Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
121 Cards in this Set
- Front
- Back
|
Eukaryotes |
Cells with organelle bound membranes; high SA:V ratio (larger cells); have mitochondria (and chloroplasts) |
|
|
Prokaryotes |
Cells without internal membranes (low internal complexity); no mitochondria; low SA:V ratio; smaller size; single celled |
|
|
Archaea |
Single celled; no internal membranes; prokaryotic but more closely related to eukaryotes; often extremophiles |
|
|
Chemorgano |
Energy from organic chemicals |
|
|
Chemolitho |
Energy from inorganic chemicals |
|
|
Phototroph |
Energy from light |
|
|
Autotroph |
Carbon from inorganic compounds |
|
|
Heterotroph |
Carbon from organic compounds |
|
|
Endosymbiosis |
Symbiotic relationship where one organism lives inside another |
|
|
Theory of eukaryotic development #1 |
Endosymbiosis. Primitive eurkaryote evolves from archaea but is likely energy starved. Engulfs a bacteria which produces energy (eventually becomes a mitochondria). |
|
|
Theory of eukaryotic development # 2 |
An archaea engulfs a bacterium develop an endosymbiotic relationship. Eventually eukaryotes evolve from there. |
|
|
Support for endosymbiotic theory of eukaryotic evolution |
1. Chloroplasts/mitochondria are about the same size as modern day prokaryotes 2. Chloroplasts/mitochondria have their own DNA and divide by binary fission like bacteria 3. Chloroplasts/mitochondrial ribosomes are more similar to those of bacteria |
|
|
5 kingdom classification |
Based on morphology and nutritional/metabolic needs |
|
|
Phylogenetics |
Looks at the similarities in ribosomal RNA to classify organisms |
|
|
Electrochemical gradient |
Across a membrane. Gradient w 2 components: 1. Electrical gradient (positive H+ repel each other) 2. Concentration gradient
Stores PE, much like a dam. Used to synthesize ATP. |
|
|
Calculating energy across a membrane |
Free Energy = RTln(Y/X) |
|
|
ATP |
Energy currency of cells. Used for immediate needs. The negative phosphate groups repel each other, but are held close, and thus hold a lot of PE. Once a phosphate is detached it floats around as an inorganic molecule |
|
|
Phospholipid |
Composed of a hydrophilic head and a hydrophobic fatty acid tail. The tail has a hydrocarbon backbone. The tail may vary in the number of carbons and double bonds. Amphipathic. |
|
|
Membrane bilayer |
Composed of phospholipids. Heads face out to interact w water. Tails are in the centre, hidden from water. |
|
|
Saturated |
All the carbons in a fatty acid are fully bonded with hydrogen (no double bonds). More electrons mean greater van der waals interactions between the tails and no kinks mean the tails fit closely together. The melting point is high and the membrane more rigid. |
|
|
Unsaturated |
Double bonds b/w Cs in the fatty acid tails. Creates kinks which don't allow the tails to sit closely together. Lower melting point and more fluid membranes. |
|
|
Opsin |
Pigment molecule of H. Halobium. Attached to integral membrane protein bacteriorhodopsin (H+ pump). |
|
|
Bacteriorhodopsin |
Integral membrane protein attached to pigment molecule opsin. Is an H+ pump. |
|
|
Antennae pigments |
Absorb light E and transfer it to special rx centre chlorophylls. E transfer not in straight line. Passes E to neighbouring molecules in a random fashion until it reaches rx centre. Located in thylakoid. |
|
|
Reaction centre chlorophyll |
Bound to protein complexes PS1 and PS2. Located in thylakoid membrane. |
|
|
Thylakoid |
Disc shaped structures in chloroplast. Chlorophyll is embedded in thylakoid membrane. Site of photosynthesis. |
|
|
Free energy |
Amount of PE (and some KE and entropy) that can be freed up to do work. Must be negative (exergonic) for a rx to be spontaneous. |
|
|
PE in a molecule |
Stored in bonds. More bonds = more PE Non polar covalent bonds = more PE |
|
|
Sources of cell E |
1. e- position (polar v non polar bonds) 2. e- position (in E levels of an atom) 3. Redox rxs 4. Electrochem gradients acress a membrane |
|
|
Function of membranes |
1. Compartmentalize the cell 2. Selective permeability - maintain homeostasis - allow for concentration difference inside v out 3. Sites for comms. and rxs |
|
|
Fluid mosaic model |
Lipids and proteins coexist in membranes. Molecules can move within membrane, which is constantly in flux. |
|
|
Integral protein |
Spans membrane. |
|
|
Peripheral protein |
Either inside or out of membrane |
|
|
Amphipathic |
Have both a hydrophobic and hydrophilic part. |
|
|
Micelle |
Spherical phospholipid monolayer formed spontaneously in water. |
|
|
Liposome |
Spherical bilayer (like a cell) formed spontaneously in water. |
|
|
Sterols |
Amphipathic. In phospholipid membrane. Prevents freezing (keeps PLs from getting too close) and melting (keeps the gaps small). |
|
|
Selective permeability |
Hydrophobic region creates a barrier: 1. Small, uncharged, or barely polar molecules can pass (O2, H2O, CO2) 2. Large, charged, polar cannot pass (Na+, H+, glucose) |
|
|
Isotonic |
Solution has same concentration as the cell. |
|
|
Hypotonic |
Solution has a lower concentration than the cell |
|
|
Hypertonic |
Solution has a higher concentration than the cell. |
|
|
Entropy |
The "disorder" of the universe. All rxs must have positive total entropy (Ssystem + Ssurroundings). |
|
|
Go |
Free energy change under standard lab conditions. Is not the same as G b/c conditions in a cell (temperature, substrate concentration) may be different. Can adjust to cellular concentrations: G = Go + RTln((X)/(Y)) @ equilibrium G = 0, Q (X/Y) = Keq Go = -RTlnKeq |
|
|
Complex 1 |
First e- acceptor for NADH in ETC (is reduced). Is oxidized by CoQ e- taxi. Pumps H+ into IMS. |
|
|
Complex 2 |
First e- acceptor for FADH2 in ETC (is reduced). Reduces CoQ e- taxi. Does not pump H+. |
|
|
Complex 3 |
Reduced by CoQ (from both complex 1 and 2) and oxidized by CytC. Pumps H+ in IMS. |
|
|
Complex 4 |
Reduced by CytCred and oxidized by O2 (forms H2O). Pumps H+ across IMS. |
|
|
CoQ |
Ubiquinone. E- taxi. Hydrophobic. Operates within IMM. Accepts e-s from complexes 1 and 2 and transfers to 3. Reduced = CoQh. |
|
|
Spontaneous rx |
Goes "downhill" in G. |
|
|
Coupled rx |
Single rx in which 2 things are happening (same time and place) |
|
|
Pushing and pulling a rx |
Manipulate the concentrations of products and substrates so that the rx occurs spontaneously. High (substrate) pushes the rx forward. Low (products) pulls it forward. |
|
|
Activation energy |
G*. Activation barrier. Energy required to start a rx by overcoming and partially breaking the substrate bonds. Change in AE does NOT change the G of the rx. |
|
|
Transition state |
Reactants when old bonds are breaking and new bonds are forming. At the top of the energy barrier. |
|
|
Enzyme |
Protein catalysts that speed up otherwise slow bio rxs by lowering the AE. Ribozymes are RNA catalysts. |
|
|
Active site |
Enzyme region that interacts w a specific substrate. The enzyme and substrate react here, forming a substrate-enzyme complex. |
|
|
Induced fit |
ES complex changes the conformation of the enzyme to fit the transition state (not the substrate) and therefore causes the substrate bonds to weaken (reduces the AE). Once the rx complete the enzyme changes back to original conformation. |
|
|
Enzyme velocity |
Depends on: 1. (enzyme) - linear relationship 2. (substrate) - plateaued curve 3. Inhibitors and activators |
|
|
Enzyme kinetics |
Enzyme velocity: how fast it catalyzes a rx. |
|
|
Vmax |
Max velocity of catalysis; enzymes are saturated with substrate. |
|
|
Km (Michaelis constant) |
Quantifies affinity enzyme has for a substrate. (substrate) at 1/2vmax. A large km = poor affinity, low km = high affinity. |
|
|
Reversible competitive inhibitor |
Chemically similar to substrate. Binds at active site in competition w substrate. The chemical at the highest concentration wins. Vmax remains the same, and km increases. |
|
|
Reversible non competitive inhibitor |
Not similar to substrate. Binds at site other than active site. High (substrate) does not reverse. Vmax decreases, km stays the same. |
|
|
Irreversible inhibtor |
Can be noncompetitive or competitive. Forms a covalent bond w enzyme (reversible inhibitors = hbonds and van der waahls). |
|
|
Allosteric enzymes. |
Regulatory. Used by cells to control rate of entire biochem pathway. May inhibit or activate. |
|
|
Feedback inhibition |
Allosteric inhibitor is the final product in a pathway (acts on enzyme early in the pathway). |
|
|
Amino acids |
1. AA polymer = protein 2. Consists of a. Amino group b. Central C c. Carboxyl group d. H group d. R group (only difference b/w AAs) |
|
|
R groups |
Differentiating group of AA. 1. Hydrophobic 2. Hydrophilic |
|
|
Peptides |
Linked AA. Held together by peptide bonds (covalent) b/w C-N (carboxyl and amino groups). |
|
|
PQ (plastiquinone) |
Hydrophobic e- taxi in thylakoid mem. b/w PS2 and Cyt complex |
|
|
PC (plastocyanine) |
Hydrophilic e- taxi b/w Cty C complex and PS1. |
|
|
Cyt complex |
Central protein in thylakoid ETC. Reduced by PQ and oxidized by PC. |
|
|
Energetic coupling |
Spontanepus rx drives nonspontaneous rx; net of 2 rxs must have -G. Enzymes often E coupling devices. |
|
|
Polypeptide |
A polymer of more than 10 AAs (all enzymes) |
|
|
Oligopeptide |
Polymer of less than 10 AAs |
|
|
Protein |
Polypeptide folded into 3D shape |
|
|
Primary active transport |
Uses ATP directly to move a molecule across a membrane against its gradient. Are energy coupling devices. Ex. Na/K pump couples with ATP hydrolysis. |
|
|
Secondary active transport |
Uses the movement of one molecule down it (gradient) to move a second solute against its (gradient). Are energy coupling devices 1. Symport: both solutes move in sane direction 2. Antiport: solutes move in opposite directions |
|
|
Primary protein structure |
Linear AA sequence |
|
|
Secondary protein structure |
Helices and sheets (hbonds of backbone b/w carbonyl and amide groups) |
|
|
Tertiary protein structure |
3D shape due to interaction b/w R groups. Hbonds, ionic bonds, covalent, ver der waahls. |
|
|
Quaternary structure |
Multiple 3D subunits interacting. Homo (same), hetero (dif) subunits + # + (units = mer) |
|
|
Enzymes as ECDs |
Transfer E released from one rx to help complete 2nd rx. Do this by: 1. Becoming phosphorylated (changes conformation) 2. Becoming reduced (redox and ETC) |
|
|
Enthalpy (H) |
Sum of all PE and all KE. Heat of rx. Exo/endothermic |
|
|
Spontaneous rx |
A rx that can occur (may be slow though). Has -G (exergonic). Determined by entropy. |
|
|
Entropy (S) |
Dispersion/disorder of E. Must always increase. S is always + for spontaneous rx. Stotal = Ssystem + Ssurroundings. G also measures entropy change. |
|
|
Gibbs Function (G) |
E free to do work (E that can be dispersed). Also measures entropy. Must be - for spontaneous rx. Stot = Ssurr - Ssys G = -TSsurr - TSsys G = -TStot |
|
|
Steady state system |
Rate inflow = rate outflow Ex. Metabolic homeostasis (pools of metabolic intermediates where rate of intermediate production = consumption) |
|
|
Chemoorgabotroph metabolic pathways |
Fermentation, anaerobic and aerobic respiration All include glycolysis |
|
|
Glycolysis |
Occurs in cytosol. Anaerobic 10 connected rxs to breakdown glucose each w own enzyme. Input: 1 glucose, 2 ATP, 2NAD+ Output: 2 NADH, 4 ATP, 2 pyruvate
|
|
|
E extraction from glucose |
1. Glycolysis 2. Pyruvate oxidation 3. Krebs 4. Oxphos Stepwise to control E release |
|
|
1st phase of glycolysis |
Prime the pump. Input 2 ATP to attach 2 P to glucose |
|
|
2nd phase glycolysis |
Lysing (splitting) the glucose into 2 3C molecules. |
|
|
3rd phase glycolysis |
Energy generation/payoff. Produces 1NADH and 2 ATP per pyruvate (3C) formed (2 pyruvate formed). NAD+ carrier reduced. ATP made by substrate level phosphorylation |
|
|
Substrate level phosphorylation |
ADP phosphorylated to ATP by a P donated by a an organic substrate. Coupled by an enzyme. |
|
|
Possible pyruvate pathways after glycolysis |
1. Fermentation: absence of O2 2. Aerobic respiration 3. Anaerobic respiration: only prokaryotes |
|
|
Fermentation |
When O2 limiting, used to keep glycolysis going. Does not produce ATP!!! Pyruvate is reduced by NADH to produce NAD+ (recycled to glycolysis). Not eukaryotes preference. Humans: happens in muscles. |
|
|
Recycling NADH |
Need to recycle to NAD+ for glycolysis 1. Pyruvate oxidation (no O2) 2. O2 as OA: Oxphos (many steps); O2 final e- acceptor. |
|
|
Pyruvate oxidation |
2nd stage of cell respiration. "Bridge" rx. Won't occur if O2 not present (cell would run out of ATP). Occurs in mit. matrix. Oxidized to acetyl-CoA by NAD+ and input CoA. Produces NADH, CO2, acetyl-CoA per 1 pyruvate. |
|
|
Acetyl-CoA |
Produced by pyruvate in MM by oxidation w NAD+. |
|
|
Krebs/citric acid |
Fuel molecules from glucose fully broken down to produce ATP and e- carriers. 8 connected rxs. Oxidize acetyl-CoA to CO2. 1 turn per acetyl-CoA (2 turns per glucose). Produces/acetyl-CoA: 1GTP by subs level phos + e- carriers (3 NADH + 1FADH2) Not just for E: intermediates to make other molecules |
|
|
ETC |
Occurs on IMM (euks) and plasma mem (pros). Does two things: 1. Transports e- from e- carriers (FADH2 and NADH) to O2 2. Generates electrochem gradient (pmf) across IMM using E from e- transfer -H+ moved from Matrix to IMS Overall result: G released w e- flow and used to pump H+ H+ also removed from matrix by formation of H2O |
|
|
Mitochondrion |
Double mem. Location of pryuvate oxidation, krebs, and oxphos. |
|
|
Cyt C/ Cty Cred |
Hydrophilic e- taxi; exists on IMS side of IMM. Shuttles e- from C3 to C4. Contains cytochrome |
|
|
OxPhos |
Use of ETC to generate pmf for ATP synthesis using inorganic phosphate. Pmf most direct source of E for OxPhos. H+ moves through ATP synthase to phosphorylate ADP. |
|
|
ATP synthase |
Enzyme (nanoturbine) used to phosphorylate ATP. Powered by pmf. 2 subunits: 1. F0: forms channel that rotates as ions pass through. 2. F1: sticks into matrix. Uses rotational E to catalyze ATP synthesism. |
|
|
Aerobic respiration (Pros) |
Occurs in cytosol (glycolysis and bridge) and on plasma mem (ETC). Otherwise is is the same as aerobic respiration in euks. |
|
|
Anaerobic respiration |
Only in pros. Not fermentation. Uses final e- acceptors other than O2. Ex. SO4- and NO3- Otherwise is the same as aerobic respiration. |
|
|
Chemolithotrophy |
Only in pros. Uses primary e- donors that are inorganic (eg NOT FADH2 or NADH). Ex. H2S, Fe 3+, H2, NH3 Does NOT use glyc, bridge, krebs DOES use ETC/Oxphos Aerobic or anaerobic. Final e- acceptor is O2 or another molecule. |
|
|
E dif in metabolic pathways |
Primary e- donors of final acceptors generate pmfs of dif strengths. Weaker pmf = less ATP. Org molec have more PE than inorg O2 is stronger acceptor than all other acceptors |
|
|
Rubisco |
Enzyme that catalyzes the 1st dark rx (Calvin cycle) where CO2 is added to C5 to produce 2 x PGA (C3) (phosphoglycerate). |
|
|
Calvin cycle |
Dark rxs. 1. Fixation (use rubisco to attach 6 CO2 to 6 C5 to form 12 x PGA (phosphglycerate, C3)) 2. Reduction (12 ATP used and 12 NADPH to produce the intermediate 12 x G3P and 12 H2O - half the O from CO2 in this H2O). 2a. 2 of the G3P undergo gluconeogensis. 3. Regeneration: 10 x G3P use 6 ATP to regenerate the 6 x C5 *Use a lot of ATP/NADPH to make glucose 6CO2 + 12 NADPH + 12 H+ + 18ATP + 18 H2O -----) C6H12O6 + 12NADP+ + 6H2O +18ADP + P |
|
|
Light dependent rx |
Uses photons directly Oxidation of water w O2 as byproduct |
|
|
Light independent rxs |
Photons not used directly (but ATP/NADPH products of light rx are) Reduction of CO2 to form carbs |
|
|
Chloroplast |
Triple mem 1. Outer 2. Inner 3. Thylakoid Space b/w inner and thylakoid is the stroma Inside thylakoid is the lumen |
|
|
Chlorophyll |
Looks like a lipid (amphipathic) - is part of thylakoid mem Major pigment |
|
|
Carotenoids |
Accessory pigments |
|
|
Photosystem |
Antenna pigments grouped around rx centre |
|
|
Antenna pigments |
Channel E (don't pass e-). Excited e- in one pigment passes E to neighbour (excites it's valence e-) when it returns to ground state. |
|
|
Rx centre chlorophyll |
Can donate high E e- (redox) |
|
|
Photophosphorylation |
ATP synthesis w ATP synthase (inorganic P) using E from a pmf that was pumped using E from the sun |
|
|
Ways to make ATP |
1. Subs level phos 2. Oxphos 3. Photophos |
