Medical Biochemistry Final | Borgon UCF

What are diastereomers?

stereoisomers that are not mirror images

What are enantiomers?

mirror images that have identical physical properties (not polarized light), and react identically with achiral reagents, but may have different biological activity

What is free energy?

energy available to do work

Energy change is expressed as change in what?

ΔG, ΔG=ΔH-TΔS

The system moves towards equilibrium conc. where ΔG equals what?

0

What is activation energy?

the minimum amount of energy needed to start a chemical reaction

What lowers activation energy?

enzymes

ΔG's are additive, what does that mean?

Even if the last reaction is positive, the overall summation of ΔG's can be negative-> favorable

ΔG tells the direction of reactions as they go towards_______, but not how to ______ reactions up.

equilibrium ;speed

What 5 things increase reaction rates?

- Higher temperatures, but molecules may not be stable

- Higher concentration of reactants, but costly as more valuable starting material is needed

- Lower concentration of products by downstream reactions

- Change the reaction by coupling to a fast one

- Lower activation barrier by catalysis

What is a catalyst?

substance that increases the rate of a chemical reaction

What lowers the activation free energy ΔG⁺⁺?

Catalysts

What can catalysts not do?

alter ΔG⁰ and go against equilibrium

What are the six enzymatic catalysis benefits?

- Reaction acceleration under mild conditions

- High specificity

- Regulation

- Coupling reactions to ATP hydrolysis

- Avoiding side reactions

- Substrate channeling

Regulation of enzyme synthesis or degradation will change what?

Its concentration

Regulation of enzyme activity is often via ________

modifications

Covalent modification (phosphorylation) can do what to proteins?

activate or inactivate

Allosteric feedback inhibition regulates enzymes by causing what changes?

conformational

What is the central dogma?

DNA-transcription-RNA-translation-protein

What is the RNA world hypothesis?

States the earliest self-replicating entity used RNA both to store genetic information and to conduct cellular processes.

What is the endosymbiotic theory?

theory that eukaryotic organelles such as mitochondria and chloroplasts from ancient free living prokaryotes invaded primitive eukaryotic cells

Hydrogen bonds are due to what?

dipole moment of NH/OH molecules

What are ionic bonds?

electrostatic interactions between permanently charged species, or between the ion and a permanent dipole

What are Van der Waals forces?

weak interactions between all atoms,

regardless of polarity, attractive (dispersion) and repulsive (steric)

component

What is the hydrophobic effect?

the ordering of water molecules around nonpolar

substances

When are hydrogen bonds the strongest?

when the bonded molecules are oriented to maximize electrostatic interaction (ideally in a line, not bent), >30 degrees and bond weakens

What happens in the hydrophobic effect?

Water forms highly ordered cages around hydrophobic groups, pushing them together (van der waals) to maximize self water interactions

When lipid molecules cluster, what happens to the overall entropy of the system?

It increases due to less ordering of water

How does the hydrophobic effect stabilize macromolecules?

Hydrophobic amino acids are buried within proteins and pack together via van der Waals interactions,

contributing greatly to folding and stability

What do buffers do?

resist changes in pH

What happens if pH changes?

- H-bond donors/acceptors are affected

- solubility of polar molecules are changed

- active site change

- structure destabilizes

What do all amino acids have (not proline)?

an acidic carboxyl group, a basic amino group, and an α-hydrogen connected to the α-carbon

What are peptides?

small condensation products of amino acids

Why does equilibrium favor amino acids?

it consumes a water

What four functions do peptides have?

Hormones and pheromones, Neuropeptides, Antibiotics, and Protection

Why is protein synthesis unfavorable?

requires activation with ATP

What three things are used to purify proteins?

size, ion exchange (charge), and affinity chromatography

What happens in SDS-PAGE?

Proteins separated based on size alone (SDS gives uniform negative charge for consistent charge-to-mass ratio); proteins migrate via electrophoresis through gel)

What can SDS-PAGE be used for?

Estimates molecular weight

What happens in western blotting?

Uses antibody to tag specific protein on a membrane (after it ran on a different gel)

What information does western blotting give?

Molecular weight and an antibodies specificity for identification

What happens in an ELISA test?

Antibodies to identify target proteins in wells or on a membrane are used

What is determined in isoelectric focusing?

the pI of a protein

What is 2D gel electrophoresis?

a combination of isoelectric focusing and SDS PAGE electrophoresis. Separates a sample on size and charge

Protein concentration can be determined in a __________.

spectrophotometer

A peptide bond is a _______ double bond.

partial

What conformation are peptide bonds mostly in? What geometry do they have?

Trans (sterics); rigid and nearly planar

Is rotation around the peptide bond permitted?

no

What is the phi angle?

angle around the alpha carbon-amide nitrogen bond

What is the psi angle?

angle around the alpha carbon-carbonyl carbon bond

What is the alpha helix?

a delicate coil held together by hydrogen bonding between every fourth amino acid

The peptide bonds are aligned roughly _______ with the helical axis.

parallel

Side chains point out and are roughly ______ with the helical axis.

perpendicular

An alpha helix has how many amino acids per turn?

3.6

What is a beta sheet?

A sheet like arrangement of backbone is held together by H bonds between the backbone amines in different strands

In a beta sheet, side chains protrude from the sheet alternating in ______ and ______ direction.

Up; down

In parallel beta-sheets, the H-bonded strands run in what direction? Are the H-bonds bent or linear? How strong are they?

Same direction; bent H-bonds; weaker

In antiparallel beta-sheets, the H-bonded strands run in what direction? Are the H-bonds bent or linear? How strong are they?

opposite direction; linear; stronger

What are motifs?

folds

What are domains?

small stable sections of proteins

What do three things do domains provide?

compartmentalization, folding advantage, and regulation

In aqueous solutions, where do nonpolar amino acids go, and what is the effect?

They get internalized, making a hydrophobic core; makes the protein more stable (delta G is more neg for nonpolar packing)

What are the four advantages of quaternary structures?

Allows for proper folding, transcription/translation, movement/rotation, and enzyme activity and regulation

What is a subunit?

A sub unit refers to one of the functional tertiary peptides comprising the overall quaternary peptide.

What does heme keep and prevent?

Keeps Fe2+, prevents Fe3+ (not O2 binding)

How does heme prevent nonspecific irreversible binding?

It is buried within pockets

Why is heme in myoglobin?

Protein bound hemes capture oxygen, and since myoglobin is the main oxygen storage protein, this is necessary. Heme allows for the reversible binding of O2

What is myoglobin?

a monomer that facilitates O2 diffusion in muscle

What is hemoglobin?

A tetramer that transports O2 in blood

Why can't myoglobin transport O2?

It would not release it in the tissues since its pO2 affinity does not vary as much as hemoglobin

What do hemoglobin's binding sites do?

interact with each other (cooperativity)

What is positive cooperativity?

first binding event increases affinity at remaining sites

What is negative cooperativity?

first binding event reduces affinity at remaining sites

What is the Bohr effect?

Tissues generate H+ (lowers pH near tissues relative to lungs), H+ binds to Hb (stabilizes T state), releases O2 in tissues

AKA: pH difference between tissues and lungs increase the efficiency of O2 transport

What is 2,3 bisphosphoglycerate (BPG)?

A negative heterotropic regulator of Hb function that helps prevent hypoxia

How does 2,3-BPG regulate hemoglobin?

It binds to the positively charged central cavity of beta subunits of Hb in T state, and stabilizes the T state causing O2 release

What is allosteric regulation?

Protein's function at one site is affected by binding of a regulatory molecule on a different site.

When are amino acids directly modified?

Post-transcriptionally

How can amino acid modifications impact proteins?

it can activate/inhibit the protein by changing its shape, changing its surface to allow/prevent interactions with binder partners, or tag it for destruction.

How does the hydrolysis of ATP into ADP create movement?

It causes a conformational change that generates a mechanical force

What does phosphorylation do?

Changes the charge of a protein, decreases hydrophobicity, allows for large structural movements, and can change the proteins surface/interface, which can affect interactions

What do kinases do?

add phosphates

What do phosphatases do?

remove phosphates

What does acetylation do?

Activates or inhibits protein function, and N-terminal acetylation serves as protection or targeting to the Golgi

The acetylation of lysine does what?

Lysine's positive charge is neutralized, changing interactions, and allows DNA to separate from proteins and be more accessible

What does glycosylation do?

Adds sugars; helps with folding in ER, secretion, membrane, formation, and cellular adhesion

What does ubiquitination do?

adds ubiquitin to a protein, marks it for degradation after threshold is reached, alters its activity, or prevents interactions

What are conformational changes?

when proteins change shape upon substrate or binding partner interactions

What is phototransduction?

Conversion of light stimuli into an electrical signal, causes conformational changes in the retina

What does mechanotransduction do?

It involves converting a mechanical force into a biochemical signal

Where do enzyme catalyzed reactions take place?

active site

What is a substrate?

the substance on which an enzyme acts; the molecule bound in the active site

What are cofactors?

Inorganic ions that bind to enzymes temporarily and can transfer electrons for oxidation/reduction reactions

What are coenzymes?

complex organic molecules or metalloorganic molecules that help enzymes

What are prosthetic groups?

Coenzyme or metal ion that has tightly or even covalently bound to the enzyme protein

What are holoenzymes?

complete catalytically active enzymes

What are apoenzymes?

protein portion of enzyme

How do enzymes lower activation energy by stabilizing the transition state?

Weak interactions are optimized in a reaction's transition state. (weak bonds release small free energy -> -delta G)

Enzyme must be complementary to the transition state

What is the lock and key model?

Enzymes are specific to the substrate they bind to. (complementary shapes)

What is the induced fit model?

the active site molds around the substrate to form the enzyme-substrate complex. (change in conformation)

Induced by multiple weak interactions (lock and key in transition state)