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Exam 2 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Enzymes become ___ at high substrate concentration

A

Saturated

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2
Q

ΔG tells us what? what does it not tell us

A

-if the reaction will occur
-nothing about the RATE

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3
Q

what is a catalyst

A

something that speeds up a rxn but reamins unchanged when the rxn is over
lowers activation energy

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4
Q

what does a catalyst not affect

A

ΔG, equilibrium point, add energy

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5
Q

what are enzymes

A

proteins that act as biological catalysts

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6
Q

what are ribozymes

A

RNA molecules that act as biological catalysts

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7
Q

what is the activation energy

A

energy barrier must be overcome before a reaction can occur, even for spontaneous

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8
Q

what might activation energy represent

A
  • energy needed to bring substrates into transition state
    -unfavorable chemical environment for rxn
    -physical separation of reactants
    -other factors that hinder progress of reaction
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9
Q

for uncatalyzed rxns where does the activation energy come from

A

random thermal energy

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10
Q

what can overcome activation energy

A

heat

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11
Q

what do high temperatures do to cellular structures

A

denature them by destroying the hydrogen bonds

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12
Q

how do catalysts work

A

-bringing reactants together
-altering chemical environments around reactants
-bringing substrates into transition state
-doing other things to remove obstacles to reaction progress

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13
Q

what3 properties do all catalysts share

A
  1. increase rxn rates by lowering activation energy
  2. form transient, reversible complexes with substrate molecules
  3. change the rate at which equilibrium is achieved not position of equilibrium
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14
Q

what is a coupled rxn

A

use of an exergonic rxn to provide energy for an endergonic rxn

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15
Q

extracellular vs intracellular

A

extracellular matrix
-collagen in animals
cytoskeleton for intracellular

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16
Q

what forms of communication do proteins use

A

receptors
antibodies (animals)
hormones
transport

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17
Q

what do proteins regulation function regulate

A
  1. gene expression
    physically by histones
    physiologically by enzymes that control transcription
  2. other proteins
    -calmodulin
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18
Q

why are histones positively charged

A

because DNA has phosphates which make them negative and the histones are positive- before phosphates are added

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19
Q

what is one example of the adhesion function in proteins

A

glycoproteins at cell surface
-stick us together

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20
Q

what is an example of storage and transport function in proteins

A

blood- transporting oxygen
storing amino acids to build new structures

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21
Q

how many amino acids are used in protein synthesis

A

20

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22
Q

at pH 7 what is ionized in the basic amino acid structure

A

amino(+) and carboxyl groups(-)

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23
Q

nonpolar amino acids have what characteristics

A

r-group is mostly hydrocarbon- nothing charged or polar

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24
Q

peptide bond characteristics

A

partial double bond characteristic - which limits rotation around the bond and how a polypeptide can fold

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25
Q

how would you describe primary structure

A

sequence of amino acids in a chain- from N to C terminus

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26
Q

peptides fold to achieve what

A

lowest free energy state

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27
Q

why does folding in protein happen

A

noncovalent bonds and hydrophobic exclusion

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28
Q

how would you describe secondary structure

A

conformation oof polypeptide strand, alpha helix and beta strand result from rotation of bonds around alpha-c in chain

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29
Q

alpha helix structure charcteristics

A

right handed spiral- held by v.d.w forces and hydrogen bonds- side chains point out from helix axis

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30
Q

what category of amino acids would most likely be found in a alpha helix

A

nonpolar group of amino acids

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31
Q

how many amino acids are needed to cross the bilayer as part of an alpha helix

A

3.6 on each fold or turn
5.56 turns to get across nonpolar
=20 aa needed to span the bilayer- round up

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32
Q

beta strand characteristics

A

-stretched chain
-no H-bonds within strand but do link neighboring strands
-side chains (R) point up and down

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33
Q

what would loops and turns on a protein be caused by

A

proline
charged side chains

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34
Q

why are loops and turns on a protein important

A

bending and folding of polypeptide
-short stretches that connect alpha helices and beta strands

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35
Q

what are intrinsically disordered proteins and what do they lack

A

random coils - gain structure when environment changes, abundant in cells,
-tertiary structure, hydrophobic and aromatic amino acids

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36
Q

how would IDP’s be able to have a predictive function

A

can adapt some order if mixed with particular lipids that are membrane formers can adapt to that structure

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37
Q

what are motifs

A

modular
-common patterns of secondary structures
-may have functional significance

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38
Q

what are domains

A

stable, independently folding protein regions
-may have functional significance

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39
Q

what three things always affect noncovalent bonds

A

ph, temp, and salt concentration

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40
Q

how would you explain pic of motif

A

either a beta sheet or alpha helices anti parallel both ways but can see it in beta sheet

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41
Q

what structure does carbonic anhydrase have

A

beta sheets

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42
Q

when something is hydrophobic is it polar or nonpolar

A

nonpolar (tails in a membrane)

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43
Q

what are the 3 noncovalent bonds that help proteins fold

A

hydrogen bonds, van der waals attraction, electrostatic connections

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44
Q

what is denaturation and is it reversible

A

unfolding that disrupts function, may be reversible may not be

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45
Q

what are examples of things that would cause denaturation

A

heat, alcohol, acids, bases, heavy metals, reducing agents, detergent

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46
Q

in tertiary structures disulfide bridges

A

stabilize- must have a cysteine to do oxidation and reduction

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47
Q

proteins bind to

A

ligands

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48
Q

enzymes bind to

A

substrates to catalyze reactions

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49
Q

what does enzymes binding to substrates do

A

decreases activation energy and increases reaction rates

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50
Q

what does the sentence enzymes are reusable explain

A

they return to their initial state after releasing reaction products.

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51
Q

what does the sentence enzymes are specific in activity mean

A

each catalyzes one type of reaction for a single type substrate

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52
Q

how do enzymes recognize substrates

A

by their shape and chemical properties

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53
Q

what is the active site

A

where substrate binds and catalysis occurs

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54
Q

what do enzymes have that contribute to activity that are nonproteins

A

cofactors

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55
Q

what are the 2 types of cofactors

A

inorganic (metal ions)
organic

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56
Q

what is a prosthetic group

A

organic cofactor- molecule is tightly bound to protein and required for activity

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57
Q

what is a coenzyme

A

cofactor- not tightly bound to protein-, carries substrates to or products from enzymes

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58
Q

coenzymes are or are derived from

A

vitamins

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59
Q

what is a lysozyme

A

cleaves a polysaccharide chain

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60
Q

what bonds do lysozymes cleave

A

beta 1-4 linkages

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61
Q

enzymes become ____ at high substrate concentration

A

saturated

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62
Q

what is vmax

A

maximal velocity - how fast

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63
Q

what is km

A

substrate concentration when v=1/2 vmax

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64
Q

km is related to enzymes

A

affinity for substrate

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65
Q

if there is high affinity km will be

A

low

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66
Q

why would isomers have different affinity

A

structure between different isomers

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67
Q

can too high of a temperature or ph affect enzyme activity

A

yes too high of a temp can cause a huge drop in function
-each enzyme has an optimal curve for environment they have evolved

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68
Q

how does ph affect structure and function

A

affect the charge on basic and acidic amino acids
optimal curve, pH maximum correlates to in vivo environment of enzyme

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69
Q

what kind of environments do lysozymes operate in

A

acidic, so too high of a pH affects structure and function
ionic strength also affects activity

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70
Q

what 2 things regulate protein abundance

A

-gene expression
-proteolysis

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71
Q

what is gene expression

A

turns on gene to make more protein and more enzymes

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72
Q

what is proteolysis

A

degrade proteins in regulated manner

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73
Q

what is the main type of covalent modification in regulation of protein activity

A

phophorylation and dephosphorylation
-fast

74
Q

what does the protein kinase do

A

phosphate added to amino acids with OH

75
Q

what does phophotase do

A

removes phosphates

76
Q

which amino acids can be targeted by protein kinases

A

those with OH groups-tyrosine, serine, thereonine

77
Q

allosteric proteins can change shape when changes

A

its job

78
Q

where is the allosteric site located

A

regulatory domain

79
Q

what does an allosteric site bind

A

allosteric regulator

80
Q

how is allostery a regulation method

A

the change in shape affects the active site and whether the substrate can bind or not

81
Q

allosteric activators increase the affinity for substrate so what about the km

A

km decreases

82
Q

what is a competitive inhibitor

A

binds to active site of enzyme and blocks substrate binding
-may be an alternative substrate, looks like one
-if binds covalently then it is a toxin

83
Q

nonpolar side chains make the amino acids hydrophobic or hydrophillic

A

hydrophobic which forms the core of many proteins

84
Q

secondary and tertiary structure difference in bonding how

A

secondary- bonds between hydrogens
tertiary- bonds between R groups

85
Q

nonpolar molecules are hydrophobic or hydrophillic

A

hydrophobic- in membranes the tails

86
Q

how does a competitive inhibitor affect the value of km and vmax

A

km- increase
vmax- no change

87
Q

is competitive inhibition reversible

A

yes, add more of desired substrate to out compete then inhibitor

88
Q

what is competing in competitive inhibition

A

two substrates competing for the active site

89
Q

what is non-competitive inhibition

A

inhibitor binds to regulatory site and decreases enzymes ability to catalyze rxn

90
Q

how does noncompetitive inhibition affect km and vmax

A

no change in km but decreases vmax

91
Q

what are examples of noncompetitive inhibitors

A

toxins, heavy metals

92
Q

is noncompetitive inhibition reversible

A

no- toxins affect protein structures

93
Q

what is feedback inhibition

A

products of metabolic pathways act as inhibitors of enzymes
- bind to allosteric site to cause conformational change

94
Q

calcium in calmodulin properties

A

calcium regulates the proteins structure
it is a motif that is part of the protein structure
-calcium affects the shape and function

95
Q

what does the plasma membrane do and what is the labeled function

A

separates cell contents from outside environments
-compartmentation

96
Q

how does compartmentation function in biological membranes

A

-separate different part of the cell from one another
- allows different reactions with different membranes to exist within cell

97
Q

how does the function of metabolism work in biological membranes - 3 ways

A

-some rxns and pathways function in nonpolar environment, enzymes in membrane catalyze
- organization of some metabolic pathways
- enable electrochemical gradients to exist

98
Q

what is an example of metabolism in biological membranes

A

mitochondria forming ATP

99
Q

can prokes have a electrochemical gradient

A

yes even though no strong permeability barrier or compartments

100
Q

what is the only membrane that prokaryotes have? why is that important?

A

plasma membrane and they use it to maintain electrochemical gradients

101
Q

what are examples of communicators in biological membranes

A

plasma membrane, hormone signals

102
Q

what is the structure of biological membranes

A

fluid mosaic model
- bilayer of hydrophillic and hydrophobic lipids forms matrix

103
Q

where are proteins located in membranes

A

on and in bilayer

104
Q

how are carbohydrates related to membranes

A

found on the outer surface of plasma membrane
-glycocalyx and glycoproteins (furry)

105
Q

what is the wight vs molar ration between proteins and lipids in the membranes

A

weight ratio- 1:1
molar ratio -1:50

106
Q

how would ratios of components vary in membranes

A

-depend on type of membrane, cell, tissue, organ, species, and environment
- highest protein content
-molar vs weight ratio

107
Q

what are the ways that membrane proteins attach to membrane

A

peripheral proteins
integral membrane proteins

108
Q

what are integral membrane proteins

A

tightly associated with membrane structure

109
Q

what are peripheral proteins

A

are held on surface by non-covalent bonds

110
Q

properties of hydrophobic (nonpolar) regions in the core of bilayer

A

-hydrophobic aa
-membrane spanning a-helices and b-barrels are common
-amphipathic a-helices and b-barrels can form channels through membranes

111
Q

how would you calculate how many amino acids needed to span a bilayer

A

bilayer across divided by vertical rise
and then times 3.6

112
Q

what is an example of a channel protein in a membrane

A

beta barrel filled with water molecules which is an polar structure - forms a hydrophillic core!

113
Q

outer leaflet vs inner leaflet

A

outer- glycocalyx, layer of carbs- more saturated fatty acids- sphingomyelin, PC
inner- less saturated, PE, PS

114
Q

how does protein asymmetry occur

A

as they are being synthesized

115
Q

If protein asymmetry is the orientation of proteins in membranes and is specific across bilayer, how are they determined?

A

when proteins are made and inserted into membrane layer- different things on different sides

116
Q

what may asymmetry be due to among different parts of cell surface

A
  • tight junctions that seal cells together
  • linkage to cytoskeleton
    -membrane rafts
117
Q

what are membrane rafts important for

A

cell signaling

118
Q

what do membrane rafts often contain

A

lipids with lower fluidity - saturated

119
Q

what is a membrane raft

A

where membrane lipids have similar physical and chemical properties aggregate

120
Q

what physical properties allow the fluid phase to have a high degree of motional freedom

A
  • around c-c bonds in fatty acids
    -rotation of entire molecule
  • lateral diffusion
121
Q

what is the gel phase when talking about physical properties of membranes

A

slower movement, tightly packed lipids

122
Q

what are the physical properties of membranes

A
  1. the phase transitions between fluid and gel
  2. fluid phase has more freedom
  3. gel phase
    4.fluid gel transition
  4. non bilayer phases exist
123
Q

what is the fluid-gel transition being influenced by and is it reversible?

A

temperature
yes
-think of butter

124
Q

what is the importance of non bilayer phases existing

A
  • membrane fusion
  • 2 membranes next to eachother fusing, one must break out
125
Q

membranes with less fluidity would take longer to do what

A

recover from bleached light

126
Q

when talking about the fluid- gel phase transition what helps keep the membranes fluid

A

double bonds - wider curve

127
Q

what does tm depend on in the fluid- gel phase

A

of unsaturated c-c bonds

length of fatty acid
-position of double bond
-headgroup
-solution properties

128
Q

the more carbon atoms more or less fluid

A

less

129
Q

what are consequences of fluid-gel phase transitions

A

-membrane functionality
-change in permeability , 100% less permeable in gel phase
-protein function - increased or decreases, depends on interactions with lipids

130
Q

how do sterols interfere with the gel phase

A

fluidity buffer, lower fluidity

131
Q

protein diffusion is determined, in part, by lipid ____. also depends on whether protein is ____ by attachment to _____ of extracellular matrix

A

fluidity, anchored, cytoskeleton

131
Q

if some proteins were anchored and bleached would it recover faster or slower

A

slower

132
Q

what is homeoviscous adaptation

A

organisms can change membrane composition to keep them fluid as environment changes
-seasonal, homeothermic

133
Q

as winter approaches, what type of lipid is most liely to accumulate

A

unsaturated fatty acids- lower boiling point, more fluid

134
Q

what types of cells have the cytoplasmic enzyme complex and what does it make

A

prokaryotes and eukaryotes
-in eukaryotes it makes saturated and monosaturated fatty acids

135
Q

what does the chloroplastic pathway make

A

prokaryotes -polyunsaturated fatty acids

136
Q

where does fatty acid synthesis occur

A

in cytosol not a membrane

137
Q

what leaflet is facing the cytosol

A

outer leaflet

138
Q

fatty acids added to membrane lipids in where

A

outer leaflet of er- biogenesis

139
Q

is the er or golgi symmetrical or asymmetrical

A

asymmetrical

140
Q

what do scramblase and flippase do in membrane biogenesis

A

1st step- scramblase- moves fatty acids to some inner leaflet
flippase- moves some back to get correct positioning

141
Q

what carries lipids and proteins to endomembrane system

A

vesicles

142
Q

what do lipid transfer proteins do

A

move lipid molecules from er to organelles NOT in endomembrane system

143
Q

what is included in the endomembrane system

A

er, golgi, endosomes, lysosomes, nuclear envelope

144
Q

polypeptides are inserted into the membrane as they are

A

synthesized

145
Q

vesicles with proteins in membrane bud off and move to____. more glycosylations and other _____ can occur

A

golgi, modifications

146
Q

membrane lipids and proteins move to ___ ______ as vesicles

A

plasma membrane

147
Q

where are proteins for membranes that are not included in the endomembrane system made and taken to

A

made on soluble ribosomes
taken to target membrane with chaperone proteins

148
Q

ion concentrations are ______ inside and outside of the cell

A

different

149
Q

lipid bilayer in terms of transport

A

permeability barrier for large, polar, and charged molecules
-semi permeable

150
Q

what is stored in gradients

A

potential energy (free energy)

151
Q

uncharged solutes make what type of gradient

A

chemical concentration gradients

152
Q

what type of gradient to charged solutes make

A

electrochemical gradients
-free energy has voltage gradient

153
Q

passive or active transport depends on what

A

change in G

154
Q

is active transport exergonic or endergonic

A

endergonic

155
Q

does diffusion require energy- what does it depend on

A

no, depends on random thermal energy

156
Q

is diffusion spontaneous or nonspontaneous

A

spontaneous

157
Q

as diffusion occurs is the change in G moving closer or farther from 0

A

closer- less negative

158
Q

Jj=Dj x ΔG /distance - what does each part of the equation mean
-ficks 1st law of diffusion

A

Jj= amount of j crossing a given area per unit of time
Dj= diffusion coefficient- depends on permeability- slope
distance= thickness of barrier

159
Q

what is simple diffusion

A

through the membrane= passive movement through lipid bilayer

160
Q

a membrane that has transporter proteins and enzymes is going to have a higher or lower Dj

A

higher

161
Q

what is facilitated diffusion? is it spontaneous? does it require energy? what does it require?

A

-passive movement of polar or charged molecules across membrane
-spontaneous
-no energy needed
-requires transmembrane protein

162
Q

how do transporters (carriers) work?

A

bind solute on one side of membrane
- solute falls off and diffuses away
-undergo conformation change that opens binding site

163
Q

how are the transporters for facilitated diffusion enzyme like (4)

A
  • specific for specific solutes
    -recognize solutes by chemical properties
    -saturate at high conc.
    -competitive inhibition by similar solutes
164
Q

uniport vs cotransport

A

uniport- transport single solutes
cotransport- moves 2 solutes

165
Q

channels are mainly for what type of transport and what does it not bind

A

ion- do not bind solute

166
Q

porins vs aquaporins in proteins for facilitated diffusion or passive transport

A

porins - large channels opening 4nm
aquaporins = water channels
-bacteria, endosymbiosis theory
facilitate water diffusion when simple diffusion is not fast enough

167
Q

an ion channel has a ____ filter that controls which ____ ions it will allow to cross the membrane

A

selectivity, inorganic

168
Q

what is a gated channel

A

opens/shuts to control solute movement

169
Q

what is active transport

A

requires input of energy to overcome unfavorable free energy gradient

170
Q

active transport moves solutes….

A

against their gradient- coupled rxn

171
Q

energy usually comes from

A

directly or indirectly from ATP

172
Q

what is direct active transport

A

transport protein uses ATP hydrolysis to get energy
-binding site for ATP
-establishes membrane potential

173
Q

5 characteristics for the P-type pump in direct active transport

A

-pump is phosphorylated by ATP
-single polypeptide with 8-10 trasnsmembrane helices
-all pump cations
-all inhibited by vandate
-located in plasma membrane and er

174
Q

p type pumps bind what during transport cycle

A

phosphate of atp

175
Q

what face does atp bind on

A

cytosolic

176
Q

what is a sodium-potassium ATPase

A

a p type pump that pumps 3 Na+ out and 2K+ into animal cells

177
Q

hydrolysis and binding of atp causes what

A

shape change

178
Q

what is the v type pump in direct active transport

A
  • not phosphorylated by atp- makes atp
    -multi subunit proteins
    -unaffected by vandate
    -all pump H+ out of cytosol- into vacuole
179
Q

characteristics of v type pump and H+-ATPase

A

-pumps H+ out of cytosol into organelles and vesicles
-helps regulate cystolic ph
-can acidify some vesicles
-active transporter

cell biology (4 decks)

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