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1
Q

macromolecules that can’t form polymers

A

lipids

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2
Q

what is the most abundant molecule in organisms

A

proteins, then nucleic acids

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3
Q

what is one way organisms benefit from consuming other organisms

A

all organisms are composed of the same macromolecules composed of roughly the same proportions

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4
Q

process by which monomers are added to a growing polymer

A

dehydration synthesis or condensation. an OH is removed from the monomer and a hydrogen from the polymer, forming a bond and releasing water

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5
Q

hydrolysis is the process of

A

breaking down a polymer to a monomer and. polymer minus 1. the water attacks the bond and leaves h on polymer and oh on the monomer

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6
Q

direction of protein synthesis

A

n terminus to c terminus, numbered 1 to n from n to c

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7
Q

protein structure

A

primary - sequence, secondary - backbone, tertiary - r group, quaternary - other polypeptides

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8
Q

types of primary structure

A

alpha helices and beta pleated sheets, both arise from hydrogen bonds on the backbone

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9
Q

proline can form what kind of secondary structure

A

none, it has a ring in its structure and so the nitrogen is not bonded to any hydrogens

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10
Q

types of tertiary interactions

A

hydrophobic interactions, ionic, disulfide, hydrogen bonds between r groups or between r groups and backbone

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11
Q

what is coiled coils?

A

happen when there are hydrophobic aas at every 4th position (one rotation is 3.6 aa), gives rise to fibrous structural proteins like keratin in hair

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12
Q

is folding a reversible process

A

typically yes

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13
Q

what are protein chaperones?

A

proteins which allow for the folding of new proteins (isolating them when they are newly syntehsized as polypeptides)

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14
Q

what are the building blocks of nucleotides

A

phosphate linked (to the 5 carbon) of a 5 carbon sugar linked to a nitrogenousbase(to the 1 carbon)

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15
Q

differences between ribose and deoxyribose

A

ribose is only in RNA whereas DNA has exclusively deoxyribose. ribose has a hydroxyl group on the 2 carbon whereas deoxyribose does not (deoxy, de oxy)

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16
Q

what is atp

A

energy rich molecule fro the 2 phosphate bonds on an adenine base

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17
Q

what are they pyrimidines and what are the purines

A

pyrimidines CUT purines (AG)

pyrimidines are smaller, bigger name
purines are bigger, CUT into pyrimidines

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18
Q

direction and mechanism of nucleotide synthesis

A

5’ to 3’, phosphodiester linkage formed between hydroxyl on 3 carbon and oxygen on phosphate of next molecule

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19
Q

big names of people involved in DNA structure discovery

A

rosalund franklin, Francis crick, James Watson

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20
Q

number of hydrogen bonds between purines and pyrimidines

A 
GC 3
AT 2(same as AU)
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21
Q

how is DNA structured

A

double stranded, antiparallel, and helical.

has major and minor grooves when looked at from a fixed orientation

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22
Q

describe tRNA’s hairpin structure

A

there is a single stranded loop portion as well as a double stranded portion

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23
Q

anabolic reactions

A

synthesize molecules and requires energy

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24
Q

catabolic reactions

A

breakdown molecules and release energy

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25
Q

energy coupling

A

endergonic and exergonic reactions (catabolic and anabolic) are paired to make endergonic proceed spontaneously

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26
Q

driving forces of spontanaeity

A

enthalpy and entropy yield a relationship with temperature which is described by Gibbs free energy equation. negative energy is good

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27
Q

conditions for standard free energy

A

37 deg and 1 m of all reactants, actual g usually differs

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28
Q

can rate be predicted if free energy is known

A

no it cannot

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29
Q

function of catalysts

A

enzymes who catalyst reactions, don’t impact rate or overall change in free energy

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30
Q

how do catalysts function

A

bringing molecules together, charge isolation, mechanical strain to induce reaction

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31
Q

what are cofactors

A

things necessary for catalysis that are not polypeptides or enzymes. often are metal ions

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32
Q

differences between allosteric and competitive inhibition

A

competitive requires equal or greater concentration of regulatory molecule whereas allosteric does not

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33
Q

aldehydes vs ketones

A

carbonyl groups that are terminal for aldehydes or central for ketones

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34
Q

optical isomers exhibit chirality

A

this leads to stereoisomerisation

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35
Q

differences between alpha and betaglucose

A

are in equilibrium with the linear molecule, alpha hydroxyl points down (same orientation as 4 hydroxyl) whereas beta does the opposite

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36
Q

amylose

A

a starch (hydrocarbon) is linear and only has alpha linkages (helical)

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37
Q

amylopectin

A

another starch (like amylose) but can be moderately branched, is glycogen in animals (helical)

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38
Q

glycogen

A

storage of glucose subunits, alpha linkages, branched, functionally and structurally similar to amylopectin (helical)

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39
Q

cellulose

A

is symmetrical and is completely linear, exhibits strong h bonding due to its linear shape. beta 1 4 linkages

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40
Q

uses of lipids

A

energy, cell membranes, carotenoids (energy capture)hormones and vitamins, thermal and electrical insulation, hydrophobicity

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41
Q

composition of fatty acids

A

carboxyl group and a hydrocarbon tail

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42
Q

fats and phospholipids

A

form between fatty acids and glycerol molecule

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43
Q

phospholipid structure

A

choline head atop a phosphate molecule, attached to a diglyceride glycerol

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44
Q

formations of a phospholipid bilayer

A

thermodynamically favoured

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45
Q

fluid mosaic model

A

paints a picture of the membrane model. phospholipids and most proteins can float around as much as they want but don’t flip to the other side very often at all.

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46
Q

describe saturation of different fats

A

highly saturated means no double bonds in the hydrocarbon chain, makes it very non polar in that region, leads to IMFS

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47
Q

saturation of the bilayer

A

leads to reduced fluidity and permeability in saturated bilayers, the opposite is true for unsaturated ones

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48
Q

what does it mean to be amphipathic

A

having a region which is polar and others that are not

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49
Q

how does the amphipathicity of some proteins play into the mosaic model

A

the polar ends will reside on the outsides and the polar component of the layer with non polar components transversing the hydrophilic portions of phospholipid layer

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50
Q

meaning of peripheral or transverse(integral) proteins

A

peripheral is on either side, whereas transverse cut all the way through

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51
Q

permeability of different molecules and elements in thebilayer

A

gases molecules pas easily through, uncharged polar get through because of their small size, large uncharge have trouble and ions basically don’t

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52
Q

factors controlling rates of diffusion

A

distance between molecules, temperature, size of molecule and the steepness of the concentration gradient

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53
Q

osmosis mechanism

A

osmosis is the transfer of water through a semipermeable membrane, where water flows from low to high solute concentration (high to low water concentration)

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54
Q

types of non diffusion passive transport (name 2)

A

facilitated diffusion occurs by

  1. channel proteins - which allow for the flow of ions, usually voltage gated
  2. carrier proteins -binds the substrate and assists it out of the cell ( or in)
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55
Q

types and definition of active transport

A

requiring energy directly or indirectly. ex na k pump which pumps both ions across their gradients, described as active transport
secondary active transport are symporters and anti porters for example.
symport - same direction
antiport - opposite directions. the driver molecule always follows its gradient, assisting the target to move against

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56
Q

what drives glucose transport in gut cells:

A

sodium concentration (symport)

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57
Q

describe diffusion limit in context of cell size

A

cells must be small in order to permit adequate permeation of nutrients by diffusion.pertains to the sa/v ratio

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58
Q

describe the organizational plan of prokaryotes

A

small, no organelles, no nucleus. typically 10x smaller in diameter, 1000x in volume

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59
Q

describe the organizational plan of eukaryotes

A

large, many organelles, nucleus

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60
Q

describe the endomembrane system

A

says that the nucleus is continuous with the cytosol. rough ER is continuous with the nuclear membrane, Golgi apparatus communicates by vesicles. the cell membrane is also a part

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61
Q

describe the nucleolus

A

the origins of ribosome synthesis, location of high density DNA. outside the nucleolus but in the nucleus is loosely packed DNa
. IT IS SURRounded by the nuclear envelope

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62
Q

describe the rough ER

A

highly folded, many ribosomes, all membrane proteins are produced here

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63
Q

where is translation always started

A

in the cytosol, however the signal hypothesis says that it deposits proteins into the lumen of the ER by SRP receptors

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64
Q

describe smooth ER

A

lipids are synthesized here, detoxification occurs here. less ribosomes

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65
Q

are the proportions of organelles dependent on cell types

A

yes

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66
Q

cis/trans faces of Golgi apparatus

A

cis faces nucleus, trans faces membrane. Golgi is the sorting station for anabolic pathways

67
Q

result/description of the pulse chase experimetn

A

basically the protein secretion pathway was validated,. used fluorescent things to monitor motion

68
Q

describe receptor mediated endocytosis

A

macromolecules bind to surface receptors, an endoscope forms, digestive enzymes get added to the endoscope, turns the endosome into a lysosome,

69
Q

what is phagocytosis

A

consumption of other cells, lysosomes fuse with the foreign body to digest them

70
Q

what is the purpose of autophagy

A

recycling old organelles for their materials

71
Q

how do vesicles know where to go in the cell

A

cytoskeleton

72
Q

what are plastids

A

chloroplasts and mitochondria, they have DNA and reproduce independent of the host

73
Q

what are cristae and the matrix

A

cristae is the inner membranes, the others is the matrix. Krebs, dna, and protein synthesis all occur in the matrix

74
Q

what are thylakoids and stroma

A

thylakoids are membranes in chloroplasts, storm is the intracellular space.

75
Q

evidence for endosymbiotic theory

A

own genome, own ribosomes (similar to bacteria), genes similar to bacteria, unique lipid synthesis and protein import

76
Q

describe microfilaments

A

made of actin monomers, pull, present in cell division, move stuff around

77
Q

intermediate filaments

A

are made of karatin or others, thicker than microfilaments, thinner than microtubules, maintain cell Shae by also pulling, anchor things

78
Q

microtubules

A

alpha beta tubulin dimers, pushes and resists compression, move chromosomes, tracks for intracellular support

79
Q

how many directions can myosin move actin in

A

one

80
Q

what is cytokinesis assisted by

A

actin myosin interactions

81
Q

microtubules start ___ and go outwards

A

at the nucleus

82
Q

kynesin and dyenin in microtubules are functionally similar to what with actin

A

myosin. dyenin and kinesin also go in opposite directions

83
Q

cilia and flagella are made of

A

microtubules

84
Q

what are axonemes

A

typical structures of flagella, 9 microtubule pairs sorted around 2 in the middle

85
Q

explain the role of collagen

A

fixing cells inter cellularly, is a secreted protein, (run in parallel and perpendicular),

86
Q

what is integrin

A

a dimeric protein that attaches fibronectin (extra cell) to microfilaments in the cell

87
Q

what are focal adhesions

A

connections between in the cell and out of (ecm) ie integrin

88
Q

cell-cell adhesion

A

stable binding of certain types of cells which can lead to like sperm egg fusion, DNA exchange, phagocytosis

89
Q

what are tight junctions

A

water tight seals as a cell-cell junction. example forcing solutes to force through epithelial cells to be sorted.

90
Q

gap junctions are important because

A

they provide cytosolic connections between cells

91
Q

describe feedback/endproduct inhibition

A

inhibition of surplus production, by inhibiting an enzyme earlier in the pathway

92
Q

cooperative allostery

A

control is much better, reduces enzyme activity at much lower concentrations

93
Q

net energy trapped from respiration

A

29

94
Q

NAD+ is a carrier which means

A

it is a cofactor which can carry electrons and release a proton upon reduction

95
Q

two phases of glycolysis

A

investment of ATP to activate sugar to split c6 to c3, and the payoff

96
Q

in glycolysis, hexokinase adds a phosphate to glucose to

A

trap it in the cell, decrease cellular glucose concentration,

97
Q

phosphofructokinase phosphorylates

A

the 6 c molecule again

98
Q

g3p (a 3 c molecule in glycolysis) is oxidized by NAD+

A

once for each molecule (2 per glucose)

99
Q

discuss the investment and payoffs of glycolysis

A

invest 1 glucose, 2 atp, get back 4 atp, and 2NADH and also 2 pyruvate

100
Q

glycolysis happens where

A

in the cytoplasm

101
Q

what is pyruvate oxidation

A

removal of CO2, making a 2c molecule, adding acetyl and reducing one NAD+ per pyruvate

102
Q

dehydrogenase does what

A

removes co2 and reduces nad+

103
Q

what is the end of the ETC

A

oxygen gets reduced and turns into water, is the final electron receptor

104
Q

why does the ETC not short circuit?

A

enzyme specificity! the electrons from NADH can’t just jump to o2, even though this is more favourable

105
Q

how does cyanide act

A

it binds to active site of cytochrome c, this does not allow for pumping of hydronium

106
Q

what is the greater contributor to the PROTON MOTIVE FORCE

A

diffusion is much weaker than the voltage difference

107
Q

how many hydronium are consumed by atp synthase to produce 1 atp by oxidative phosphorylation

A

3 lol

108
Q

is oxidative phosphorylation and ETC independent

A

yes lol

109
Q

what is energy uncoupling

A

the uncoupling of etc and atp production, h+ move across the membrane . this allows for the production of heat

110
Q

how is respiration regulated

A

glycolysis - atp with phosphophructokinase
krebs - high NADH and H+ inhibits the first dehydrogenase of the cycle
ETC- low proton gradient results in faster ETC, too high slows it

111
Q

in the absence of oxygen in respiration ->

A

increases proton gradient in the inter membrane space, which inhibits ETC flow, resultantly increases NADH concentration and inhibits dehydrogenase in krebs

112
Q

what is the premise of fermentation

A

in the lack of oxygen, benefit from the atp yield of glycolysis by oxidizing pyruvate with NADH to start the cycle over again. it frees up NAD+ to oxidize glucose

113
Q

alcohol fermentation

A

is the same as lactate fermentation except you remove a carbon and are left with ethanol

114
Q

what happens if inadequate food is available? what is used first!

A

glycogen stores from muscle and liver undergo glycogenesis. then fats are used, then lastly proteins

115
Q

NADP is only used in

A

anabolic pathways

reactions driven by its excess

116
Q

plant cells typically have how many chloroplasts

A

40 to 50, but depends on the cell location and function

117
Q

what are the three things that can happen to an excited electron in chlorophyll molecules

A
  1. can just decay and give off light and heat
  2. can decay by resonance, shifting energy to an adjacent molecule
  3. decay by successive electron transfers
118
Q

the antenna system in photosynthesis is embedded

A

in the thylakoid membrane

119
Q

the reaction centre in the light harvesting complex is

A

the final electron acceptor, which promotes the electron to pheophytin

120
Q

the reaction centre acts like an energy sink (antenna molecules resonate electrons to it because…)

A

it has the longest wavelength (lowest energy) of the complex

121
Q

describe the scheme of phosphorylation in photosynthesis

A

electrons are excited and brought to reaction centre in PS2, where electrons are promoted to pheophytin, carrying electrons to plastoquinone

as plastoquinone moves to the cytochrome complex, it pumps protons into the thylakoid lumen
atp is then produced in the stroma

122
Q

describe noncyclic electron transfer

A

the ideal working of the system, splitting of water in ps2 happens to donate electrons to the system, oxidative phosphorylation occurs because of the transfer of electrons moving protons, ,, the electrons then move to ps1 to get excited again and move into the ETC

123
Q

what establishes the proton gradient in the thylakoid membrane

A

splitting of water increases thylakoid concentration, using of nadp and h in the stroma decreases stroll concentration, plastoquinone directly increases the concentration

124
Q

describe cyclic electron flow

A

instead of ferreredoxin taking electrons from ps1 to etc, brings them back to pq to pump more protons. this makes atp but doesn’t reduce the nadp

125
Q

what is rubisco

A

Ribulose-1,5-bisphosphate carboxylase/oxygenase,

the most abundant protein in the world

a 5 carbon molecule

126
Q

describe the Calvin cycle of carbon fixation

A

3co2 are added to 3 rubisco, then split to yield 63pg. this is the fixation step
you reduce these molecules by phosphorylating and and reducing from nadph to g3p
for every 3co2 that enter, you release 1 g3p to synthesisze carbohydrates
phosphorylate the g3pps again and bring them together to make your 3 rubisco again

127
Q

what is photorespiration

A

so rubisco has a higher affinity for oxygen than co2, too much o2 halts the Calvin cycle essentially by forcing the plant to release co2 and consume atp without fixing any carbon

128
Q

cell theory states

A

all organisms consist of cells
cells divide to produce new cells
higher organisms fuse cells to produce offspring

129
Q

what are mitotic chromosomes

A

sister chromatids in mitosis

130
Q

cell cycle phases

A 
S phase or interphase (stationary/replication)
is broken into G1, S, G2
M phase (mitosis/meiosis)
131
Q

cancer can be

A

unregulated g1 s checkpoint fail because of excess cyclin E

132
Q

what does hydroxyurea do

A

blocks replication inS phase so can’t proceed to G2,

however caffeine disables this checkpoint, allowing this to proceed, but then mitosis can’t happen rip

133
Q

cyclins and cdks are involved in

A

cell cycle regulation

134
Q

describe the g2 checkpoint

A

checks if chromosomes have correctly replicated and if DNA is undamaged.

135
Q

metaphase checkpoint:

A

checks that all chromosomes are attached to the spindle apparatus

136
Q

the G1 checkpoint

A

checks to see if cells are big enough and have enough nutrients, also for integrity of DNA

137
Q

DESCribe mitosis

A

IPMAT

prophase: condensing of chromosomes, spindle apparatus begins to form
pro metaphase: nuclear envelope breaks down, kinetochore microtubules begin to make contact
metaphase: chromosomes migrate to middle of cell at the division/metaphase plate
anaphase: pulled to opposite sides of cell upon centromere dissolution
telophase: assembly of membrane, spindle apparatus disintegrates

138
Q

centrioles are

A

the units in centrosomes

139
Q

cytokenesis is

A

the purse string closing of actin myosin to separate cells

140
Q

syncytial means

A

multinucleated

141
Q

in humans, somatic cells are _____ and gametes are _____

A

diploid, haploid

142
Q

what is meiosis

A

imagine doing mitosis twice with double the material. 1 cell yields 4 haploid gametes

143
Q

describe meiosis 1

A

tetrad ( pair of homologs x4)
cross over in prophase 1
between non sister chromatids
break and repair chiasmata

144
Q

meiosis 2:

A

mitosis with half the dna

145
Q

risk of Down syndrome depends on

A

age of mother, nondisjunction in meiosis

146
Q

odd ploidy organisms tend to be sterile because:

A

problems in meiosis1 separation

the ratio of homologs is more important

147
Q

the probability of two independent events is

A

the product of the probability of those events happening in isolation

148
Q

umber of gamete genotypes

A

its 2^n gamete genotypes where n is the number of independently assorting genes

149
Q

colorblindness has

A

only males of unaffected parents are colourblind, females who are colourblind must have affected fatehrs

150
Q

why does the Y chromosome always have the colourblindness alleel

A

it doesn’t, but it doesn’t have a colourblindness gene so there is no possibility for it to be good vision dominant

151
Q

difference between dominant alleles linked in cis and trans

A

cis means the dominant (when considering 2 genes) are on the same chromatid, trans is the opposite

152
Q

what are the factors that contribute to the heredity of a trait

A

number of genes controlling the trait, alleles in the population per gene, environmental effects

153
Q

miescher was the first to

A

purify dna

154
Q

explain Griffiths transformation principle

A

a chemical component of one cell is capable of influencing another cell

155
Q

Hershey and chase showed that

A

dna is the genetic material of cells

156
Q

at /gc _____between organisms

A

varies

157
Q

Watson and crick used Rosalind franklins X-ray crystallography measurements to

A

untangle the structure of dna

158
Q

explain how we found out that DNA replication was semiconservative

A

meselson stahl experiment: make DNA with heavy nitrogen, let it replicate, you’ll end up with light dna and intermediate dna ice u centrifuge in a slowing medium

159
Q

explain the role of helicase

A

unwinds the dna during replication

160
Q

explain the role of topoisomerase

A

to cut and anneal a strand to relieve tension during replication

161
Q

synthesis of dna occurs in the

A

5prime 3prime direction

162
Q

describe the lagging strand

A

the strand which is opposite the 5’ 3’ strand and must have inttermittent placement of primers to allow for replication

163
Q

describe DNApolymerase1 and dna ligase

A

the protein responsible for excising rna fragments and replacing the with dna, ligase fuses the backbones

164
Q

how are errors corrected in replication

A

proofreading by dnap3, mismatch repair (single nucleotide) and excision repair (in somatic cells, ripping out chunks)

BIOL111 (1 decks)

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