biology- cell & molec Flashcards
(178 cards)
1
Q
catabolism
A
break down
2
Q
anabolism
A
build up
3
Q
oxidation
A
loss of electrons
more bonds to oxygen
4
Q
reduction
A
gain of electrons
more bonds to hydrogens
5
Q
enzymes
A
protein catalysts
6
Q
Vmax
A
enzymes processing substrate as fast as they can
7
Q
active site
A
site where enzyme binds
8
Q
inhibitors
A
bind to wrong active sites that slow down reactions
9
Q
competitive inhibition
A
inhibitor and substrate compete for the enzyme doesn't change vmax (rate) new Km (concentration) value increases
10
Q
non-competitive inhibition
A
- inhibitor can bind to the enzyme at the binding site at the same time as the substrate but not to the active site
- doesn’t bind to active site but somewhere else
- binding happens but reaction doesnt
- vmax decreases
- km unchanged
- EI and EIS complexes enzymatically inactive
11
Q
uncompetitive inhibition
A
inhibitor cannot bind to the free enzyme, only to the ES complex
the complex formed is enzymatically inactive
rare kind of inhibition
may happen in multimeric enzymes
12
Q
mixed inhibition
A
like noncompetitive
EIS complex has residual enzymatic activity
does not follow the MIchaelis-Menten Equation
13
Q
enzymes work by lowering the _____
A
activation energy and increase the rate of reaction
14
Q
enzymatic catalyzed reactions form products faster, making reactions reach their ______ more rapidly
A
equilibrium
15
Q
T/F enzymes are not conumed by the reactions they catalyze
A
true
16
Q
how do enzymes differ from other catalysts
A
they are highly specific for their substrates due to their complementary shape, charge, and hydrophilic/hydrophobic characteristics
17
Q
michaelis-menten equation
A
v=(vmax [S])/(km + [S])
18
Q
cooperativity
A
when a substrate binds to one enzymatic sub-unit/binding site, which induces the rest of the subunits to be stimulated and become active
19
Q
example of cooperativity
A
hemoglobin shows positive cooperativity for oxygen because it is more accepting to oxygen after one oxygen molecule binds
-transports 4 oxygen subunits while myoglobin only transports 1 subunit
20
Q
what demonstrates cooperativity?
A
ligands
21
Q
negative cooperativity
A
as ligands bind to the protein, the protein’s affinity for the ligand decreases
22
Q
types of enzyme regulation
A
- allosteric
- phosphorylation
- zymogens
- cofactors
- association with other peptides
23
Q
allosteric regulation
A
other molecules bind to enzyme in places other than active site
-ex: feedback inhibition
24
Q
phosphorylation
A
adding a phosphate group
- covalent modification (make covalent bond)
- ser, thr, tyr residues can be phosphorylated by kinases (using ATP hydrolysis) or phophorylases
- phosphatases pull phosphate off
- phosphorylation can either activate or inhibit an enzyme depending upon the enzyme
25
zymogens
inactive precursors that become active upon proteolytic cleavage
-ex: proteins cleave in stomach
26
cofactors
involvement of metal ions or organic molecules (coenzymes)
27
association with other peptides
individual peptides come together to form a bigger one
| -one of the peptides will have a regulatory feature that regulates catalytic activity
28
gibbs equation
G=H-TS
29
delta G is negative means
spontaneous reaction
30
delta G positive means
not spontaneous
31
thermodynamics
tells you if a reaction will happen or not
32
H - and S +
spontaneous at all temps
| exothermic
33
H means
enthalpy
34
S means
entropy
35
H + S -
nonspontaneous at all temps
| endothermic
36
H + S +
spontaneous at all high temps
37
H - S -
spontaneous at all low temps
38
standard conditions
1 atm
1 molar gas
all reactants and products present at 1 M concentration
39
Q
products/reactatns
40
what happens to delta G if you shift the equilibrium to the right
more negative
41
shift equilibrium to left?
more positive
42
catalyst
lowers activation energy
provides an alternate pathways
helps get to equilibrium faster
can work in both directions
43
what does adding a catalyst do to delta G?
doesnt change it at all
44
what is the only thing that can change delta G
temp
45
path of glucose catabolism (aerobic)
1. glucose
2. glycolysis (cytosol)
3. pyruvate (mitochondrial matrix)
4. acetyl coA
5. TCA (kreb's) cycle (mitochondrial matrix)
6. electron transport chain (mitochondrial inner membrane)-oxidative phosphorylation
7. ATP synthase
46
yield for glycolysis
per glucose:
2 ATP (net)
2 NADH
2 pyruvate
47
what does glucose use in glycolysis? what is the cost?
2 ATP, 4 ADP, 2 NAD+
48
anaerobic catabolism of glucose
1. glucose
2. glycolysis (cytosol)-substrate level phosphorylation
3. 2 pyruvate
3a. reduces to lactate using NADH---> NAD+
3b. OR reduces/ferments to ethanol and CO2 using NADH---> NAD+
49
mitochondrial structure
outer membrane, intermembrane space, inner membrane, matrix
50
commitment step in glycolysis
fructose-6-phosphate turns into fructose-1,6-biphosphate
ATP--->ADP
irreversible step
51
Pyruvate dehydrogenase complex (PDC or PDH complex)
responsible for bringing glycolysis into Krebs
52
yield of krebs
```
per acetyl coA:
GTP=ATP
3 NADH
2 CO2
FADH2
```
53
start of krebs
acetyl coA + oxalo-acetate----> citrate
54
how many oxidation steps of krebs
4
55
ADP
low energy
turns catabolism on
biosynthesis inhibited
56
ATP
high energy
turns catabolism off and anabolism on
biosynthesis activated
57
gluconeogenesis
production of glucose
reverse of glycolysis
occurs mainly in liver (but also kidneys)
58
glycogen metabolism
- glucose polymer for glucose storage in the liver and muscles
- insulin activates glycogen synthesis
- glucagon and epinephrine promote degradation
59
cori cycle
lactate transported to the liver for conversion back to glucose
60
formula for catabolism of glucose
C6H12O6 + 6 O2---> 6 CO2 + 6H2O
61
where do the electrons come from to deposit in the electron transport chain
oxygen and turn into H2O
62
oxidations in electron transport chain
NADH--NAD+
| FADH2--FAD
63
what has a high H+ concentration in the electron transport chain
intermembrane space
64
what has a low H+ concentration in the electron transport chain
matrix--higher pH
65
path of electron transport chain from NADH
1. NADH ---> NAD+
2. complex 1
3. coQ
4. complex 3
5. cytochrome C
6. complex 4
7. oxygen making water
66
path of electron transport chain from FADH2
1. FADH2--->FAD
2. complex 2
3. coQ
4. complex 3
5. cytochrome C
6. complex 4
7. oxygen making water
67
what powers ATP synthase
electrochemical potential from electron transport chain
| voltage gradient
68
NADH=
2.5 ATP
69
FADH2=
1.5 ATP
70
dietary uptake of lipids
triacylglycerides use lipases (in lumen of small intestine) and turn into monoacylglyerides and fatty acids (translported into electrocytes) and then turn into triacylglycerides then using chylomicrons (packaged with choleserol) turn into adipose tissue
71
what breaks triacylglyerides apart?
lipases
72
what stores more energy--fats or carbohydrates
fats
73
liver turns glyerol into what
glycolysis or gluconeogenesis
74
fatty acids turn into what
acetyl coA to CAC cycle
75
what is the body's response to fasting, exercise, or stress?
glucagon and epinephrine activate the triacylglyerides to be converted to fatty acids and glyerol by hormone-sensitive lipases
76
adipose tissue to energy production path
triacylglycerides converted to fatty acids and glycerol by hormone-sensitive lipases
- activated by glucagon and epinephrine in response to fasting, exercise, or stress
- glycerol transported to the liver for glycolysis or gluconeogenesis
- fatty acids transported through the bloodstream to tissues in need (heart and primary muscles)
77
beta oxidation activated by
hooking up fatty acid with acetyl coA
78
oxidations in beta oxidation
1. FAD turns into FADH2
| 2. NAD turns into NADH
79
virus
- nonliving
- parasitic
- structure-nucleic acids encased in a protein capsid (enveloped or nonenveloped)
- genome-linear or circular (dsDNA, ssDNA, dsRNA, or ssRNA)
- relatively small genomes that can often be read in different reading frames
- typically uses host's replication, transcription, and translation machineery
- much smaller than prokaryotic or eukaryotic cells
80
bacteriophage
head with capsid protein coating and contains genome
| tail punctures and injects DNA into bacteria
81
animal virus
envelope outside
capsid protein with coat containing genome
endocytosis thru cell membrane
not all have envelope
82
lytic cycle
1. adsorption-bind cell surface via tail (host cell specific interactions)
2. penetration-puncture cell wall and membrane and inject genome into host cell
3. hydrolase (a viral gene product) is produced and degrades the host's genome
4. replication of the viral genome (many copies) and synthesis of much capsid protein
5. assembly of new virus particles
6. production of lysozyme to degrade the cell wall resulting in cell lysis and release of virus particles
* *disadvantage of this cycle--kills host cell and eventually kills them all
83
lysogenic cycle
1. adsorption-bind cell surface via tail (host cell specific interactions)
2. penetration-puncture cell wall and membrane and inject genome into host cell
3. integration of the phage genome into the host genome
4. dormancy-viral genes not expressed by viral genome is transmitted to all progeny during cell division
5. activation- excision of viral DNA and entrance into lytic cycle
84
bacteriophage life cycles
lytic or lysogenic
85
how do viruses of eukaryotes enter and exit the cell
they have a lipid bilayer envelope and enter the host cell via endocytosis and exit by budding out of the host cell
86
host cells contain what that will degrade the viral DNA
restriction enzymes
87
bacteria do what to distinguish their own DNA from foreign DNA
methylate their own DNA
88
transduction
transer of genetic material via a virus in the lysogenic cycle
89
virus types
1. +RNA virus
2. -RNA virus
3. retroviruses
90
+RNA
genome is single stranded (ssRNA) which can serve directly as mRNA
-must code for an RNA-dependent RNA polymerase for viral replication
91
-RNA
viral genome is ssRNA which is anti-sense (-) and therefore complementary to the mRNA coding for viral genes
- must code for an RNA-dependent RNA polymerase and include this polymerase in its capsid to be infectious
- needs enzyme in capsid
92
retrovirus
-have enzyme called reverse transcriptase which converts +RNA to dsDNA
then incorporates itself into the host's genome
-must encode an RNA-dependent DNA polymerase (reverse transcriptase)
-specificity
93
prokaryotes
- no nucleus
- no membrane bound organelles
- no mitosis
- one chromosome--dna in cytoplasm
- coupled transcription and translation
94
cell wall of prokaryotes made out of
peptoglycand
95
eubacteria vs archaebacteria
eubacteria--true bacteria
| archaebacteria--separate domain, eukaryotes more related, extreme conditions
96
classifications of bacteria
1. cocci (spherical)
2. bacilli (rod)
3. spirilla (spiral shaped)
97
gram positive bacteria
stain dark purple during gram staining
| have cell membrane and cell wall (peptidoglycan)
98
gram negative bacteria
stain pink during gram staining
| have cell membrane, cell wall, and outer lipopolysaccharide layer (LPS) (contains endotoxins)
99
flagellar propulsion
bacterial flagellum used by motile bacteria for locomotion
decide what direction to move in using chemotaxis--either toward chemoattractants or away from chemorepellants (sensed by chemoreceptors)
-powered by ATP hydrolysis
100
bacterial growth
fission
| reproduction simply through growth, DNA replication, and cell division
101
4 phases of bacterial growth
1. lag phase
2. log phase
3. stationary phase
4. death phase
102
endospores
dormant form produced by some bacteria under harsh conditions
- have a thick peptidoglycan coat and can survive through extreme conditions
- can survive boiling
103
aerobes
can survive in an oxygen environment
104
anaerobes
do not require oxygen to survive
105
facultative anaerobes
can carry out metabolic processes with or without oxygen
| can use oxygen as final electron acceptor
106
conjugation
way for bacteria to share genetic information adding to diversity
common way of conferring antibiotic resistance genes
107
fungi
some unicellular (yeast)
most are multicellular
eukaryote (nucleus and organelles)
cell wall made of chitin
108
asexual reproduction of fungi
1. budding--a fungi cell simply grows out of an existing fungal cell until distinct
2. spore formation--produced by mitosis, spore will germinate under favorable conditions to become active
109
sexual reproduction of fungi
1. 2 haploid gametes
2. fusion to become dikaryon
3. fusion of nuclei
4. diploid zygote made
5. meiosis
6. haploid progeny
110
nucleus
- storage of DNA, site of transcription
- surrounded by nuclear envelope (2 lipid bilayers) through which nuclear pores regulate traffic of large molecules
- contains the nucleolus (dark spot which is the site of rRNA synthesis
111
ribosomes
translation of mRNA into proteins (present in both pro- and eukaryotes)
112
rough ER
ER associated with ribosomes that is involved in synthesis and glycosylation of peptides to form glycoproteins destined for secretion or integration into the membrane
113
smooth ER
- synthesis of lipids (membrane) and hormones often for export from the cell
- breakdown of toxins in liver cells
114
golgi apparatus
modification (glycosylation) and packaging of proteins into vesicles for secretion or transport to cellular destinations (like lysosomes)
115
mitochondria
- site of ATP synthesis via ATP synthase as a result of oxidative phosphorylation (PDC, Krebs, and electron transport chain)
- site of fatty acid catabolism (beta oxidation)
- have their own DNA (circular) and ribosomes for self-regulation
116
lysosomes
- contains acid hydrolases (digestive enzymes) and have pH=5
- degradation of old organelles or phagocytosed materials
- produced from the golgi apparatus
- not present in plant cells
117
perioxosomes
- involved in the breakdown (involving hydrogen peroxide) of many substances including fatty acids, amino acids, and various toxins
- carry out the glyoxalate cycle in germinating plant seeds
118
centrioles
source of the spindle apparatus used for cell division (acts as microtubule organizing center)
not present in plant cells
119
vacuoles
fluid filled membrane bound vesicles used for transport, storage of nutrients and other substances, pumping excess water out of a cell, and cell rigidity (in plants)
120
chloroplasts
site of photosynthesis in plant cells
121
animal cells have what that plant cells dont
lysosomes and centrioles
122
plant cells have what that animal cells dont
cell walls, chloroplasts, and a central vacuole
123
bacteria cell walls material
peptidoglycans
124
archaebacteria cell walls material
polysaccharides (not peptidoglycans though)
125
fungi cell walls material
chitin
126
plant cell walls material
cellulose
127
animal cell walls material
none!
128
PDC and krebs cycle occur in
mitochondrial matrix
129
ETC complexes are located
in inner membrane of mitochondria
130
protons are pumped (actively) from _____ to the ______
mitochondrial matrix to the intermembrane space
131
ATP synthase located in the ____ and synthesizes ATP on ______
inner membrane and matrix side
132
protein trafficking
signal peptide recognized by signal recognition particle (SRP)
- binds to SRP and translation haulted and takes it to rough ER
- threads peptides into ER lumen
- signal peptide cleaved
* if peptide is destined for secretion, entire peptide ends up in ER
133
2 destinations of protein trafficking
1. plasma membrane (integral membrane or secreted)
| 2. organelles (ex. lysosomes, ER)
134
fluid mosaic model
- different components free to diffuse throughout membrane, 2D
- composed of phosphpolipids, glycolipids, and cholesterol
- cholesterol adds rigidity to the membrane
- unsaturated fatty acids increase membrane fluidity
135
what can cross the plasma membrane
hydrophobic molecules and small polar molecules (uncharged)
| ex: CO2, O2, lipids, some drugs
136
membrane proteins
1. transmembrane protein-spans the entire membrane and includes channel proteins, carrier proteins, porins
2. integral membrane protein- anchored to and embedded in the membrane
3. peripheral membrane proteins- adhere to membrane surface via electrostatic interactions
137
cell receptors
recognition glycoproteins on the cell surface that interact with hormones or other molecules and relay signals to the cell
138
function of plasma membrane
- separates living thing from environment
- gradient
- resting membrane potential
- isolate nutrients from environment
139
channel proteins
liquid membrane permiable to small, polar molecules and hydrophobic molecules
- form a barrel across membrane that allows different ions in/out
- very specific
- ions must bind first
- need hydrophobic proteins on side
140
carrier proteins
bind to whatever theyre supposed to transport on one side and then undergo a conformational change and go to the other side
141
porin
protein that forms a giant hole in membrane
allow diffusion to take place
not specific
not common in animal cells
142
membrane proteins are glycosylated at
golgi and rough ER
143
what play a big role in signaling
polysaccarides
ligand will bind to it
always on exterior of cell receptor
144
adhesion proteins
1. gap junctions- allow exchange of nutrients and cell-to-cell communication (ex. cardiac muscle cells)
2. tight junctions- completely encircle cells and seals the space between them to prevent leakage (ex. intestinal cells)
3. desmosomes- 'spot welds' between cells that adhere them to one another and give mechancal strength and anchored to the cytoskeletons of each cell (ex. skin cells)
4. plasmodesmata- narrow channels allowing the exchange of nutrients in plant cells
145
glycocalyx
carbohydrate coating on the cell wall of some bacteria and the plasma membane of some animal cells
-functions in adhesion, barrier to infection, or cell-cell recognition
146
passive transport
- don't require ATP
- go down WITH concentration gradient
- simple diffusion right across membrane
- facilatated diffusion-larger polar things using porin, carrier, channel proteins
147
active transport
- requires ATP
- go against/up concentration gradient
- primary-transport directly coupled to ATP hydrolysis (Na/K pump)
- secondary- solute being transported is not directly coupled with ATP hydrolysis; creates concentration gradient by pumping a solute across and then it will couple the actual one with ATP hydrolysis (Na/glucose transporter)
148
sodium potassium pump
- more Na on outside of cell
- more potassium inside of cell
- primary active transport
- pumps 3 Na out
- brings 2 K in
- resting membrane potential=-70 mV
- Na/glucose pump brings more Na in only if it brings glucose with it (secondary active transport)
149
cell signaling and second messengers
1. ligand binds G-protein receptor (conformational change)
2. G-protein receptor activates G-protein which binds GTP (exchanges GTP for GDP)
3. G-protein activates Adenylate Cyclase (ATP --> cAMP)
4. cAMP acts as a second messenger activating a series of proteins and transcription factors
150
plasmolysis
osmosis in hypertonic solution (higher in solute concentration, relative to cell)
-cell shrivels up
151
cytolysis
osmosis in hypotonic solution (lower in solute concentration)
-destruction of cell/ bursts
152
isotonic
cell and solute have same concentration
153
endocytosis
taking something within cell
154
phagocytosis
cell taking in solids
155
pinocytosis
cell dissolving stuff
156
receptor mediated endocytosis
cell surface already has pits coated with receptors
| sends signals that cause endocytosis to take place
157
cytoskeleton filaments (largest to smallest)
1. microtubules--made from tubulin (monomer) in a 9+2 arrangement; "railroad" for intracellular transport; found in the spindle apparatus of mitosis and in flagella and cilia
2. intermediate filaments-support and maintain the shape of the cell
3. microfilaments-made from actin and involved in cellular motility, muscle contraction, and cytokinesis
158
cell cycle (interphase)
G1-protein and nucleic acid synthesis to prepare for replication; production of organelles
S- DNA replication
G2-continued growth in preparation for mitosis
159
mitosis
1. prophase-chromosomes condense; nuclear envelope disappears, polarization of centrioles
2. metaphase-chromosomes line up on metaphase plate; spindle fibers attach at centromeres
3. anaphase-spindle fibers pull sister chromatids apart towards centrioles; cleavage furrow begins forming
4. telophase-nuclear membranes reform; completion of cytokinesis
160
cellular metabolism uses _____ to make ______
fuel to energy
161
photosynthesis
uses sun's energy to make carbohydrates by reducing CO2
| -exact opposite of cellular respirtation
162
light reactions
- require light
- goal-make energy
- H2O ----> O2
- NADP+--->NADPH (reducing agent)
163
dark reactions
- dont require light
- ATP---> ADP
- CO2--->carbohydrates
164
location of photosynthesis
in chloroplasts of plants--membrane bound organelles
inner and outer membrane
**thylakoid membrane, full of chlorophyll (light absorbing molecules)
165
location of dark reactions
stroma
166
chlorophylls absorb ____ and _____
red light (600-700 nm) and blue light (400-500 nm)
167
antennae chlorophyll molecules pass light energy to _____
reaction centers
168
photophorphorylation
photosystems are part of an electron transport chain that creates a proton gradient
-the proton gradient powers ATP synthase
169
light reaction path
1. PS II P680--water turned into O2
2. PQ (plastoquinon)
3. Cyt b6/f complex
4. PC
5. PS I P700
6. Fd (ferodoxin)
7. FNR
8. thylakoid membrane
9. atp synthase
170
final electron carrier of photosynthesis
NADPH
171
lots of H+ on what side of thylakoid membrane
lumen
172
less H+ on what side of thylakoid membrane
stroma
173
location of light reactions
lumen of thylakoid
174
go through how many rounds of dark reaction (calvin cycle) to get product?
3
175
product of dark reaction
glyceraldehyde-3-phosphate used to make carbs and glycolysis
176
RuBisCo
major enzyme used in dark reactions
starts off reaction
one of the most abundant enzymes on planet
177
carbon fixation
turning carbon dioxides into sugars
| costs a lot of ATP and NADPH which you get from light reactions which get their energy from the sun
178
3 CO2---->
1 glyceride-3-phosphate
