Exam 1 Flashcards
(211 cards)
1
Q
initial theory about species reproduction
A
spontaneous regeneration
2
Q
experiment used to disprove spontaneous regeneration
A
maggots; covered vs uncovered habitats
3
Q
Cell Theory
A
everything living is made of cells AND cells are produced from other cells (cell division)
4
Q
evolutionary evidence that cells produce to make diff kinds of cells
A
extinct species and appearance of new species (adaptation to form new species)
5
Q
Natural selection
A
1) trait variation
2) heritable traits
3) certain traits allow better survival in environment -> reproduce successful offspring
6
Q
Cells 4 functions
A
1) transform matter (build and break molecules)
2) acquire, store, and produce chemical and kinetic energy
3) acquire, save and acquire coordinate info w/ other cells and environment
4)pass info from parent -> daughter
7
Q
what do dissolved molecules do
A
diffuse between parts of cell; collide and undergo chem rxn
8
Q
diffusion
A
move things over short distances from region of high conc -> low conc
9
Q
water adhesion
A
polar water molecules electrically attracted to polar and charged molecules (ex. miniscus)
10
Q
water cohesion
A
polar water molecules bind to other water molecules by H bonds (ex. round water droplets; water sticks to itself)
11
Q
why does ice float in water?
A
the orientation of hydrogen bonds causes molecules to push farther apart, which lowers the density of ice, making it float in water.
12
Q
hydrocarbon
A
molecule made of exclusively hydrogen and carbons
13
Q
saturated hydrocarbon
A
all carbon carbon single bonds
14
Q
unsaturated hydrocarbon
A
includes some c-c double bonds; kinks in chain
15
Q
atomic force microscopy
A
measure forces exerted by atoms
16
Q
4 functions of carbon containing organic molecules
A
1) structure (see if it will dissolve in water)
2) reactants to make product molecules
3) energy stored in bonds
4) control of chemical reactions
17
Q
hydrophobic interactions
A
water molecules would rather be by other water molecules than hydrophobic molecules; most stable with smaller surface where hydrophobic molecule and water meet
18
Q
amphipathic molecules
A
have both hydrophilic and hydrophobic regions
19
Q
plasma membrane
A
amphipathic molecules that separate intracellular cytoplasm/cytosol from extracellular cell well or extracellular matrix
20
Q
first law of thermodynamics
A
energy cannot be created or destroyed
21
Q
second law of thermodynamics
A
entropy (randomness/disorder) is always increasing
22
Q
potential energy
A
the stored ability to cause motion/ release energy
23
Q
kinetic energy
A
energy of motion
24
Q
Spontaneous rxn
A
rxn that releases PE from its bonds (reactant energy> product energy) and entropy increases (more disorder/ little molecules)
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Exergonic rxn
spontaneous (releases energy); neg delta G
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endergonic rxn
non spontaneous (requires energy); pos delta G
27
Which bond has more PE: C-H or C-O
C-H because the electrons are shared more equally (non polar) so the bond is stronger, meaning more energy is released when broken.
28
Anabolic reaction
ADD: many small molecules -> bigger one(s)
*endergonic rxn
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Catabolic Reaction
CUT: bif molecule(s) breaks up into smaller ones (increasing disorder and bonds breaking -> EXERGONIC)
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reaction coupling
exergonic (spontaneous) reaction run with endergonic reaction and act as energy source.
31
coupling reaction in cells
ATP + H2O -> ADP + Pi (inorganic phosphate) + energy
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ATP and glucose coupling rxn
Glucose + ATP -> Glucose 6-phosphate + ADP
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ADP -> ATP + H2O; catabolic or anabolic?
anabolic (endergonic)
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ATP + H2O -> ADP; catabolic or anabolic?
catabolic (exergonic)
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Activation energy
energy needed to start the reaction; energy barrier
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catalyst
provides alt pathways; lowers the EA to speed up the reaction
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enzyme
biological catalyst
name: ___ase
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carbohydrate C:H:O ratio
1:2:1
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lipid C:H:O ratio
1:2:few
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Carbohydrate monomer
monosaccharide; general formula CH2O
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protein monomer
amino acid (amino group, carboxylic acid group, alpha carbon, and side chain)
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nucleic acid monomer
Nucleotides (nitrogenous base, 5 carbon sugar, phosphate group)
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What type of bond links protein monomers together into a polymer?
Peptide bonds:
carbonyl group and amine group dehydration rxn to yield C-N peptide bond and H2O
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polymer formed by protien monomers (amino acids)
polypeptide
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What type of bond links carbohydrate monomers together into a polymer?
glycosidic bond:
hydroxyl groups on sugars dehydration rxn to yield H2O + sugar- O - sugar
46
polymers formed by carbohydrate monomers
Polysaccharids
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What type of bond links nucleic acid monomers together into a polymer?
Phosphodiester Bonds:
sugar -phosphate - sugar
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carbohydrate functions
- breakdown sugar to get energy
-store energy
-make support structures
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carbohydrate plants make to store energy
starch
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carbohydrates animals make to store energy
glycogen
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carbohydrate support structures ex
-cellulose: used in cell walls of plant cells
-chitin: used in cell walls of fungi and insect exoskeleton
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protein functions
determined by R group properties (acidic/basic, hydrophobic/phillic, etc)
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nucleic acid functions
store genetic material
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Protein primary structure
sequence of amino acid
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Protein secondary structure
H bonding between carbonyl groups and amide group
*alpha helix and beta pleated sheet structure
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Protein tertiary structure
interactions between R groups (ionic, H bonds, VDW, disulfide bridge covalent interaction, etc)
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Protein quaternary structure
multiple polypeptide subunits make loosely packed arrangement
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Chaperone
proteins that help other proteins correctly fold
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condensation rxn/ dehydration rxn
removes water from molecule; anabolic rxn small mol -> bigger mol
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hydrolysis rxn
breaks down polymers -> monomers; catabolic (cuts water and polymer molecule)
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Monosaccharides structure
3-7 carbon long hydrocarbon chain with 1 carbonyl group and many hydroxyl groups (can be linear or cyclical)
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amino acid structure
alpha carbon, hydrogen, amine group, carboxylic acid, r group
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Nucleotide structure
nitrogenous base, 5-carbon monosaccharide (ribose or deoxyribose) and 1-3 phosphate groups
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Deoxyribonucleic Acid
DNA; any 4 deoxyribose nucleotide (A,T,G,C)
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Ribonucleic Acid
RNA; any of 4 ribous nucleic acid (A,C,G,U)
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structural difference between RNA and DNA (4)
1) RNA has -OH group (reactive group) on 2' carbon making it less stable and DNA has -H on 2' carbon
2) DNA is double helix while RNA is single stranded
3) RNA has U and DNA has T
4) DNA longer strand than RNA
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protein denaturing
loss of secondary,tertiary, and quaternary structures of protein
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what factors affect protein denaturation
temperature, pH, salt concentration
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ex. of protien mutation
hemoglobin; mutation in 1 amino acid in primary structure -> change in instructions for folding and interactions -> sickle cell anemia
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2 types of enzyme inhibition
competitive inhibition and non competitive/ allosteric inhibition
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competitive inhibition
inhibitor binds to the active so substrate cannot bind
*no chemical reaction
*temporary
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non competitive/ allosteric inhibition
inhibitor binds to allosteric site and changes shape of enzyme
*chemical reaction
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Non polar R groups
C-H bonds/ rings and sometimes S and N
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uncharged Polar R groups
-OH groups
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charged polar R groups
acidic: -COOH
basic: NH3
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3 basic tenets of cell theory
All organisms are made up of cells
Cells are the fundamental unit of life (smallest entity that can be defined as living)
Structure of cells connected to function
Cells come from pre existing cells
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differences between prokaryotes and eukaryotes (organization, compartmentalization, size)
Prokaryotes: have cell wall to maintain shape, nucleotide rather than nucleus’s, non membrane bound organelles
Eukaryotes: contain nucleus and other membrane bound organelles, larger
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Feedback inhabition
Allows cells to control the amounts of products produced from metabolic processes; regulates production
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Protein functions (3)
-regulate other proteins and molecules (bind to target and chem modify; add, activate, inactivate, destruct, etc)
-provide structural support (ex fibers, collagen, etc)
-use energy from atp and act as motors/ pumps to drive rxn
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Structural difference between dna and rna
DNA backbone has -H and RNA backbone/ sugar has -OH
*different nitrogenous bases bind
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Dna nitrogenous bases; complementary pairs
A and T
C and G
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RNA nitrogenous bases; complementary pairs
A and U
C and G
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Complementary nucleotides
Bind via hydrogen bonds; lock and key mechanism
*new strand created complementary to templet strand
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DNA transcription
DNA template splits and makes mRNA sequence
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DNA translation
mRNA directions go to ribosome and create protein polypeptide
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DNA replication
Hydrogen bonds between bases break and sequence used as code to create complementary strands which create 2 double started structure identical to the original
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Ribozymes
RNA enzymes
*floppy rna strands binds with itself
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Fatty acid
Long hydrocarbon chain with carboxyl group at end
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Lipid functions
Storing and releasing energy from breaking hydrophobic bonds
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Triglycerides
3 fatty acids linked by a glycerol
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What type of lipids are membranes made up of
Phospholipids;
Polar head from phosphate group and long hydrophobic fatty acid tails
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Phospholipid hydrophobic interactions in water
-micelle: heads on outside of half circle
-liposome: micelle with hydrophobic hole region in center
-bylayer sheet
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Cell membrane / plasma membrane
Amphipathic structure that separates inside of the cell from outside of the cell; defines boundaries of cell
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Glycolipids
lipids with saccharides instead of phosphate hydrophilic head
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Steroid
lipid with hydrocarbon ring structure
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Cholesterol in membranes
Membrane becomes more solid at high temperatures and more fluid at low temperatures; more resistant to temp change so stabilizes membrane
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Permeability of lipid bilayer
-non polar molecules pass through easily
-small polar molecules (ex. h2o) pass through
-dissolved gases
-large polar molecules and ions CANNOT pass through on own
-amphoteric molecules; depends on size/ significance of polar group
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do steroids pass through lipid bilayer
most do!
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do phospholipids pass THROUGH lipid bilayer
no
100
Isotonic
solute conc same inside and outside of cell
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Hypotonic
solute conc lower outside of the cell; blown up
102
How do cells respond to hypotonic conditions
-plant: cell walls create turgor pressure to block water entry
-animal: contractile vacuoles pump out water
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hypertonic
solute conc higher outside of cell; shriveled
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Osmosis
diffusion of water across membrane
high -> low water conc
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trans membrane proteins
proteins embedded in lipid bilayer to facilitate movement
*hydrophobic R groups near lipid tails
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facilitated diffusion
creates pathway to help diffusion along
*along/down conc gradient
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types of facilitated diffusion proteins
-channel/ pores
-carrier proteins; lock and key interactions
-specialized carrier proteins/channels (ion channels, macromolecule carriers, etc)
108
aquaporins
pores/ channels for water
*speeds up osmosis
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active transport
energy required to move substances across membrane
*AGAINST conc gradient
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secondary transport/ cotransport
diffusion of molecule down conc gradient drives/ provides energy for active transport of another molecule against conc gradient
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primary transport
ATP used to move substances across membrane through active transport
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Symporter
type of co transported that cotransports in the same direction
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antiporter
type of co transported that cotransports in the opposite direction
114
how to couple primary and secondary transport
use pump (primary active transport) to drive cotransport of substance against gradient.
115
3 domains of life
bacteria, archara (both prokaryotes) and eukaryotes
116
what makes eukaryotes different than prokaryotes
-bigger/more complex
-can deform and pince off bits of membrane; vesicle/vacuole
-has organelles
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organelle
specialized membrane bound compartments in a cell (only in eukaryotes)
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endocytosis
membrane pinching off and capturing substance from outside of cell
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exocytosis
membrane fusion releases vesicle contents to the outside of the cell.
120
Semi autonomous organelles
prokaryote resembling structure inside of the cell
*mitochondria and chloroplast
121
Semi autonomous organelle functions
-double membrane bounded
-split/ replicate like prokaryotes
-has own dna and ribosomes -> produce protien
122
theory of Semi autonomous organelle evolution
Endosymbiont;
bacteria enters eukaryote -> helped cell produce ATP -> evolved to make Semi autonomous organelles
*symbiotic relationship
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3 steps of respiration
1) glycolysis (happens in cytoplasm)
2) citric acid/ krebs cycle (in mitochondrial matrix)
3)Oxidative phosphorylation (across inner mitochondrial membrane)
124
substrate level phosphorylation
when a phosphoryl group is transferred from a high energy substrate to ADP -> ATP and coupled with release of energy
*happens in glycolysis and krebs cycle
125
cell membrane with saturated fatty acid tail favored at....
high temp
126
cell membrane with unsaturated fatty acid tail favored at....
low temp
127
Oxidizing agent
substance that is reduced (gains e-)
ex. electron carriers
128
reducing agent
substance that is oxidized
ex. sugars
129
e- carrier cycle
get e- energy from C-H bonds -> break bonds to produce energy by e- being released
130
glycolysis
6-carbon glucose produces 2 3-carbon pyruvates
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glycolysis requirements
requires phosphates from 2 ATP molecules
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glycolysis yeilds
-4 ATP (2 net ATP yield bc 2 ATP put in)
-2 NADH
- 2 pyruvate (per 1 glucose)
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Pyruvate Oxidation
pyruvate loses 1 Carbon -> CO2
pyruvate - 1C then binds to Coenzyme A -> produce Acetyl- CoA
134
Pyruvate oxidation steps
One, carbon dioxide is released from pyruvate. Two, the remaining portion of pyruvate (an acetyl group) is oxidized (donates an electron) to form NADH from NAD+. Three, the oxidized acetyl group binds with Coenzyme A to make acetyl CoA.
135
pyruvate oxidation yield
-2 Acetyl-CoA
-2 CO2
-2 NADH
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Citric Acid Cycle
1) Acetyl-CoA (2 carbons) added to 4-carbon compound -> 6-carbon citric acid
2) 6 carbon citric acid looses 2 carbons -> 2 CO2 and high energy e-
3) regenerate starting 4 carbon and get ATP
137
Citric acid cycle requirements
2 Acetyl-CoA
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Citric Acid Cycle yeilds
- 2 ATP
- 6 NADH
- 2 FADH2
- 2 CO2
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Oxidative Phosphorylation
oxidation of the electron carriers using oxygen that produces the most ATP
140
how much ATP does oxidative phosphorylation yield
26-34 ATP per glucose
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2 parts of oxidative phosphorylation
electron transport chain and ATP synthase
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Electron transport chain
-series of H+ pumps in inner membrane that use energy from high energy e- to pump H+ into intermembrane space
-as chain continues, e- loose energy; oxygen takes low energy e- -> H2O
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ATP synthase
facilitated diffusion of H+ through channel -> spins channel protein to catalyze ATP synthase
-H+ diffuses back across inner membrane
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Chemiosmosis
H+ going from high conc to low conc
*drive synthesis of ATP
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Cellular respiration efficiency
40%
146
cellular respiration products
30-38 ATP
10 NAD+
2 FAD
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what other energy sources other than carbohydrates/ glucose can be turned into ATP?
fats and proteins
148
how do proteins enter cellular respiration
amino acids broken down (dispose of NH3) and in pyruvate oxidation to Acetyl CoA and Citric Acid Cycle.
149
how do fats enter cellular respiration
fats split into fatty acid and glycerol; glycerol provides Pi for glycolysis and fatty acid -> Acetyl CoA
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aerobic
with oxygen
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anerobic
without oxygen
152
fermentation (2 types)
1) lactic acid fermentation
2)ethanol fermentation
way to get NAD+ back from NADH without O2
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lactic acid fermentation
reduce pyruvate with e- from NADH; yields 2 lactate + 2NAD+ + 2ATP
*lactic acid can turn back to pyruvate when oxygen is present
154
ethanol fermentation
take CO2 off pyruvate -> oxidize and yield ethanol, 2NAD+ and 2 ATP
155
ATP production respiration vs fermentation
respiration: 30-36 ATP per glucose
fermentation: 2 ATP per glucose
156
anaerobic respiration
e- from ETC taken off my different e- acceptors (not O2)
ex. CO2, S, SO4, etc
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phototroph
organisms that get their energy from the sun
158
chemotroph
organisms that get their energy from molecules
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heterotroph
organisms that get an organic carbon
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autotrophs
organisms that get an inorganic carbon source-> turn into usable organic carbon on own.
161
chloroplast
semi autonomic organelle in plants and some protists (single celled eukaryotes) used to undergo photosynthesis
162
stroma
space inside the inner membrane of chloroplasts
163
Thylakoid
membrane wrapped disks/ flattened stacks called gana
164
lumen
part of chloroplast where thylakoids are
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photosynthesis: light reaction
use light energy to make ATP
166
photosynthesis: dark reaction
use ATP as an energy source to make energy for cell
167
Photosystems
use light to excite and donate e- to e- acceptor -> run through ETC
*photosystem 2 then photosystem 1
168
pigments
absorb/ collect light energy
*main pigment is chlorophyll a
169
why are leaves green
chlorophyll a pigment does not absorb green light; green light reflected back
*fall leaves different colors because other pigments absorb different wavelengths of light
170
accessory pigments
chlorophyll b, carotenoids, etc
171
photosystems 2
place where donated e- replaced by stealing e- from H2O
172
oxygenic
generates oxygen
173
photosystem 2 products
2e- , 2 H+ , 1/2 O2
174
how does photosystem 2 work?
gives high energy e- to ETC and pumps H+ into thylakoid; used H+ gradient to drive ATP synthase
175
photosystem 1
excites low energy e- from ETC (after pumping H+) using light energy
*2 schemes
176
photosystem 1: non cyclical/ Z scheme
excited e- go to NADP+ to make NADPH -> goes to calvin cycle
*makes ATP VIA H+ PUMPS AND NADPH
177
photosystem 1: cyclical scheme
takes excited e- back to proton pump (cyclical) -> uses them to pump H+ -> H+ gradient drives ATP synthase
*maes ATP W/OUT NADPH ELECTRON CARRIERS
178
does the cyclical or non cyclical scheme of photosystem 1 make more ATP?
cyclical scheme
179
what inputs are needed for the calvin cycle
9 ATP and 6 NADPH (*more ATP!)
180
Calvin Cycle job
fixes (binds/adds) inorganic carbon from CO2 to organic molecules to build them up
181
calvin cycle 3 steps
1) carbon fixation
2)reduction
3)regeneration
182
calvin cycle: carbon fixation
rubisco enzyme adds CO2 to RuBP (5-carbon structure) -> to yield 3-carbon structures
*to get product, 3 carbons are needed so CO2 added 3 times (run cycle 3 times)
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calvin cycle: reduction
use e- from 6 NADPH and 6 ATP to produce 6 G3P (3-carbon) which is used to make sugars
184
calvin cycle: regeneration
5 of the 6 G3P's use 3 ATP to regenerate 3 RuBP (5-carbon structures)
185
rubisco
enzyme that adds CO2 to RuBP (5-carbon); performs carbon fixation
186
photorespiration
brings in O2 rather than CO2; breaks down sugar into CO2 rather than building sugars
*alternate to Calvin cycle
187
when does photorespiration happen
when there is more O2 than CO2; ratio is messed up
*specifically impacts land plants!!
188
How to keep CO2 conc high/ limit photorespiration
C4 and CAM: fix and store CO2 and release before Calvin cycle
*temporary other source of CO2; increases conc of CO2 relative to conc of oxygen
189
LCA
last common ancestor
190
anoxygenic photosynthesis
e- from H2, HS, Fe2+ instead of H2O
191
archaea photosynthesis
use bacteriorhodopsin (a light-driven proton pump, transporting protons out of the cell, and exemplifies vectorial catalysis) but no PS1 or PS2
192
elements of metabolism shared by all 3 domains of life
glycolysis, citric acid cycle/ reverse citric acid cycle, ATP synthase / ETC (chemiosmosis) and *fermentation
193
Chemolithotropes
get their energy from minerals/ high energy e- from inorganic molecules
*"rock eaters"
ex. deep ocean organisms (no sunlight)
194
anaerobic fermentation
energy and e- from ORGANIC molecules use organic molecules as acceptors (not O2)
*substrate level phosphorylation
195
chromosomes
in nucleus; 2 of each type in parent cell -> after meiosis, only 1 of each in daughter cell
*map genes along different positions along chromosomes
196
one gene one enzyme hypothesis
one mutated gene affects only 1 biochemical reaction and 1 specific enzyme/protein
*genes instructions for making proteins
197
what are chromosomes made up of
DNA and proteins
198
tetranucleotide model
only, WRONG theory that said that 4 different nucleotides just attached in a four way attachment
199
Avery 1944 experiment
take smooth cell (with cell wall) and remove proteins and RNA with protease and RNAse to see if rough -> smooth transformation still occurs
*negative result! transformation still occurs
200
rough to smooth bacteria transformation
smooth bacteria DNA exposed to rough bacteria -> interpreted ito rough bacteria -> transformation of colony
201
rules for genetic discovery experiments (validity)
1) testable hypothesis
2) Occams Razor
3)neutral laws don't change reproductivity
202
Occam's Razor
simplest explanation of facts in best
203
Virus
particle (NOT CELL!!) that contains proteins and genetic material (nucleic acids); take over host cell machinery to make viral proteins
204
bacteriophage
virus that infects bacteria; take over and destroy
205
Hershey-Chase 1952
infects bacteria with virus and makes either protein or DNA radioactive to pinpoint which macromolecule goes in bacteria
*2 experiments
206
how to make proteins radioactive
35 S
207
how to make DNA radioactive
32 P
208
chargaff's analysis of DNA (1947)
- 4 different nucleotides present in different conc
-conc of each nucleotide varies between species
-nucleotides are code for carrying material
209
chargaff's rule
%A = %T
%C = %G
210
C4 mechanism
neighboring cells releases stored co2 to cells undergoing photosynthesis -> co2 can out compete o2
211
CAM mechanism
during night time (not doing photosynthesis) store co2 and store in chloroplast
