Name the two subcategories of oxidoreductases and define them.
Define oxidoreductase as well
Oxidoreductase - enzyme in redox rxn
Dehydrogenase - transfers electrons and hydrogens from donor to another molecule (oxidizes donor)
Oxidase - transfers electrons and hydrogens from donor to oxygen (oxidizes donor)
2. Hydrolase - where is donor group transferred to? cleaves what type of bonds?
3. Lyase - cleaves what type of bonds? What else does it do (2)?
Transferase - transfers part of one molecule to another X-Y + Z --> X + Y--Z
Hydrolase - cleavage of bonds w/ addition of water (cleaves C-O, C-C, C-N, etc) The donor group is transferred to water.
Lyase - cleaves C-O, C-C, C-N, leaving double bonds or adding groups to double bonds.
Define isomerase and name 3 subcategories.
Isomerase - changes geometric/spatial configuration of a molecule
Epimerase, racemase, mutase
What is analogous to a ligase?
Ligase - uses the energy derived from hydrolysis of high energy bond (ATP) to join 2 molecules)
Define (1) Kinase (2) Phosphatase
Kinase - adds PO3 (phosphate) group to a molecule, generally obtains PO3 from ATP.
Phosphatase - removes phosphate group from molecule.
What is the general structure of sugar? Draw.
Be able to identify glucose linkages (1,4 & 1,6)
Identify this structure:
Fatty acid (saturated)
Can also be unsaturated.
Identify this structure:
Identify this structure:
Where will peptide bond form?
Identify this type of structure!
Sterol: ex. Cholesterol, bile acids, cortisol, estrogen, testosterone, vitamin D, purine, pyrimidine
Name the 4 categories of amino acids and their defining characteristic
What are differences between polar and nonpolar compounds? (2 diff)
Polar compounds are hydrophilic and water-soluble
Nonpolar compounds are hydrophobic and fat-soluble
Define the following:
2. Binding affinity
Substrate and reactant are the same thing (both on left sides of equation), except called substrate when rxn is done by enzyme.
Binding affinity - strength of binding by noncovalent interactions between two molecules
- 1. Precursor - a substance from which another is formed
- 2. Product - something manufactured from substrate by enzyme
Define Km vs. Vmax
Seen on what type of graphs? (What is the x and y axis)
Km - roughly an inverse measure of binding affinity bt substrate and enzyme (lower Km, higher affinity)
Also, Km = the substrate concentration that produces a Vi that's half of Vmax
Km stands for Michaelis-Menten Constant
Vmax - maximum velocity of the rxn.
1. Cell differentiation
- 1. Cell Diff - normal process by which a less specialized cell develops/matures to possess a more distinct form and function.
- 2. Mitogen - substance that induces/stimulates mitosis
- 3. Mitogenesis - Induction of mitosis in cell
Define in vivo vs in vitro
In Vivo - experimentation done in or on living tissue of a whole, living organism as opposed to a partial/dead organism.
In vitro - experimentation done in controlled environment outside of living organism, for example in petri dish or test tube.
What are three descriptions of enzymes?
- 1. Help reactions go faster by lowering activation energy
- 2. Are specific for their substrates
- 3. Active site mechanism is like lock and key
What are two major types of short term regulation? Name two subcategories of the 2nd one.
- 1. Substrate availability
- 2. Conformational change - allosteric binding sites (immediate) and covalent modification (second to minutes)
What is the mechanism behind allosteric regulation?
What is the result? (3)
What can effectors be? (3)
How soon does the effect take place?
Mechanism: Effector molecule binds noncovalently to enzymes at a site other than active site, changing the shape of the active site.
Results: This binding causes change in affinity of enzyme for its substrate or alters its rxn rate (maximal activity) OR BOTH.
Effectors: substrates, products, or other small molecules
The effect takes place immediately.
What is the mechanism behind covalent modification?
What specific type of covalent modification?
Catalyzd by what type of enzymes? Requires what else, usually? (1)
Mech: Phosphate has negative charge and alters enzyme shape or conformation
Usually, phosphorylation or dephosphorylation
Catalyzed by protein kinases and phosphatases (ATP and ADP too)
How long does it take for covalent modification to occur?
seconds to min
Name three types of broad regulation that are NOT short term and give examples of each.
- 1. Long term (gene expression) - SREBP
- 2. Permanent compartmentation - Enzymes are segregated into specific cells/compartments/organelles; transcription
- 3. Variable compartmentation - GLUT 4 recruitment for intracellular pool
Name the main form of long term regulation.
What are the effects of this kind of regulation?
How does it render these effects?
How long does it take for these things to work?
Gene expression - can increase/decrease amount of enzyme present in cell.
By altering rate of transcription/translation to get new protein synthesis
Hours to days
What are regulation sites in a metabolic pathway likely to be? (4)
- 1. Rate-limiting step
- 2. Committed step
- 3. Irreversible rxn (ATP consuming)
- 4. At a branch point in pathway
Active vs passive transport?
Active transport requires energy, requires movement of molecules against electrochemical gradient.
Passive transport does NOT require energy, molecules travel from higher concentration to lower concentration through concentration gradient.
What are two types of enzyme regulation outside of the first couple listed?
Rate of enzyme synthesis and degradation
What can block a pathway? (2)
Enzyme deficiency (partial or total) OR drug
Why is specific transport needed?
To control import!!
To increase entry of molecule in short supply, in response to physiological condition (glucose entry into muscle),
increase/decrease entry of useful but pot toxic molecule (iron), in response to specific & changing cell requirements (cholesterol)
Maintain membrane polarization (Na+/K+), export molecules in a regulated way (HCl secretion), maintain intra/extracellular concentrations.
Define passive transport. What's another word for it?
- Passive movement according to concentration gradient across membrane
- - molecules pass freely through the lipid bilayer
- - no need for protein transporter
What is the only thing needed for diffusion across a lipid bilayer?
Something to drag them out of the lipid on the other side of membrane
What happens in mediated transport? (5)
Requires molecule to specifically bind to a transporter, probably with a change in the transporters shape.
The molecule is moved to the opposite side of the membrane in the process.
The molecule then disassociates from the transporter which changes its shape back to its conformation.
Diffusion vs mediated transport in terms of molecule movement?
Diffusion - movement of molecules increases in proportion to EC concentration, no binding site needed. When the concentrations inside and outside become equal, its in equilibrium.
Mediated transport - movement of molecules reaches max value when all available transport proteins are saturated. Any increase in EC concentration will not change rate of entry into cell.
What are the two types of mediated transport?
What do they have in common? (5)
- (1) Facilitated diffusion aka passive trasnport
- (2) Active transport
- - Binding resembles substrate-enzyme interaction:
- - Has specific binding site
- - Is saturable (so there's a max rate of transport - Vmax)
- - Has a binding constant/affinity for its solute (Km)
- - Can be inhibited by structurally similar competitive inhibitor
What determines rate of facilitated or passive transport? (4)
- 1. Concentration gradient across membrane
- 2. Amount of carrier - KEY CONTROL STEP!
- 3. Rate of solute-carrier interaction
- 4. Rate of conformational change for the loaded & unloaded carrier
What are differences between facilitated/passive transport and active transport?
1. Facilitated: high conc to low conc until both sides are equal, doesn't req energy, bidirectional
2. Active: against electrochemical gradient, usually unidirectional, requires energy
How much of total energy expenditure does maintenance of electrochemical gradient take up?
Maintenance of electrochemical gradient takes 30-40% of total energy
What's the difference between primary active transport and secondary active transport?
Primary active - DIRECTLY coupled to hydrolysis of ATP
Secondary active - uses ion concentration gradient (set in place by primary active transport) as energy source.
Transporter binds to ion, movement can be in same direction (co-transport) or opposite (counter-transport)
Is [Na+] high inside or outside of cells? What about [K+]?
Na+ --> EC
What are the differences between allosteric and covalent modification?
- (1) Requires effector molecule vs. kinases or phosphatases
- (2) Binds noncovalently to site different from active site vs binds covalently to serine, threonine, or tyrosine residues.
- (3) Effector changes shape of substrate binding site vs phosphate group has negative charge changing enzyme shape/conformation
- (4) Immediate effect vs seconds to minutes