Midterm 1 - Biochemistry Flashcards
1
Q
Hydrogen Bonding
A
Polarity of water
2
Q
4 emergent properties of water essential to life
A
- Cohesion
- Moderation of temperature
- Insulation by floating ice
- The solvent of life
3
Q
Autoionization
A
Water ionizes into H+ and OH- (acid/base properties)
4
Q
Characterize fructose, glucose, galactose
A
fructose: ketohexose
glucose: aldohexose
galactose: aldohexose
5
Q
Difference between glucose and galactose
A
Stereoisomers
Switching of OH group at 4’C
6
Q
Reactions of monomers to polymers (and the reverse)
A
Dehydration or condensation
hydrolysis
7
Q
Polysaccharides
A
Linked by glycosidic linkages
e.g. cellulose, starch, glycogen, chitin
structural support, energy storage
8
Q
Important lipids
A
Triacylglycerols (glycerol + 3 fatty acids)
Phospholipids (phosphate groups + 2 fatty acids)
Steroids (four fused rings with attached chemical groups)
9
Q
Important lipids functions
A
triacylglycerols: energy source
phospholipids: lipid bilayers of membranes
Steroids: component of cell membranes (cholesterol); signaling molecules (hormones)
10
Q
Protein functions
A
- catalysts
- structural support (collagen, elastin, etc)
- storage protein (ovalbumin)
- tranport proteins (hemoglobin)
- hormonal proteins (insulin)
- receptor proteins
- contractile and motor proteins (actin and myosin, flagellin)
- defensive proteins (antibodies)
11
Q
DNA function
A
store all hereditary information
12
Q
RNA function
A
carries protein-coding instructions from DNA to protein synthesizing machinery
13
Q
A- B- glucose
A
alpha glucose: 1’OH opposite side of 5’C
beta glucose: 1’OH same side as 5’C
14
Q
4 major classes of macromolecules
A
carbohydrates
lipids
proteins
nucleic acids
15
Q
Monomer - linkage - polymer
A
monosaccharides - glycosidic - polysaccharides
fatty acids - ester - triacylglycerols
amino acids - peptide - polypeptides
nucleotides - phosphodiester - polynucleotides
16
Q
Quality of microscopy
A
magnification, resolution, contrast
17
Q
scanning electron microscopy (SEM)
A
surface of the specimen –> “3D” image
18
Q
transmission electron microscopy (TEM)
A
electron beam through the specimen –> internal structure
19
Q
cell fractionation
A
ultracentrifuge to separate organelles within cells
used to characterize functions of organelles
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
21
Q
Eukaryotic cells
A
DNA in nucleus bound by nuclear envelope
membrane bound organelles
cytoplasm between plasma membrane and nucleus
10-100 microm
22
Q
defining life
A
- compartmentalization (cells)
- hierarchical complexity (tissues –> organs)
- sensitivity
- reproduction
- energy utilization
- homeostasis
- adaptation
23
Q
cellulose bonding
A
beta 1-4 glycosidic bonds
H-bonds
24
Q
branched polysaccharide bonding
A
alpha 1-4 glycosidic bonds + alpha 1-6 glycosidic bonds
25
Eukaryotic cell organelles
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
26
nucleus components
nucleolus
nuclear envelope
chromatin
nuclear lamina (composed of proteins) maintains the shape of nucleus
27
nuclear envelope
```
nuclear envelope
double layer (each lipid bilayer)
nuclear pores regulate entry and exit of molecules (responding to signals)
```
28
ribosome
```
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)
```
29
endomembrane system
```
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
```
30
endoplasmic reticulum
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)
31
golgi apparatus
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
32
2 sides of golgi apparatus
cis face - receiving
| trans face - shipping
33
lysosome
digestive compartments:
(phagocytosis)
lysosome fuses with food vacuoles and digests molecules
(autophagy)
recycle the cell's own organelles and macromolecules
34
mitochondria function
chemical energy conversion:
(found in nearly all eukaryotic cells)
cellular respiration
ATP synthesis
35
mitochondria structure
double membrane
smooth outer membrane, folded inner membrane --> cristae (folded to maximze surface area for ATP syn.)
2 compartments: intermembrane space and mitochondrial matrix
36
chloroplast function
capture of light energy;
| sugar synthesis
37
chloroplast structure
double membrane
matrix: stroma
granum (grana): containing thylakoid
38
peroxisome
oxidation:
single membrane
H2O2 --> H2O
39
cytoskeleton
```
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
```
40
microtubules
shaping the cell
guiding movement of organelles
separating chromosoms during cell division
directional, tubulin dimers give rise to +/- ends
+ growing; - shrinking
41
centrosomes and centrioles
microtubules grow out from a centrosome near nucleus
| centrosome has a pair of centrioles
42
cilia & flagella
locomotor appendages:
microtubules sheathed by plasma membrane
basal body anchoring the cilium or flagellum
motor protein dynein (bending movements)
43
microfilaments
contain actin and myosin
44
intermediate filaments
more permanent than the other two
| support shape, fix organelles
45
extracellular components
```
cell walls - plants
extracellular matrix (ECM) - animals
intercellular junctions
```
46
cell wall function
protect plant cell
maintain shape
prevent excessive uptake of water
47
cell wall structure
```
cellulose fibers embedded in polysacc. & proteins
many layers:
primary cell wall
middle lamella
secondary cell wall (only some cells)
```
48
extracellular matrix structure
glycoproteins (collagen, proteoglycan, fibronectin)
| ECM proteins bind to receptor integrins in plasma membrane
49
extracellular matrix structure function
support
adhesion
movement
regulation
50
intercellular junction
plasmodesmata (plant cells)
tight junctions (animal cells)
desmosomes (animal cells)
gap junctions (animal cells)
51
plasmodesmata
channels that perforate plant cell walls
| water, small solutes pass from cell to cell
52
tight junctions
membranes of neighboring cells pressed together
prevent leakages of extracellular fluid
one single line in picture
53
desmosomes
anchoring junctions
fasten cells into strong sheets
intermediate filaments visible in pictures
54
gap junctions
communicating junctions
provide cytoplasmic channels between adjacent cells
2 lines with channels in picture
55
fluid mosaic model
membrane is a fluid structure with a mosaic of proteins embedded
56
2 types of membrane proteins
peripheral proteins - bound to surface
| integral proteins - penetrate the hydrophobic core - transmembrane proteins span the membrane
57
functions of membrane protein
1. transport
2. enzymatic activity
3. signal transduction
4. cell-cell recognition
5. intercellular joining
6. attachment to cytoskeleton and ECM
58
sidedness of membranes
distinct inside and outside
asymmetrical distribution of proteins, lipids, and carbohydrates is determined when synthesized in ER and golgi apparatus
59
passive transport
diffusion, osmosis
60
tonicity
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
effect of tonicity on cells
hypotonic - lysed (animal) or turgid (plant, normal)
isotonic - normal (animal) or flaccid (plant)
hypertonic - shriveled or plasmolyzed
62
facilitated diffusion
passive transport aided by proteins
| e.g. aquaporins, ion channels (gated channels)
63
active transport
against gradient
requires energy, usually ATP
e.g. ion pumps: Na/K
64
driving force of ion diffusion
electrochemical potential:
1. ion concentration gradient
2. membrane potential
65
electrogenic pump
proteins that generate voltage across a membrane
animals: Na/K pumps
plants, fungi, bacteria: proton pump
66
transport of macromolecules
bulk transport via vesicles
exocytosis: vesicles fuse with membrane, release
endocytosis: takes in molecules by forming vesicles from plasma membrane
67
types of endocytosis
1. phagocytosis: pseudopodium --> food vacuole
2. pinocytosis: vesicle
3. receptor-mediated endocytosis
68
effect of temperature on membrane fluidity
high temperature --> more thermal energy --> phospholipids rearrange more rapidly --> more fluidic
69
effect of cholesterol on membrane fluidity
high temperature - stabilize membrane --> more rigid
| low temperature - prevent clustering --> more fluidic
70
channel protein vs. carrier protein
channel vs. conformational changes for carrying
71
definition of metabolism
the totality of an organism's chemical reactions
72
definition of metabolomics
the study of all small molecules (metabolites) in a cell
73
2 types of metabolic pathway
catabolic (breaking down)
| anabolic (synthesis)
74
is metabolism at equilibrium?
NO or you will be dead
75
are all enzymes proteins?
no
| there are also RNA enzymes
76
enzymes as catalysts - properties
do not alter reaction equilibrium
alter reaction rates
remain unchanged after reaction
77
induced fit model of enzymes
substrate --> induce conformational change of enzymes --> enhance catalytic ability
78
what if an enzyme binds too well to the substrate
actually raise E --> no reaction
79
how does ATP perform work
ATP drives endergonic reactions by phosphorylation, making the recipient less stable
80
3 types of cellular work that require ATP
mechanical, transport, and chemical
81
3 types of enzyme inhibitors
1. competitive (*similar shape & properties)
2. non-competitive (e.g. allosteric)
3. uncompetitive (bind to ES complex)
82
cofactors, coenzyme, prosthetic groups
cofactors: nonprotein enzyme helpers (inorganic & organic)
coenzymes: organic cofactor (e.g. vitamin)
prosthetic groups: tightly-bound cofactors
83
apo-enzyme vs. holoenzyme
apo-enzyme: an inactive enzyme lacking cofactors
| holoenzyme: complete enzyme with its cofactor
84
how to regulate metabolism
1. switching on/off the genes that encode specific proteins
| 2. regulate enzyme activity
85
feedback inhibition
the end product of a metabolic pathway shuts down the pathway - prevents a cell from wasting chemical resources by over synthesizing products
86
2 types of allosteric regulation
| 1 special case
(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
example of cooperativity in Hb
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
mechanisms for enzyme to lower Ea
1. orienting substrates correctly
2. straining substrate bonds
3. providing a favorable microenvironment
4. forming transient covalent bonds with the substrate
89
3 types of catabolic pathway
produce ATP:
fermentation (partial degradation of sugars, occurs without O2)
aerobic respiration (organic molecules + O2)
anaerobic respiration (organic molecules + non-O2)
90
NAD+
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
3 stages of celluar respiration
1. glycolysis (sugar --> 2 pyruvate, in cytoplasm)
2. citric acid cycle (completes breakdown of glucose)
3. oxidative phosphorylation (most of ATP synthesis)
92
substrate-level phosphorylation
substrate + P + ADP --> product + ATP
| glycolysis and citric acid cycle
93
glycolysis - 2 phases
energy investment
| energy payoff
94
energy investment phase of glycolysis - energy flow
2 ATP --> 2 ADP + 2 P
95
energy payoff phase of glycolysis - energy flow
4 ADP + 4 P --> 4 ATP
| 2 NAD+ + 4 e- + 4 H+ --> 2 NADH + 2 H+
96
overall output of glycolysis
glucose --> 2 pyruvate + 2 H2O
4 ATP generated - 2 ATP used --> 2 ATP
2 NAD+ + 4 e- + 4 H+ --> 2 NADH + 2 H+
97
glycolysis steps
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
Warburg effect
tumor cells x200 glycolysis
| low O2 environment, tumor associated pyruvate kinase, damage/shutdown of mitochondria
99
pyruvate going into citric acid cycle
presence of O2, going into mitochondria
| pyruvate (cytosol) --(transport protein, loses CO2, NAD --> NADH + H+, Coenzyme A added)--> acetyl CoA
100
citric acid cycle: where and products
aka Krebs cycle or tricarboxylic acid (TCA) cycle
mitochondrion matrix
1 ATP, 3 NADH, 1 FADH2 per turn (2 turns per glucose)
101
2 parts of oxidative phosphorylation
1. electron transport chain
2. chemiosmosis
coupled together for ATP synthesis
102
electron transport chain - where, how, final electron carrier
cristae of mitochondrion
multiprotein complexes (including cytochrome)
O2
*generates no ATP, releases energy from NADH and FADH2
103
chemiosmosis - what, how to produce ATP
electron transfer chain --> protein pumps H+ from mitochondrial matrix to intermembrane space
H+ moves back --> passing through ATP synthase --> phosphorylation of ADP --> ATP
104
proton motive force
H+ gradient across the membrane
| able to do work (drive ATP synthase)
105
bacteria cellular respiration - where
inner membrane surface
106
anaerobic respiration final electron acceptor
non-O2, e.g. sulfate
107
generation of ATP in fermentation
only substrate-level phosphorylation
108
2 types of fermentation
1. alcohol fermentation (2 pyruvate --> 2 acetaldehyde + 2 CO2 --> 2 ethanol)
2. lactic acid fermentation (2 pyruvate --> 2 lactate)
109
fermentation - final electron acceptor
acetaldehyde (alcohol fermentation)
| pyruvate (lactic acid fermentation)
110
energy production of fermentation vs. aerobic respiration
fermentation: 2 ATP
| aerobic respiration: 30-32 ATP
111
fermentation - where
cytosol
112
types of anaerobes
1. obligate anaerobes
| 2. facultative anaerobes (e.g. muscle cells, yeast)
113
catabolism - proteins and fats
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
regulation of cellular respiration
feedback regulation
ATP regulates phosphofructokinase (allosteric inhibitor)
F6P -(PFK)-> F1,6BP is the commitment step
115
definition of autotroph vs. heterotrophy
autotrophs sustain themselves without eating anything derived from other organisms
heterotrophs obtain their organic material from other organisms
116
the driving force of organic molecule synthesis
light energy harvested by chlorophyll
117
CO2 entry or O2 exit
stomata
118
where are chloroplasts found?
in cells of mesophyll, the interior tissue of leaves
119
2 stages of photosynthesis - what and where
1. light reactions (thylakoid)
| 2. Calvin cycle (stroma)
120
what color of light is reflected by chlorophyll?
green
121
overview of light reaction
split H2O
release O2
reduce NADP+ to NADPH
generate ATP from ADP by photophosphorylation
122
overview of Calvin cycle
forms sugar from CO2 (carbon fixation)
| uses ATP and NADPH
123
3 pigments in chloroplasts
chlorophyll a, chlorophyll b, and carotenoids
124
absorption spectra of the three chloroplast pigments
1. chlorophyll a: purple + red
2. chlorophyll b: purple-blue + orange
3. carotenoids: purple + blue
125
Engelmann's experiment
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
the functions of the three chloroplast pigments
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
chlorophyll structure
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
2 parts of a photosystem
reaction-center complex surrounded by light-harvesting complexes
129
electron transfer in photosystem II --> I --> NADP+
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
2 types of photosystems
1. photosystem I
| 2. photosystem II (functions first)
131
names of chlorophyll a's in photosystems I and II
photosystem II: P680
| photosystem I: P700
132
cyclic electron flow
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
chemiosmosis in chloroplast vs. in mitochondria
chloroplasts: light as energy source
mitochondria: food as energy source
chloroplasts: thylakoid in --> out diffusion --> ATP
mitochondria: cristae out --> in diffusion --> ATP
134
Calvin cycle entering & exiting materials
entering: CO2
exiting: G3P (1 G3P takes 3 CO2)
135
3 phases of Calvin cycle
1. carbon fixation (catalyzed by rubisco)
2. reduction
3. regeneration of CO2 acceptor (RuBP)
136
Calvin cycle output per 3 CO2
3 CO2 --> 1 G3P
9 ATP --> 9 ADP
6 NADPH --> 6 NADP+
137
problem with photosynthesis in hot, dry climate
closing of stomata to prevent water loss
- -> CO2 decreases, O2 increases
- -> photorespiration
138
photorespiration
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
difference between C3 and C4 plants
C3: rubisco binds to CO2 --> 3C compound
C4: PEP -(PEP carboxylase)-> 4C compound
PEP carboxylase has higher affinity to CO2 than rubisco
140
C4 pathway difference
CO2 incorporated into 4C compound (in mesophyll)
- -> enters bundle sheath cells
- -> pyruvate + CO2
- -> CO2 completes Calvin cycle
141
CAM plants pathway
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
