid formed

A

byproduct of cellular respiration (CO2) combines with water

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59
Q

what is Gibbs free energy

A

amount of energy in a reaction available to do chemical work

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60
Q

protein composition

A

20 different amino acids linked together in polymers

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61
Q

generic formula for amino acids

A

variable R group

x-amino group

tetrahedral x-carbon

x-carboxyl group

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62
Q

unique feature of each amino acid

A

it’s side chain! gives it it’s physical/chemical properties that distinguish it from the other 19 AAs

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63
Q

acidic amino acids (x2)

A

aspartic acid: asp (D)

glutamic acid: glu (E)

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64
Q

why are some amino acids classified as acidic?

A

they have carboxylic acid functional groups in their side chains → acidic

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65
Q

in acidic amino acids, how many functional groups can act as acids

A

three!

the 2 backbone grows and the R group

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66
Q

what are asparate and glutamate

A

anionic (deprotonated) forms of the acidic AAs

this is how they are observed at physiological pH

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67
Q

basic amino acids (x3)

A

lysine: lys (K)
arginine: arg (R)
histidine: his (K)

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68
Q

pKa values of the side chains in basic AAs

A

lys (K): 10

arg (R): 12

his (H): 6.5

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69
Q

why is histidine unique

A

has a side chain with a pKa close to physiological pH

classified as a base but can act as both

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70
Q

hydrophobic (non polar amino acids) (x7)

A

glycine: gly (G)
alanine: ala (A)
valine: val (V)
leucine: leu (L)
isoleucine: ile (I)
phenylalanine: phe (F)
trypyophan: trp (W)

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71
Q

AAs with aliphatic (alkyl) side chains

A

non polar AAs

gly, ala, val, leu and ile

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72
Q

AAs with aromatic side chains

A

phe, trp (non polar)

and try (polar)

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73
Q

hydrophobic group & force

A

the larger the hydrophobic group, the greater the hydrophobic force repelling it from water

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74
Q

polar amino acids (x5)

A

serine: ser (S)
threonine: thr (T)
tyrosine: tyr (Y)
asparagine: asn (N)
glutamine: gln (Q)

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75
Q

what makes an AA polar

A

has an R group that is polar enough to from hydrogen ions with water but does not act as an acid or base

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76
Q

which AAs are modified by the attachment of a phosphate group by a kinase

A

serine, threonine + tyrosine (polar)

this modification is important → regulates protein activity

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77
Q

sulfur-containing amino acids (x2)

A

cysteine: cys (C)
methionine: met (M)

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78
Q

properties of cysteine

A

contions a thiol (alcohol with a S atom instead of O)

polar

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79
Q

properties of methionine

A

contains a thioether (ether with a S instead of O)

non polar

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80
Q

proline

A

has an amino group that is covalently bound to its non polar side chain → creates a secondary alpha amino group

important in protein folding

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81
Q

what are essential AAs

A

AAs that cannot be synthesized by humans → must be obtained by diet

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82
Q

nine essential amino acids

A

lysine

histidine

threonine

valine

leucine

isoleucine

phenylalanine

tryptophan

methionine

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83
Q

what 2 groups do AAs contain

A

acidic carboxylic group

basic amino group

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84
Q

zwitterion

A

a molecule with positive and negative charges that balance → no overall net charge

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85
Q

the pH of which a molecule is uncharged is..

A

the isoelectric point (pI)

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86
Q

how to calculate the pI of a molecule with 2 functional groups

A

average the pKas of the 2 functional groups

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87
Q

what is a peptide bond

A

links amino acids together

formed between the carboxyl group of one AA and the alpha-amino group of another AA (loss of water)

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88
Q

backbone of a polypeptide

A

N-C-C-N-C-C pattern formed from the AAs

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89
Q

when is an individual AA termed a residue

A

when it is part of a polypeptide chain

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90
Q

N-terminus

A

amino end of a polypeptide

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91
Q

C-terminus

A

carboxylic acid end

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92
Q

proteolysis/proteolytic cleavage

A

hydrolysis of a protein by another protein

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93
Q

what is a proteolytic enzyme/protease

A

the protein that does the cutting in proteolysis

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94
Q

which peptide bond is usually cleaved by enzymes

A

the peptide bond adjacent to a specific AA

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95
Q

which amino acid can form disulphide bonds

A

cysteine

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96
Q

how is a disulphide bond formed

A

thiol of one cysteine reacts with the thiol of another cysteine to make a covalent sulfur-sulfur bond

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97
Q

purpose of a disulphide bond

A

stabilizes tertiary protein structure

98
Q

cystine vs cysteine

A

once a cysteine residue becomes disulfide-bonded to another cysteine residue, it becomes cystine

99
Q

what is denaturation

A

the disruption of a protein’s shape without breaking peptide bonds

100
Q

conditions in which proteins are denatured (x4)

A

urea (disrupts hydrogen bonding interactions)

extremes of pH

extremes of temperature

changes in salt conc.

101
Q

primary protein structure

A

AAs bonded to each other in the polypeptide chain aka sequence

102
Q

secondary protein structure

A

folding of polypeptide chain into shapes stabilized by hydrogen bonds between backbone NH and CO groups

103
Q

2 types of secondary protein structures

A

alpha helix

beta pleated sheet

104
Q

why do proline residues never appear within the alpha helix

A

the formation of a peptide bond with proline eliminates the only H on the N (disrupts the backbone H-bonding in the polypeptide chain)

kinks the polypeptide chain

105
Q

why is an alpha helix a favourable structure for a hydrophobic transmembrane region

A

all the polar NH and CO groups in the backbone are H-bonded to each other in the inside of the helix and so don’t interact with the hydrophobic membrane interior

106
Q

hydrogen bonding in beta pleated sheets

A

H-bonding occurs between residues distant from each other or on separate polypeptide chains

107
Q

types of beta sheets

A

parallel pleated sheet: adjacent polypeptide strands running in the same direction

antiparallel pleated sheet: polypeptide strands running in opposite directions

108
Q

tertiary protein folding

A

3D shape of a protein

109
Q

what drives the folding into tertiary structures

A

interactions of R groups with each other and with the solvent (water)

110
Q

hydrophobic R groups (tertiary)

A

tend to fold into the interior of the protein (away from the solvent)

111
Q

hydrophilic R groups (tertiary)

A

tend to be exposed to water on the surface of the protein

112
Q

hydrophobic effect

A

how hydrophobic/philic R groups tend to fold

113
Q

quaternary protein structure

A

interactions between polypeptide subunits

the arrangements of subunits in a multisubunit complex is quaternary structure

114
Q

forces that stabilize tertiary and quaternary structures

A

van der Waals

hydrogen bonds

disulfide bonds

electrostatic interactions

115
Q

what does a hydrolase do

A

hydrolyzes chemical bonds

116
Q

what does an isomerase do

A

rearranges bonds within a molecule to form an isomer

117
Q

what does a ligase do

A

forms a chemical bond

118
Q

what does a lyase do

A

breaks chemical bonds by means other than oxidation or hydrolysis

119
Q

what does a kinase do

A

transfers a phosphate group to a molecule from a high energy carrier, such as ATP

120
Q

what does an oxidoreductase do

A

runs redox reactions

121
Q

what does a polymerase do

A

polymerization

122
Q

what does a phosphatase do

A

transfers a phosphate group to a molecule from inorganic phosphate

123
Q

what does a protease do

A

hydrolyzes peptide bonds

124
Q

what is reaction coupling

A

a favourable reaction is used to drive an unfavourable one

125
Q

why is reaction coupling possible

A

free energy changes are additive

126
Q

how does ATP hydrolysis drive unfavourable reactions (x2)

A

causes a conformational change in a protein

transfer of a phosphate group from ATP to a substrate

127
Q

how are carbohydrates broken down to CO2

A

oxidation (aka combustion or burning)

128
Q

why are carbohydrates the principle energy source for cellular metabolism

A

the oxidation of carbohydrates to CO2 releases large amounts of energy

129
Q

what is a monosaccharide

A

a single carbohydrate molecule → aka simple sugar

130
Q

monosaccharide formula

A

CnH2nOn

131
Q

examples of monosaccharides

A

fructose, glucose, ribose

132
Q

monosaccharides to polysaccharide

A

monosaccharide → disaccharide → oligosaccharide → polysaccharide

133
Q

what is a glycosidic linkage

A

bond between 2 sugar molecules

covalent bond formed in a dehydration reaction (requires enzymatic catalysis)

134
Q

glycogen and starch

A

glycogen → energy storage in animals

starch → energy sto=rage in plants

135
Q

cellulose

A

polymer of cellobiose

cellobiose does not exist freely in nature (only as cellulose)

wood + cotton are made of this

136
Q

roles of lipids

A

in adipose cells, triglycerides store energy

in cellular membranes, phospholipids constitute a barrier between intracellular and extracellular environments

cholesterol serves as the building block for hydrophobic steriod hormones

137
Q

fatty acid structure

A

composed of long unsubstituted alkanes that end in a carboxylic acid

138
Q

why are only even numbered fatty acids made in human cells

A

they are synthesized 2 carbons at a time from acetate

139
Q

saturated vs unsaturated fatty acids

A

saturated: no C=C bonds, bound to maximum Hs
unsaturated: one or more double bonds (almost always Z aka cis)

140
Q

what drives hydrophobic tails into the center of a micelle

A

hydrophobic interaction

141
Q

composition of a triglyceride

A

3 fatty acids esterified to a glycerol molecule

142
Q

why is it important to store fatty acids as triglycerides

A

free fatty acids are reactive chemicals

143
Q

what enzyme hydrolyzes fats

A

lipases

144
Q

why are fats more efficient energy storage molecules than carbohydrates

A

packing and energy content W

145
Q

packing - fats

A

the hydrophobicity of fats allows them to pack together closer than carbohydrates

146
Q

energy content - fats

A

fat molecules can store more energy than carbohydrates (more energy carbon-for-carbon than a carbohydrate)

147
Q

what are membrane lipids

A

phospholipids derived from diacylglycerol phosphate

148
Q

how is a lipid bilayer formed

A

hydrophobic interactions drive the formation of the bilayer and stabilized by van der Waals forces between the long tails

149
Q

why do unsaturated fatty acids prevent a solid membrane

A

unsaturation in phospholipid fatty acids increases membrane fluidity → disrupts orderly packing of hydrophobic lipid tails

150
Q

what increases membrane fluidity

A

decreasing the length of fatty acid tails

double bonds in phospholipid fatty acids

cholesterol

151
Q

how does cholesterol affect membrane fluidity

A

at low temps → increases fluidity (membrane antifreeze)

at high temps → reduces membrane fluidity

152
Q

terpenes

A

compounds built from isoprene units

formula: (C5H8)n

153
Q

how are terpenes classified

A

they can be linear or cyclic and are classified by the number of isoprene units they contain

mono = 2

sesqui = 3

di = 4

154
Q

squalene

A

a triterpene (6 isoprene units) and it is used in the manufacture of steroids

155
Q

what is a terpenoid + example

A

species built from an isoprene skeleton & functionalized with other elements (O, N, S)

vit A

156
Q

what are steroid hormones made of + examples

A

cholesterol

testosterone and estradiol

157
Q

structure of steroids

A

tetracyclic ring system

158
Q

where does cholesterol come from

A

diet + synthesis in liver

159
Q

how is cholesterol carried in the blood

A

packaged with fats and proteins into lipoproteins

160
Q

characteristics of phosphoric acid

A

inorganic (doesn’t contain carbons)

can donate 3 protons

161
Q

orthophosphate

A

aka just phosphate

162
Q

pyrophosphate

A

2 orthophosphates bound together via an anhydride linkage

163
Q

why do the phosphate anhydride bonds store so much energy

A

when phosphates are linked together, their negative charges repel each other

orthophosphate has more resonance dorms (lower free energy than linked phosphates)

orthophosphate has a more favourable interaction with water than linked phosphates

164
Q

composition of nucleotides

A

ribose sugar group

purine/pyrimidine base joined to carbon 1

1 or 2 or 3 phosphate units joined to carbon 5

165
Q

ATP phosphoanhydride bonds

A

energy extracted from the oxidation of food is immediately stored here → later used to power cellular processes

166
Q

maltose

A

glucose + glucose

167
Q

sucrose

A

glucose + fructose

168
Q

lactose

A

glucose + galactose

169
Q

4 lipids in the body

A

triglycerides

phospholipids

terpene

cholesterol

170
Q

importance of folding in enzyme function

A

for the proper formation of the active site → directly involved in catalysis

171
Q

active site model

A

states that the substrate and active site are perfectly complementary

172
Q

induced fit model

A

states that the substrate and active site differ and that the binding of the substate induces a conformational change in the enzyme

173
Q

stereospecificity

A

the ability to distinguish between stereoisomers

174
Q

aspartic acid

A

asp (D)

acidic AA

175
Q

glutamic acid

A

glu (E)

acidic AA

176
Q

lysine

A

lys (K)

basic AA

177
Q

arginine

A

arg (R)

basic AA

178
Q

histidine

A

his (H)

basic AA

179
Q

glycine

A

gly (G)

hydrophobic + non polar

180
Q

alanine

A

ala (A)

hydrophobic + non polar

181
Q

valine

A

val (V)

hydrophobic + non polar

182
Q

leucine

A

leu (L)

hydrophobic + non polar

183
Q

isoleucine

A

ile (I)

hydrophobic + non polar

184
Q

phenylalanine

A

phe (F)

hydrophobic + non polar

aromatic

185
Q

tryptophan

A

trp (W)

hydrophobic + non polar

aromatic

186
Q

serine

A

ser (S)

polar

187
Q

threonine

A

thr (T)

polar

188
Q

tyrosine (Y)

A

tyr (Y)

aromatic

189
Q

asparagine

A

asn (N)

polar

190
Q

glutamine

A

gln (Q)

polar

191
Q

cysteine

A

cys (C)
sulfur containing

192
Q

methionine

A

met (M)

sulfur containing

193
Q

proline

A

pro (P)

has a ring structure

194
Q

characteristics of proteases

A

have an active site with a serine residue whose OH group can act as a nucleophile (attack the carbonyl carbon of an AA residue in a polypeptide chain)

195
Q

what is a recognition pocket

A

pocket in an enzyme’s structure that attracts certain residues on substrate polypeptides

196
Q

cofactors - enzymes

A

metal ions/small molecules that are required for activity in many enzymes

197
Q

an organic cofactor is a…

A

coenzyme

198
Q

4 ways to regulate enzyme activity

A

covalent modification

proteolytic cleavage

association with other polypeptides

allosteric regulation

199
Q

covalent modification

A

different groups attached to proteins that regulate their activity

e.g. phosphoryl group (added by a protein kinase) can activate/inactivate an enzyme

200
Q

action of protein phosphatase

A

reversal of protein phosphorylation

201
Q

proteolytic cleavage

A

inactive forms (zymogens) are activated by cleavage by a protease

202
Q

association with other polypeptides

A

some enzymes have catalytic and regulatory subunits

some proteins require association with another peptide to function

203
Q

allosteric regulation

A

modification of active-site activity through molecules with other specific sites on the enzyme (allosteric sites)

alters the enzyme to increase/decrease catalysis

204
Q

negative feedback/feedback inhibition

A

end product will shut off an enzyme early in the pathway

205
Q

feedforward stimulation

A

stimulation of an enzyme by its substrate or a molecule used in the synthesis of the substrate

206
Q

enzyme kinetics

A

study of the rate of formation of products from substrates in the presence of an enzyme

207
Q

reaction rate

A

amount of product formed per unit time

208
Q

Vmax

A

the reaction rate at which the enzyme is saturated

adding substrates doesn’t increase the reaction rate

209
Q

Michaelis constant

A

the substrate conc. where the reaction velocity is half its maximum g

gives info about the affinity of an enzyme for its substrate

210
Q

what does a low Km mean

A

not much substrate is needed to get the reaction rate to half the maximum rate

enzyme has a high affinity for the substrate

211
Q

cooperativity

A

binding of substrate to one subunit modulates the affinity of other subunits for substrate

212
Q

2 types of cooperativity

A

pos and neg

213
Q

positive cooperativity

A

binding of a substrate to one subunits increases the affinity of the other subunits

tense → relaxed

214
Q

negative cooperativity

A

binding of a substrate to a subunit reduces the affinity of other subunits

215
Q

distinction between allosteric binding and cooperativity binding

A

cooperativity binding occurs at the active site

allosteric occurs at other sites

216
Q

competitive inhibitors

A

inhibitors that compete with substrate for binding at the active site

can be overcome by adding more substrate (outcompete)

Km is increased with competitive inhibitors

217
Q

noncompetitive inhibitors

A

bind at the allosteric site, not active

adding more substrate won’t help

lowers Vmax

doesn’t usually alter Km

substrate still binds but catalytic activity is prevented

218
Q

uncompetitive inhibitors

A

inhibitors that can only bind after the enzyme-substrate complex has formed

bind to allosteric sites

decreases Vmax

decreases Kmax

219
Q

what is Km

A

conc. of substrate that allows for the enzyme to reach half Vmax

lower Km = higher affinity

220
Q

mixed-type inhibition

A

inhibitor can bind to either the unoccupied enzyme OR the enzyme-substrate complex

221
Q

when does Km increase for mixed-type

A

if the enzyme has a greater affinity for in its free form → lower affinity for the substrate

similar to competitive inhibition

222
Q

when does Km decrease for mixed-type

A

if the enzyme-substrate complex has a greater affinity for the inhibitor → greater affinity

similar to uncompetitive inhibitor

223
Q

mixed type - equal affinity

A

it would be a non-competitive inhibitor

224
Q

Lineweaver-Burk plot

A
225
Q

slope of L-B plot

A

Km / Vmax

226
Q

y intercept of L-B plot

A

1 / Vmax

227
Q

x intercept of L-B plot

A

-1 / Km

228
Q

competitive inhibitors..

A

do not affect Vmax but increase Km

229
Q

noncompetitive inhibitors..

A

decrease Vmax but don’t change Km

230
Q

uncompetitive inhibitors..

A

reduce Km and Vmax

231
Q

mixed type inhibitors..

A

reduce Vmax but have variable effects on Km

232
Q

do catalysts affect thermodynamics

A

no, only kinetics

233
Q

characteristics of enzymes (3)

A

increases the rate of reaction

cannot be used up

specific for a specific reaction

234
Q

where do substrates bind

A

active site

235
Q

easiest way to turn an enzyme on/off

A

phosphorylation

236
Q

2nd most common way to regulate enzyme activity

A

allosteric regulation

237
Q

purpose of pos feedback

A

drives a reaction to a certain end point

e.g. contractions → birth

238
Q

Vmax depends on..

A

enzymes!

the specific enzyme & enzyme conc.

239
Q

decreased Km..

A

increased enzyme affinity for substrate

240
Q

all biologically produced amino acids have ___ configuration

A

L

241
Q

which AA plays a central role in the formation of alpha helices and beta sheets

A

proline

Biology - MCAT (11 decks)

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