Ek Bio Lecture 1 (Molecular Bio, Cellular Respiration)

Front 1

Function of:
Fatty Acids
Triacylglycerides
Steroids
Lipoprotein

Back 1

Fatty Acids: Some function as local hormones
Triacylglycerides: Energy, insulation/padding
Steroids: regulate metabolic activities
Lipoprotein: Transport hydrophobic lipids in bloodstream

Front 2

Structure of:
Phospholipid
Glycolipid
Steroid
Eicosanoid
Lipoprotein

Back 2

Phospholipid: 2 FA's, glycerol, phosphate, head group
Glycolipid: Glycerol, FA's, one or more carbs
Steroid: 4-ringed structures
Eicosanoid: 20 carbon FA
Lipoprotein: Lipid core surrounded by phospholipids and apoproteins (Chylamicrons, VLDL, LDL, HDL)

Front 3

Hydrogen bonding occurs where in proteins?

Back 3

Between H on amine group and O of carbonyl on both beta-pleated sheets and alpha-helices

Front 4

Five forces that create tertiary protein structure.

Back 4

Five forces that create tertiary protein structure:
1. Covalent disulfide bonds between cysteines
2. Electrostatic/ionic interactions mostly between acidic/basic side chains
3. H bonds
4. Van der Waals forces
5. Hydrophobic side chains pushed away from water toward center of protein

Front 5

What protein interactions do each of the following denaturing agents disrupt?
Urea
Salt/pH change
Mercaptoethanol
Organic Solvents
Heat

Back 5

Urea- H bonds
Salt/pH change- electrostatic interactions
Mercaptoethanol- Disulphide bonds
Organic Solvents- Hydrophobic forces
Heat- all forces

Front 6

Cytochrome

Back 6

Protein which requires a prosthetic heme group to function. Ex: Hemoglobin, Cytochrome C, Cytochromes of ETC

Front 7

Conjugated Protein

Back 7

Protein with non-proteinaceous parts
Ex: glycoprotein

Front 8

Function of liver/enterocytes related to non-glucose monosaccharides

Back 8

Converts them to glucose

Front 9

If cell has sufficient ATP, glucose is...

Back 9

polymerized into glycogen.

Front 10

Digestive tract epithelial cells and proximal tubule of kidney can...

Back 10

absorb glucose against concentration gradient via secondary active transport down concentration gradient of sodium.

Front 11

Amylose

Back 11

Form of starch, isomer of cellulose, branched or unbranched

Front 12

Amylopectin

Back 12

Form of starch, resembles glycogen but has different branching structure

Front 13

Nucleotide

Examples

Back 13

Five C sugar
Nitrogenous base
Phosphate group

Ex: ATP, cAMP, NADH, FADH2

Front 14

Polymers of nucleotides include...

Back 14

Nucleic acids, DNA, and RNA

Front 15

Phosphodiester bond involves...

Back 15

phosphate group of one nucleotide and 3rd carbon of pentose of other nucleotide

Front 16

Minerals

Back 16

Inorganic ion used to create electrochemical gradients, strengthen matrix, cofactors

Front 17

Saturation Kinetics

Back 17

As the relative concentration of substrate increases, the reaction rate also increased, but to a lesser and lesser degree until Vmax

Front 18

Turnover Number

Back 18

Number of substrate molecules one enzyme active site can convert to product in a given unit of time when an enzyme solution is saturated with substrate

Front 19

Vmax is proportional to...

Back 19

[Enzyme]

Front 20

Michaelis Constant (Km)
Does not change with...

Back 20

The [substrate] at which run rate is equal to 1/2Vmax.

Does not change with increasing [enyzme]. Therefore, a good indicator of enzyme's affinity for its substrate.

Front 21

Categorize and define Cofactors

Back 21

Cofactor is a non-protein component required by some enzymes for optimal activity.
Cofactors consist of minerals and coenzymes. Coenzymes consist of cosubstrates and prosthetic groups. Cosubstrates reversibly bind to enzyme, transfer chemical group to other substrate, and then are reverted back to original form by another enzymatic rxn. Ex: ATP
Prosthetic groups, on the other hand, remain covalently bonded to enzyme throughout rxn.

Front 22

Vitamin

Back 22

Essential organic molecule, often coenzymes.

Front 23

Apoenzyme
Holoenzyme

Back 23

Apoenzyme: Enzyme w/o its cofactor
Holoenzyme: Enzyme w/ its cofactor

Front 24

Irreversible Inhibitor

Back 24

Agent that binds irreversibly to enzyme, disrupting function. Tend to be highly toxic.
Ex: Penicillin

Front 25

Three Classes of enzyme inhibitors.

Back 25

Irreversible inhibitors
Competitive inhibitors
Noncompetitive inhibitors

Front 26

Competitive Inhibitor

Back 26

Compete with substrate by binding reversibly with non covalent bonds to active site.
Do not affect Vmax, but raise Km.
Overcoming inhibition by increasing [substrate] is a typical sign of a competitive inhibitor.

Front 27

Noncompetitive Inhibitor

Back 27

Bind noncovalently to enzyme at a spot other than active site and change conformation. Do not prevent substrate from binding, and they bind just as readily to enzymes that have a substrate as to those that don't. Do no often resemble substrate so can bind to more than one enzyme usually. Vm is lowered and Km is unaffected (no lowered affinity).

Front 28

Zymogen/Proenzyme

Back 28

Inactive form of enzyme needing irreversible cleavage by enzyme or environment (pH, etc.)
-ogen

Front 29

List and describe four ways to regulate enzymes

Back 29

Proteolytic cleavage (irreversible covalent mod.)- Proenzyme/zymogen to active form via enzyme or environment (pH, etc.)

Reversible Covalent Modification- Phosphorylation, AMP, etc. Removal of modifier almost always by hydrolysis.

Control Proteins- Protein subunits that associate with certain enzymes to activate or inhibit their activity.
Ex: Calmodulin, G-proteins

Allosteric Interactions- Modification of enzyme configuration resulting from binding of an activator or inhibitor at specific binding site on enzyme.

Front 30

Allosteric Regulation
Allosteric Inhibitors
Allosteric Activators

Back 30

Feedback inhibitors bind to enzyme causing conformational change. This activates or inhibits enzyme. Think positive and negative feedback.

Front 31

Positive/Negative Cooperativity

Back 31

Cooperativity requires multiple substrate binding sites.

Positive Cooperativity: Substrate binding to enzyme increases enzyme's affinity for substrate.
Negative cooperatively is the opposite.

Front 32

Lyase vs Ligase

Back 32

Both catalyze addition of ones substrate to double bond of second substrate.
Lyase: No ATP, aka synthase
Ligase: ATP, aka synthetase

Front 33

Metabolism

Back 33

All cellular chemical reactions (anabolism and catabolism)

Front 34

Respiration

Back 34

Second and Third stages of metabolism-- ones where you get energy

Front 35

Glycolysis

Back 35

Glucose into 2 3-carbon pyruvates, 2 ATP, 2NADH, 1 Pi, 1 H2O

All cells can do it. Second phosphate addition commits to glycolysis.

Front 36

Substrate Level Phosphorylation

Back 36

Formation of ATP from ADP and Pi using the energy released from the decay of high energy phosphorylated compounds as opposed to using the energy from diffusion.
Used in Glycolysis and TCA.

Front 37

Fermentation

Back 37

Includes glycolysis. Results in Lactic acid/Ethanol, oxidation of NADH to NAD+, CO2

Front 38

Aerobic Respiration

Back 38

If O2 is present, NADH and pyruvate move through porins (outer mitochondrial membrane) then to mito matrix. NADH sometimes needs help by ATP hydrolysis to get past inner mito membrane. Once in membrane, pyruvate converted to acetyl CoA in a rxn w/ NADH and CO2 by products.

Front 39

Acetyl CoA

Back 39

Coenzyme that transfers two carbons (from pyruvate) to oxaloacetate to begin TCA.

Front 40

The Citric Acid Cycle

Back 40

Each turn produces 1 ATP, 3 NADH, 1 FADH2, CO2

Triglycerides- Glycerol gets converted to PGAL, fatty acid gets converted to acyl CoA then 2 C's at a time are used to make acetyl CoA and go through TCA.

Amino Acids are deaminated in liver, then start as pyruvate, acetyl CoA, or in TCA directly depending on AA

Front 41

Electron Transport Chain

Back 41

Contains series of proteins including cytochromes in inner mito membrane.
First protein oxidizes NADH by accepting its high energy electrons. These are passed down the proteins and ultimately accepted by O2, forming H2O. Protons are pumped into inermembrane space as electrons are passed down. This causes a proton motive force, allowing ATP synthase to produce ATP as protons go through it. This is called Oxidative Phosphorylation.
2-3 ATP/NADH, 2 ATP/FADH2, 36 ATP total