BIS 2A Flashcards
CH3
Methyl, nonpolar
OH
Hydroxyl, polar
COOH
Carboxylic group, polar
NH3
Amino group, polar
PO4-
Phosphate group, polar
Phosphorylation
Adding of phosphate groups, endergonic
Dephosphorylation
Splitting phosphate groups, exergonic
Phosphoanhydride bond
Bond between the two phosphate groups
Anaerobic
Does not require oxygen
Aerobic
Requires oxygen
Where does glycolysis occur?
Cytoplasm
Is glycolysis aerobic or anaerobic?
Anaerobic
What happens in a coupled reaction?
The enzyme allows a favorable reaction to occur, but an unfavorable reaction occurs simultaneously, because the activation energy was too high
Substrate level phosphorylation
Phosphate is donated by a high energy carbon compound
Main purpose of fermentation…
Replenish NAD+ levels
Two different types of fermentation:
Lactic acid and ethanol
What is pyruvate and what is it used for in fermentation?
Pyruvate is an electron acceptor used in fermentation to generate lactate and oxidize NADH to NAD+
What happens to lactate in fermentation?
Secreted from cell as waste
Is fermentation anaerobic or aerobic?
Anaerobic
What process is pyruvate oxidized?
TCA Cycle
Besides fermentation, where else can we recycle NADH back to NAD+?
Electron Transport Chain
At the end of glycolysis, where are the pyruvate molecules transported to?
Mitochondria
Where does respiration and electron transport chain occur in eukaryotes
Mitochondria
What is the terminal electron acceptor for humans?
O2
In glycolysis, for every molecule that is metabolized, ___ molecules of pyruvate are produced
2
Where does the TCA Cycle occur?
Matrix of mitochondria
In the TCA cycle, one acetyl CoA will yield…
One ATP/GTP, 3 NADH, 1 FADH2
What happens to CO2 in the TCA Cycle?
It is released as gas from breathing
What is a Metabolic Intermediate
Compound that is produced by a reaction which then acts as a substrate for the next reaction
What is the reductive TCA Cycle used for?
Construct glucose and other carbon containing molecules for CO2. ATP and NADH will be inputs since it is in reverse
What does the ETC produce?
Proton gradient
What is the proton gradient used for?
Running ATP synthase
A more negative reduction potential means…
The less likely the compound will accept electrons. Stronger electron donor
Oxidized compounds will have a higher…
Reduction potential
O2 is a very strong…
Oxidizing agent (Will become reduced)
+ delta G knot prime means what for delta E knot prime
It will be negative and vice versa
The oxidant is…
the compound getting electrons
The reductant is…
the compound losing electrons
What are the two major recycable energy carriers?
NAD+ and FAD(2+)
NAD+ is used as a reactant in …
While NADH is used as a reactant in…
Glycolysis, TCA Cycle
ETC, Fermentation
More CH bonds mean…
More reduced
ETC occurs in…
The inner mitochondrial matrix
What happens in respiration?
A series of redox reactions that transfer electrons to the terminal electron acceptor
The electrons passing through the ETC gradually lose…
Potential energy
Generating ATP from ADP is called…
Oxidative phosphorylation (Redox reaction and phosphorylation)
What does the ETC begin with?
Donation of electrons from NADH and FADH2
What is aerobic respiration?
Process of using oxygen as a terminal electron acceptor in an electron transport chain
The endergonic formation of a proton gradient is powered by…
the exergonic redox reactions
What is chemiosmosis used for?
Creating 90% of the ATP during aerobic glucose catabolism
What are the fates of an excited electron?
- Go back to ground state (fluoresced)
- Transferred by resonance
- Transferred to an electron acceptor (Photochemical reaction)
Photophosphorylation
Process of transferring light energy into ATP
What is special about green sulfur bacteria
Can perform photosynthesis using low-energy infrared photons becaause they live in the absence of light
In green sulfur bacteria photosynthesis, the electrons are cyclic/non-cyclic
Cyclic
In non-cyclic photophosphorylation, electrons end up onto…
NADPH after moving through ETC
NADPH in non-cyclic photophosphorylation will be used for…
Carbon fixation
Green sulfur bacteria evolved to utilize ___ as an electron donor, while green plants cannot
H2S
What is the overall function of light dependent reactions of oxygenic photophosphorylation?
Transform solar energy into chemical compounds in the form of NADPH and ATP
The energy from light dependent reactions is used for
reactants for the light independent reactions
Photosystem I and II are found in…
the thylakoid membrane
What happens in the Calvin Cycle?
The ATP will be input and the electron is deposited onto CO2 for long-term storage in the form of a carbohydrate
Calvin Cycle takes place in the…
Stroma
What is special about the reaction center?
Close to an oxidizing agent to undergo oxidation where the light energy is transformed to stable state
Z Scheme
PSII (P680) –> ETC –> P700ox –> ETC –> donated to NADP+
Along the way, proton gradient formed
P680ox replaces its electron by…
Taking an electron from water
What happens to water molecules in PSII?
Split to create O2. O2 is then released into the atmosphere
In photosynthesis, the plant cells use the ATP and NADPH formed during photophosphorylation to…
Reduce CO2 to sugar
What are autotrophs
Organisms that can obtained their carbon from an inorganic source
What are heterotrophs
Organisms that requrie organic carbon
Calvin Cycle leads to the reduction of
CO2 to G3P
What are the three stages of the Calvin Cycle
- Carbon fixation
- Redcution of 3-PGA
- Regeneration of RuBP
Amino acids are the…
monomers that make up proteins
What is the core structure of every amino acid
Alpha carbon bonded to an amino group, caboxyl group, a hydrogen atom, and R group
What is the backbone of an amino acid
N-C-C
N terminus denotes…
The beginning of the molecule and the amino group
C terminus denotes…
The end of the molecule and the carboxyl group
Where are peptide bonds formed
When two amino acids bond. Covalent bond
What kind of reaction occurs when a peptide bond is formed
Condensation/hydrogen synthesis
What bonds when a peptide bond is formed
The carboxyl group of one amino acid and the amino group of the other amino acid
What are the most common shapes in the secondary structure
alpha helix and beta sheets
Secondary structures are held together by…
hydrogen bonds from the backbone
What is the tertiary structure?
3-D structure of polypeptide
What creates the tertiary structure?
Interactions among R groups
What kind of bonds are found in tertiary structures?
Hydrogen bonds, hydrophobic interactions, ionic bonds, disulfide bridge (covalent bond)
When is a disulfide bridge created?
When two cysteine side chains interact
What kind of proteins can refold?
Small proteins
Quaternary structure
Weak interactions between multiple tertiary structures to act as one unit
When does denaturation occur
A proteins changes in temperature, pH, or exposure to chemicals and loses its shape
What are enzymes?
Catalysts that are made of proteins often with non-protein cofactors
Enzymes have an active site providing a unique chemical environment for…
Substrates
How are enzymes regulated
Inhibition and activation
Noncompetitive inhibitors are…
allosteric
The chemical reactants to which an enzyme binds are the enzyme’s…
substrates
The substrate binds onto the enzyme’s…
Active site
What is competitive inhibition?
When an inhibitor similar enough to a substrate binds to the active site to block the substrate from binding
What happens in noncompeititve inhibition?
The inhibitor molecule binds to a location that is not the active site. The binding alters the shape of the enzyme so it doesn’t bind effectively. Also called allosteric inhibition
Competitive inhibitors affect the __ but not the __ where noncompetitive inhibitors affect the ___
Initial rate; maximal rate; maximal rate
What are allosteric activators?
Bind to locations away from the active site, inducing a changw to increase chances of substrate binding to active site
What do cofactors do?
Bind to molecules to promote optimal function
What are prokaryotes?
Single celled organisms that do not have a distinct nucleus with a membrane or other organelles
Prokaryotes are composed of two distinct groups of organisms:
Bacteria and archaea
Bacteria and archaea are ciritcal for…
recycling nutrients essential for creating new biomolecules and the evolution of new ecosystems
What is a stromatolite?
Sedimentary structure formed when minerals precipitate out of water
What began the oxygenation of the atmosphere?
Cyanobacteria
What is a cell wall?
A protective structure that allows organisms to survive in extreme conditions
What are the three common shapes of bacteria and archaea?
Cocci (spherical), bacilli (rod-shaped), and spirlli (spiral-shaped)
Which aqueous compartment does ADP synthase occur?
Stroma