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Bio 1A > Midterm 1 - Biochemistry > Flashcards

Midterm 1 - Biochemistry Flashcards

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1
Q

Hydrogen Bonding

A

Polarity of water

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2
Q

4 emergent properties of water essential to life

A
  1. Cohesion
  2. Moderation of temperature
  3. Insulation by floating ice
  4. The solvent of life
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3
Q

Autoionization

A

Water ionizes into H+ and OH- (acid/base properties)

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4
Q

Characterize fructose, glucose, galactose

A

fructose: ketohexose
glucose: aldohexose
galactose: aldohexose

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5
Q

Difference between glucose and galactose

A

Stereoisomers

Switching of OH group at 4’C

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6
Q

Reactions of monomers to polymers (and the reverse)

A

Dehydration or condensation

hydrolysis

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7
Q

Polysaccharides

A

Linked by glycosidic linkages
e.g. cellulose, starch, glycogen, chitin
structural support, energy storage

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8
Q

Important lipids

A

Triacylglycerols (glycerol + 3 fatty acids)
Phospholipids (phosphate groups + 2 fatty acids)
Steroids (four fused rings with attached chemical groups)

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9
Q

Important lipids functions

A

triacylglycerols: energy source
phospholipids: lipid bilayers of membranes
Steroids: component of cell membranes (cholesterol); signaling molecules (hormones)

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10
Q

Protein functions

A
  1. catalysts
  2. structural support (collagen, elastin, etc)
  3. storage protein (ovalbumin)
  4. tranport proteins (hemoglobin)
  5. hormonal proteins (insulin)
  6. receptor proteins
  7. contractile and motor proteins (actin and myosin, flagellin)
  8. defensive proteins (antibodies)
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11
Q

DNA function

A

store all hereditary information

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12
Q

RNA function

A

carries protein-coding instructions from DNA to protein synthesizing machinery

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13
Q

A- B- glucose

A

alpha glucose: 1’OH opposite side of 5’C

beta glucose: 1’OH same side as 5’C

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14
Q

4 major classes of macromolecules

A

carbohydrates
lipids
proteins
nucleic acids

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15
Q

Monomer - linkage - polymer

A

monosaccharides - glycosidic - polysaccharides
fatty acids - ester - triacylglycerols
amino acids - peptide - polypeptides
nucleotides - phosphodiester - polynucleotides

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16
Q

Quality of microscopy

A

magnification, resolution, contrast

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17
Q

scanning electron microscopy (SEM)

A

surface of the specimen –> “3D” image

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18
Q

transmission electron microscopy (TEM)

A

electron beam through the specimen –> internal structure

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19
Q

cell fractionation

A

ultracentrifuge to separate organelles within cells

used to characterize functions of organelles

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20
Q

Prokaryotic cells

A 
no nucleus
DNA in unbound region - nucleoid (still tightly packed)
no membrane-bound organelles
cytoplasm bound by plasma membrane
1-10 microm
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21
Q

Eukaryotic cells

A

DNA in nucleus bound by nuclear envelope
membrane bound organelles
cytoplasm between plasma membrane and nucleus
10-100 microm

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22
Q

defining life

A
  1. compartmentalization (cells)
  2. hierarchical complexity (tissues –> organs)
  3. sensitivity
  4. reproduction
  5. energy utilization
  6. homeostasis
  7. adaptation
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23
Q

cellulose bonding

A

beta 1-4 glycosidic bonds

H-bonds

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24
Q

branched polysaccharide bonding

A

alpha 1-4 glycosidic bonds + alpha 1-6 glycosidic bonds

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25
Q

Eukaryotic cell organelles

A
  1. nucleus (nucleolus, chromatin, nuclear envelope)
  2. ribosome
  3. endoplasmic reticulum (smooth ER, rough ER)
  4. golgi apparatus
  5. mitochondrion
  6. chloroplast
  7. lysosome
  8. peroxisome
  9. microfilament
  10. microtubules
  11. intermediate filaments
  12. centrosome
  13. microvilli
  14. flagellum
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26
Q

nucleus components

A

nucleolus
nuclear envelope
chromatin
nuclear lamina (composed of proteins) maintains the shape of nucleus

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27
Q

nuclear envelope

A 
nuclear envelope
double layer (each lipid bilayer)
nuclear pores regulate entry and exit of molecules (responding to signals)
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28
Q

ribosome

A 
protein factories:
made of rRNA and proteins
carry out protein synthesis
2 subunites
two types:
1. free ribosome (in cytosol)
2. bound ribosome (outside rough ER and nuclear envelopes)
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29
Q

endomembrane system

A 
regulates protein traffic and perform metabolic functions
consists of:
nuclear envelope
endoplasmic reticulum
golgi apparatus
lysosome
vacuoles
plasma membrane
either continuous or connected by vesicles
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30
Q

endoplasmic reticulum

A

biosynthesis factory:
(continuous with the nuclear envelope)
smooth ER: lipid synthesis, carbohydrate metabolism, poison detox, calcium storage;
rough ER: has ribosome secreting glyprotein, distributes transport vesicles, membrane factory
(inside: ER lumen)

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31
Q

golgi apparatus

A

shipping and receiving center:
(consisted of flattened membranous sacs called cristernae)
modifies products of ER
manufactures certain macromolecules
sorts and packages materials into transport vesicles

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32
Q

2 sides of golgi apparatus

A

cis face - receiving

trans face - shipping

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33
Q

lysosome

A

digestive compartments:
(phagocytosis)
lysosome fuses with food vacuoles and digests molecules
(autophagy)
recycle the cell’s own organelles and macromolecules

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34
Q

mitochondria function

A

chemical energy conversion:
(found in nearly all eukaryotic cells)
cellular respiration
ATP synthesis

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35
Q

mitochondria structure

A

double membrane
smooth outer membrane, folded inner membrane –> cristae (folded to maximze surface area for ATP syn.)
2 compartments: intermembrane space and mitochondrial matrix

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36
Q

chloroplast function

A

capture of light energy;

sugar synthesis

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37
Q

chloroplast structure

A

double membrane
matrix: stroma
granum (grana): containing thylakoid

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38
Q

peroxisome

A

oxidation:
single membrane
H2O2 –> H2O

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39
Q

cytoskeleton

A 
support the cell and maintain its shape
interacts with motor proteins to produce motility (consume ATP)
help regulate biochemical activities
consisted of:
microtubules
microfilaments (actin filaments)
intermediate filaments
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40
Q

microtubules

A

shaping the cell
guiding movement of organelles
separating chromosoms during cell division

directional, tubulin dimers give rise to +/- ends
+ growing; - shrinking

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41
Q

centrosomes and centrioles

A

microtubules grow out from a centrosome near nucleus

centrosome has a pair of centrioles

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42
Q

cilia & flagella

A

locomotor appendages:
microtubules sheathed by plasma membrane
basal body anchoring the cilium or flagellum
motor protein dynein (bending movements)

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43
Q

microfilaments

A

contain actin and myosin

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44
Q

intermediate filaments

A

more permanent than the other two

support shape, fix organelles

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45
Q

extracellular components

A 
cell walls - plants
extracellular matrix (ECM) - animals
intercellular junctions
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46
Q

cell wall function

A

protect plant cell
maintain shape
prevent excessive uptake of water

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47
Q

cell wall structure

A 
cellulose fibers embedded in polysacc. & proteins
many layers:
primary cell wall
middle lamella
secondary cell wall (only some cells)
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48
Q

extracellular matrix structure

A

glycoproteins (collagen, proteoglycan, fibronectin)

ECM proteins bind to receptor integrins in plasma membrane

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49
Q

extracellular matrix structure function

A

support
adhesion
movement
regulation

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50
Q

intercellular junction

A

plasmodesmata (plant cells)
tight junctions (animal cells)
desmosomes (animal cells)
gap junctions (animal cells)

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51
Q

plasmodesmata

A

channels that perforate plant cell walls

water, small solutes pass from cell to cell

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52
Q

tight junctions

A

membranes of neighboring cells pressed together
prevent leakages of extracellular fluid
one single line in picture

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53
Q

desmosomes

A

anchoring junctions
fasten cells into strong sheets
intermediate filaments visible in pictures

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54
Q

gap junctions

A

communicating junctions
provide cytoplasmic channels between adjacent cells
2 lines with channels in picture

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55
Q

fluid mosaic model

A

membrane is a fluid structure with a mosaic of proteins embedded

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56
Q

2 types of membrane proteins

A

peripheral proteins - bound to surface

integral proteins - penetrate the hydrophobic core - transmembrane proteins span the membrane

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57
Q

functions of membrane protein

A
  1. transport
  2. enzymatic activity
  3. signal transduction
  4. cell-cell recognition
  5. intercellular joining
  6. attachment to cytoskeleton and ECM
58
Q

sidedness of membranes

A

distinct inside and outside
asymmetrical distribution of proteins, lipids, and carbohydrates is determined when synthesized in ER and golgi apparatus

59
Q

passive transport

A

diffusion, osmosis

60
Q

tonicity

A

ability of a solution to cause a cell to gain or lose water

  1. isotonic - equal concentration, no net movement of water
  2. hypertonic - higher concentration outside, cell loses water
  3. hypotonic - lower concentration outside, cell gains water
61
Q

effect of tonicity on cells

A

hypotonic - lysed (animal) or turgid (plant, normal)
isotonic - normal (animal) or flaccid (plant)
hypertonic - shriveled or plasmolyzed

62
Q

facilitated diffusion

A

passive transport aided by proteins

e.g. aquaporins, ion channels (gated channels)

63
Q

active transport

A

against gradient
requires energy, usually ATP
e.g. ion pumps: Na/K

64
Q

driving force of ion diffusion

A

electrochemical potential:

  1. ion concentration gradient
  2. membrane potential
65
Q

electrogenic pump

A

proteins that generate voltage across a membrane
animals: Na/K pumps
plants, fungi, bacteria: proton pump

66
Q

transport of macromolecules

A

bulk transport via vesicles

exocytosis: vesicles fuse with membrane, release
endocytosis: takes in molecules by forming vesicles from plasma membrane

67
Q

types of endocytosis

A
  1. phagocytosis: pseudopodium –> food vacuole
  2. pinocytosis: vesicle
  3. receptor-mediated endocytosis
68
Q

effect of temperature on membrane fluidity

A

high temperature –> more thermal energy –> phospholipids rearrange more rapidly –> more fluidic

69
Q

effect of cholesterol on membrane fluidity

A

high temperature - stabilize membrane –> more rigid

low temperature - prevent clustering –> more fluidic

70
Q

channel protein vs. carrier protein

A

channel vs. conformational changes for carrying

71
Q

definition of metabolism

A

the totality of an organism’s chemical reactions

72
Q

definition of metabolomics

A

the study of all small molecules (metabolites) in a cell

73
Q

2 types of metabolic pathway

A

catabolic (breaking down)

anabolic (synthesis)

74
Q

is metabolism at equilibrium?

A

NO or you will be dead

75
Q

are all enzymes proteins?

A

no

there are also RNA enzymes

76
Q

enzymes as catalysts - properties

A

do not alter reaction equilibrium
alter reaction rates
remain unchanged after reaction

77
Q

induced fit model of enzymes

A

substrate –> induce conformational change of enzymes –> enhance catalytic ability

78
Q

what if an enzyme binds too well to the substrate

A

actually raise E –> no reaction

79
Q

how does ATP perform work

A

ATP drives endergonic reactions by phosphorylation, making the recipient less stable

80
Q

3 types of cellular work that require ATP

A

mechanical, transport, and chemical

81
Q

3 types of enzyme inhibitors

A
  1. competitive (*similar shape & properties)
  2. non-competitive (e.g. allosteric)
  3. uncompetitive (bind to ES complex)
82
Q

cofactors, coenzyme, prosthetic groups

A

cofactors: nonprotein enzyme helpers (inorganic & organic)
coenzymes: organic cofactor (e.g. vitamin)
prosthetic groups: tightly-bound cofactors

83
Q

apo-enzyme vs. holoenzyme

A

apo-enzyme: an inactive enzyme lacking cofactors

holoenzyme: complete enzyme with its cofactor

84
Q

how to regulate metabolism

A
  1. switching on/off the genes that encode specific proteins

2. regulate enzyme activity

85
Q

feedback inhibition

A

the end product of a metabolic pathway shuts down the pathway - prevents a cell from wasting chemical resources by over synthesizing products

86
Q

2 types of allosteric regulation

1 special case

A

(a regulatory molecule binds to a protein at one site and affects protein function at another site)

  1. allosteric activation (binding of an activator stabilizes the active form of the enzyme)
  2. allosteric inhibition (binding of an inhibitor stabilizes the inactive form of the enzyme)
    * cooperativity: substrate binding to active site stabilizes the active form
87
Q

example of cooperativity in Hb

A

Hb has 2 states: T & R
O2 binds to both states, but with more affinity to R state
When O2 binds, Hb changes into R state

88
Q

mechanisms for enzyme to lower Ea

A
  1. orienting substrates correctly
  2. straining substrate bonds
  3. providing a favorable microenvironment
  4. forming transient covalent bonds with the substrate
89
Q

3 types of catabolic pathway

A

produce ATP:
fermentation (partial degradation of sugars, occurs without O2)
aerobic respiration (organic molecules + O2)
anaerobic respiration (organic molecules + non-O2)

90
Q

NAD+

A

oxidized form of NADH (NADH is the reduced form)
a coenzyme in celluar respiration
electron acceptor –> reduced to NADH (stores energy) –> electron transport chain –> synthesize ATP
important for stepwise energy storage

91
Q

3 stages of celluar respiration

A
  1. glycolysis (sugar –> 2 pyruvate, in cytoplasm)
  2. citric acid cycle (completes breakdown of glucose)
  3. oxidative phosphorylation (most of ATP synthesis)
92
Q

substrate-level phosphorylation

A

substrate + P + ADP –> product + ATP

glycolysis and citric acid cycle

93
Q

glycolysis - 2 phases

A

energy investment

energy payoff

94
Q

energy investment phase of glycolysis - energy flow

A

2 ATP –> 2 ADP + 2 P

95
Q

energy payoff phase of glycolysis - energy flow

A

4 ADP + 4 P –> 4 ATP

2 NAD+ + 4 e- + 4 H+ –> 2 NADH + 2 H+

96
Q

overall output of glycolysis

A

glucose –> 2 pyruvate + 2 H2O
4 ATP generated - 2 ATP used –> 2 ATP
2 NAD+ + 4 e- + 4 H+ –> 2 NADH + 2 H+

97
Q

glycolysis steps

A
  1. glucose –(hexokinase)–> G6P (ATP –> ADP + P)
  2. G6P –(phosphoglucoisomerase)–> F6P
  3. F6P –(phosphofructokinase, PFK)–> F1,6BP (ATP –> ADP + P)
  4. F1,6BP –(aldolase)–> 2 DHAP 2 GA3P
  5. 2 GA3P + 2 P –> 2 1,3BPG (2 NAD+ –> 2 NADH + 2H+)
  6. 2 1,3BPG –(phosphoglycerokinase)–> 2 3PG (2 ADP –> 2 ATP)
  7. 2 3PG –(phosphoglyceromutase)–> 2 2PG
  8. 2 2PG –(enolase)–> 2 PEP
  9. 2 PEP –(pyruvate kinase)–> 2 pyruvate (2 ADP –> 2 ATP)
98
Q

Warburg effect

A

tumor cells x200 glycolysis

low O2 environment, tumor associated pyruvate kinase, damage/shutdown of mitochondria

99
Q

pyruvate going into citric acid cycle

A

presence of O2, going into mitochondria

pyruvate (cytosol) –(transport protein, loses CO2, NAD –> NADH + H+, Coenzyme A added)–> acetyl CoA

100
Q

citric acid cycle: where and products

A

aka Krebs cycle or tricarboxylic acid (TCA) cycle
mitochondrion matrix
1 ATP, 3 NADH, 1 FADH2 per turn (2 turns per glucose)

101
Q

2 parts of oxidative phosphorylation

A
  1. electron transport chain
  2. chemiosmosis
    coupled together for ATP synthesis
102
Q

electron transport chain - where, how, final electron carrier

A

cristae of mitochondrion
multiprotein complexes (including cytochrome)
O2
*generates no ATP, releases energy from NADH and FADH2

103
Q

chemiosmosis - what, how to produce ATP

A

electron transfer chain –> protein pumps H+ from mitochondrial matrix to intermembrane space
H+ moves back –> passing through ATP synthase –> phosphorylation of ADP –> ATP

104
Q

proton motive force

A

H+ gradient across the membrane

able to do work (drive ATP synthase)

105
Q

bacteria cellular respiration - where

A

inner membrane surface

106
Q

anaerobic respiration final electron acceptor

A

non-O2, e.g. sulfate

107
Q

generation of ATP in fermentation

A

only substrate-level phosphorylation

108
Q

2 types of fermentation

A
  1. alcohol fermentation (2 pyruvate –> 2 acetaldehyde + 2 CO2 –> 2 ethanol)
  2. lactic acid fermentation (2 pyruvate –> 2 lactate)
109
Q

fermentation - final electron acceptor

A

acetaldehyde (alcohol fermentation)

pyruvate (lactic acid fermentation)

110
Q

energy production of fermentation vs. aerobic respiration

A

fermentation: 2 ATP

aerobic respiration: 30-32 ATP

111
Q

fermentation - where

A

cytosol

112
Q

types of anaerobes

A
  1. obligate anaerobes

2. facultative anaerobes (e.g. muscle cells, yeast)

113
Q

catabolism - proteins and fats

A
  1. proteins - digested into amino acids –> glycolysis or citric acid cycle
  2. fats - digested into glycerol and fatty acids –> glycerol used in glycolysis, fatty acids broken down into 2 carbon acetyl units by beta oxidation yielding acetyl CoA
114
Q

regulation of cellular respiration

A

feedback regulation
ATP regulates phosphofructokinase (allosteric inhibitor)
F6P -(PFK)-> F1,6BP is the commitment step

115
Q

definition of autotroph vs. heterotrophy

A

autotrophs sustain themselves without eating anything derived from other organisms
heterotrophs obtain their organic material from other organisms

116
Q

the driving force of organic molecule synthesis

A

light energy harvested by chlorophyll

117
Q

CO2 entry or O2 exit

A

stomata

118
Q

where are chloroplasts found?

A

in cells of mesophyll, the interior tissue of leaves

119
Q

2 stages of photosynthesis - what and where

A
  1. light reactions (thylakoid)

2. Calvin cycle (stroma)

120
Q

what color of light is reflected by chlorophyll?

A

green

121
Q

overview of light reaction

A

split H2O
release O2
reduce NADP+ to NADPH
generate ATP from ADP by photophosphorylation

122
Q

overview of Calvin cycle

A

forms sugar from CO2 (carbon fixation)

uses ATP and NADPH

123
Q

3 pigments in chloroplasts

A

chlorophyll a, chlorophyll b, and carotenoids

124
Q

absorption spectra of the three chloroplast pigments

A
  1. chlorophyll a: purple + red
  2. chlorophyll b: purple-blue + orange
  3. carotenoids: purple + blue
125
Q

Engelmann’s experiment

A

exposing different segments of a alga to different wavelengths of light and measured the growth of aerobic bactieria along the alga as a measure of O2 production

126
Q

the functions of the three chloroplast pigments

A
  1. chlorophyll a: main photosynthetic pigment
  2. chlorophyll b: broaden the spectrum for photosynthesis
  3. carotenoids: absorb excessive light that would damage chlorophyll
    (chlorophyll b and carotenoids are accessory pigments)
127
Q

chlorophyll structure

A

2 parts: light absorbing head (porphyrin ring, CH3 for a, CHO or b, with Mg at center) + hydrophobic tail (keeps chlorophyll anchored in thylakoid membrane)

128
Q

2 parts of a photosystem

A

reaction-center complex surrounded by light-harvesting complexes

129
Q

electron transfer in photosystem II –> I –> NADP+

A

photon –> excites light-harvesting complexes

  • -> excites molecules resonance energy
  • -> energy transferred to a pair of P680 molecules in reaction-center complexes
  • -> donates electron to the primary electron acceptor
  • -> P680+ strips H2O of electron
  • -> H+ released into thylakoid lumen, O2 released as waste product (4 photons for 2 H2O or 1 O2)
  • -> Pq (plastoquinone), cytochrome complex, Pc (more H+ pumped into thylakoid)
  • -> electrons transferred to P700 –> PSII primary electron acceptor
  • -> Fd (ferredoxin)
  • -> NADP+ reductase, NADPH produced
130
Q

2 types of photosystems

A
  1. photosystem I

2. photosystem II (functions first)

131
Q

names of chlorophyll a’s in photosystems I and II

A

photosystem II: P680

photosystem I: P700

132
Q

cyclic electron flow

A

uses only PSI, produces ATP, not NADPH
generates surplus ATP, satisfying higher demand in Calvin cycle
PSI –> primary electron acceptor –> Fd –> cytochrome complex –> Pc –> PSI

133
Q

chemiosmosis in chloroplast vs. in mitochondria

A

chloroplasts: light as energy source
mitochondria: food as energy source
chloroplasts: thylakoid in –> out diffusion –> ATP
mitochondria: cristae out –> in diffusion –> ATP

134
Q

Calvin cycle entering & exiting materials

A

entering: CO2
exiting: G3P (1 G3P takes 3 CO2)

135
Q

3 phases of Calvin cycle

A
  1. carbon fixation (catalyzed by rubisco)
  2. reduction
  3. regeneration of CO2 acceptor (RuBP)
136
Q

Calvin cycle output per 3 CO2

A

3 CO2 –> 1 G3P
9 ATP –> 9 ADP
6 NADPH –> 6 NADP+

137
Q

problem with photosynthesis in hot, dry climate

A

closing of stomata to prevent water loss

  • -> CO2 decreases, O2 increases
  • -> photorespiration
138
Q

photorespiration

A

rubisco adds O2, consumes organic fuel –> produces CO2, without producing ATP or sugar
limits damaging products of light reaction to build up (evolutionary relic?)

139
Q

difference between C3 and C4 plants

A

C3: rubisco binds to CO2 –> 3C compound
C4: PEP -(PEP carboxylase)-> 4C compound
PEP carboxylase has higher affinity to CO2 than rubisco

140
Q

C4 pathway difference

A

CO2 incorporated into 4C compound (in mesophyll)

  • -> enters bundle sheath cells
  • -> pyruvate + CO2
  • -> CO2 completes Calvin cycle
141
Q

CAM plants pathway

A

crassulacean acid metabolism (CAM)
CAM plants open their stomata at night, incorporating CO2 into organic acid
stomata close during the day, CO2 released from organic acid, completes Calvin cycle

Bio 1A (2 decks)

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