ACS Biochemistry Exam

Cyanogen Bromide, Trypsin, and Chymotripsin

All are enzymes used to delineate primary structure of proteins using expected cleavage sites. Cyanogen Bromide: cleaves methionine residues on the carboxyl side. Trypsin: Cleaves after Arginine or Lysine, on the carboxyl side. Chymotripsin: Cleaves after aromatics (F/Y/W) on the carboxyl side.

Elastin Structure

Alternating hydrophilic and hydrophobic domains give elastin its key ability to stretch and compress like a rubber band: the hydrophobic domains are like a plate of spaghetti in the related state- they are gathered away from water. Upon being stretched, the molecules uncoil into an extended conformation, but immediately coil back to a hydrophobic clump once the force is removed! This combination gives elastin its rubber band-like ability.

Favorable measures of phi and psi in peptide bonds

Angle about the C-N bond, Phi, is favorable at 180, and most unfavorable at 0. Angle about the C-C=O bond, Psi, is also favorable at 180 and most unfavorable at 0.

Peptide backbone: two polypeptide angles having free rotation

Angle about the C-N bond: PHI Angle about the C-C=O bond is PSI Some measures of phi and psi are more common than others. **Rotation around the peptide bond is NOT permitted, but rotation around these bonds is**

Keq for water at 25 degrees C and in pure water

At 25 degrees C: Keq= Kw= [OH-][H3O+]= 1*10^-14 In pure water: [OH-]=[H3O+]= 1*10^-7

How to calculate PI, or isoelectric pint

Average pKa values involving the neutral species For glycine, that only has COOH and NH3 pKa's, the PI is the average between 2.34 and 9.60, so 5.97!

What do bulky side chains prefer in terms of secondary protein structure?

Beta sheets, because they can stick out the side rather than be incorporated into the helix.

Peptide bonds

Between the C and N of C=O and N-H of two adjacent amino acids.

Irreversible inhibitors: Mechanism of Action

Bind covalently to enzymes (or in some cases non-covalently, just extremely strong, making them functionally covalent).

Allosteric Effectors and Hemoglobin

Bind to different site than the liana and alter ligand binding. Several effectors alter O2 binding to maintain adequate oxygen delivery, causing the O2 binding curve for hemoglobin to shift higher or lower than p50 values. Oxygen stabilizes oxyhemoglobin, promoting oxygen binding to other subunits (curve shift LEFT, making it easier to bind O2 than release it). Other allosteric effectors stabilize deoxy-hemoglobin, promoting O2 release, including CO2, H+, and heat (curve shift RIGHT, making it easier to release O2 than bind it).

How are protein native structures stabilized?

By weak non-covalent bonding and di-sulfide bonds

The Bohr Effect: CO2

CO2 impacts oxygen binding to Hb by binding to the amino terminus of deoxy Hb to stabilize it, forming a carbamate. Thus, it shifts the curve to the right, and hemoglobin releases oxygen.

Co-enzymes vs. co-factors

Co-enyzmes are organics, and quite often loosely bind to the active site of their enzyme to aid in substrate recruitment. Examples are Vitamin B1 (Thiamine) and Vitamin B2 (riboflavin) Co-factors are metal ions, and typically do not bind to the enzyme in question. Examples are Fe2+ and Mg2+.

Four major examples of fibrous proteins

Collagen, Elastin, Keratin, and Fibroin

Blood Buffering

Components: 1) carbonic acid (H2CO3) (weak acid). pKa= 6.1. 2) Bicarbonate Ion (HCO3-), conjugate base of carbonic acid 3) H+ (hydrogen ion) If OH- (base) is added, Carbonic acid buffers it into bicarbonate ion and water. If H+ (acid) is added, bicarbonate ions and H+ buffer it to carbonic acid.

Buffers

Composed of a weak acid (HA) and its conjugate base (A-). Added acid reacts with A-, and added base reacts with HA, giving a limited overall pH change. Two main reactions: 1) When excess base is added: OH-+HA-->H2O+A- 2) When excess acid is added: H+ + A- -->HA **So, the net result is more of the weak acid and its conjugate base**

Alpha Keratin (what composes, and its fundamental structure)

Composes skin, hair, wool, feathers, nails, claws, quills, horns, hooves, etc. Fundamental structure is an alpha helix. Two alpha helixes coil together to give a two-chain coil, which then bovines with another two-chain coil to give a protofilament, which then further combine to give a protofibril.

Collagen Cross-links (what they do, steps and residues involved).

Cross-links between fibrils stabilize collagen's structure. Steps: 1) Collagen assembles into fibrils 2) Lysyl oxidase catalyzes formation of covalent links between collagen. **They involve Lys and His!**

Examples of Irreversible inhibitors: DIPF, Organophosphates, and penicillins

DIPF: an organophosphate compound that binds covalently to active site serine residues, giving a less functional enzyme. It is a "group-specific reagent". Organophosphates: Act by irreversibly inhibiting acetylchoinesterase, a cholinergic enzyme primarily found at postsynaptic neuromuscular junctions, especially in muscles and nerves, that breaks down Ach in the synapse. Thus, it acts as a "nerve agent", that blocks Ach re-uptake and induces muscular dysfunction: agitation, muscle weakness, muscle fasciculations, miosis, hypersalivation, and sweating are just some of the symptoms that result. Penicillins: react with the essential serine residue to transpeptidase, an enzyme that cross-links the peptidoglycan chains of bacterial cell walls.

How can one determine the number of chains are present in a protein?

Determine the number of N or C termini. Ex: Sanger's Reagent interacts with the amino terminal (binds to it via a C-NH bond) to show how many are present in the protein.

Sequential reactions: multi-substrate reaction mechanisms

E+ S1--> ES1--> ES1S2--> E+ P1+ P2 (ternary complex is formed)

Double displacement reactions: multi-substrate reaction mechanisms

E+S1--> ES1--> E'P1--> E'--> E'S2--> E+ P2 (No ternary complex is formed)

Acid-Base properties of amino acids

Each has at least two ionizable protons (from the COOH and NH3 groups), but most have others. COOH pKa: 2.34 NH3 pKa: 29.60

A key method in characterizing polypeptide fragments

Edman degradation: the polypeptide is treated with phenylisothiocyanate, which reacts with the N-terminal amino acid to give an N-terminal PTC derivative of the protein. This derivative forms by addition of the terminal N—H bond across the C = N of the phenylisothiocyanate. The N terminal is then cleaved under acidic conditions, resulting in the removal of exactly one amino acid monomer for identification.

Fibrous proteins (what they are, their role, and their solubility)

Elongated molecules with a single major type of secondary structure. Many have structural roles (like skin, bones, and connective tissue). They are rich in hydrophobic residues, so they are generally water insoluble.

Lineweaver-Burk double reciprocal plot

Equation: 1/V= Km+[S]/Vmax*[S]= Km/Vmax[S]+ 1/Vmax 1/[S] is plotted against 1/V0(1/uM/min), where: Vmax= y-intercept -1/Km= x-intercept Km/vmax= slope

Stereochemistry of amino acids

Every carbon except for glycine is a chiral center, giving two possible structures for each: L and D (except for glycine). L is the only one found in nature.

Fibrous vs. globular proteins

Fibrous proteins have a single major type of secondary structure, while most other proteins are folded compactly and have a mix of secondary structures.

Peptide directionality

From N to C

Ramachandran Diagrams

G. N. Ramachandran, in his 1950s experiments, used peptide models to systematically vary phi and psi. Phi and psi angles that cause atoms to collide correspond to sterically impractical conformations of the polypeptide backbone. The plots resulting from these systematic angle variations and subsequent conformations is called Ramachandran Diagram, with green regions showing favorable angle conformations (THAT INDICATE SECONDARY STRUCTURES). The two most commonly preferred secondary structures (minimize steric hindrance): alpha helixes and beta sheets.

Amino acids that are "Structure breakers"

Glycine and Proline

Alpha Keratin Cross links

Helicies and fibers are cross-linked by disulfide linkages. When getting a perm, straight hair is given a chemical treatment that reduces the disulfide bonds to S-H groups, then the desired style is given, then the S-H bonds are oxidized back to disulfide bonds, in the desired style, holding it in place.

How does hemoglobin bind oxygen, and what are some competitive inhibitors?

Hemoglobin binds O2 reversibly using its heme prosthetic group, attached to Fe2+. Other ligand compete favorably with O2, like CO, NO, and H2S.

Hemoglobin vs. Myoglobin: cooperativity

Hemoglobin has n=2.8, making it extremely cooperative. This gives it a sinusoidal curve for % saturation vs. PO2. Binding the first O2 is difficult: requires 18 mmHg. However, the second is easier, it requires 26 mmHg. From there, the last two are much easier. Myoglobin, on the other hand, is not cooperative. This gives it a hyperbolic curve for % saturation vs. PO2.

Allosterism of Hemoglobin

Hemoglobin with one Oxygen bound is almost always in the T state but has 3x the affinity of deoxy-hemoglobin, because the binding of one oxygen makes it a bit easier for a second to bind. Hemoglobin with three oxygen bound is almost always in the R state with the last site having 20x the affinity of deoxy-hemoglobin, because the binding of three hemoglobins gives the maximum chance for a fourth to bind.

Hemoglobin mutants and cooperativity

Hemoglobin's cooperativity is reduced in mutants that lack key resides involved with T-state (de-oxy hemoglobin) stabilization. Mutant without the alpha chain's C terminus reduces the hill coefficient from 2.8 to 1.7 (still cooperative, but markedly less). Mutant without the beta chain's C terminus reduces the hill coefficient from 2.8 to 1.0 (still cooperative, but much less). These mutations, therefore, make the protein more "R-like".

Two types of Allosteric Effectors

Heterotropic: distinct from the ligand itself. Homotropic: identical to the normal ligand.

What accounts for water's unique properties?

Hydrogen bonding

How can the catalytic activity of enzymes be controlled?

Inhibitors, with two general classes: Irreversible and Reversible.

Silk Fibroin structure

It has the repeating structure GLY-ALA-GLY-ALA. It is an anti-parallel (strong) beta sheet, with amorphous regions surrounding bulky residues.

Collagen structure: its components, and its basic structural unit.

Its compontents: Quaternary structure stabilized by hydrogen bonds. Its basic unit is a left-handed helix polypeptide chain, which is combined with two others into a triple-stranded collagen molecule (all right handed helixes, with glycine side chains lining the interior), which is further combined to give a collagen fibril quaternary structure. These hydrogen bonds arise from -OH groups added on to Pro and Lys, with Vitamin C required for their hydroxylation! So that's why scurvy is induced via lack of Vitamin C- collagen cannot fully form and teeth fall out, muscles and tendons loosen, etc. Its basic structural unit: a left-handed helix. There are no stabilizing hydrogen bonds within the helix, instead Proline leads to extended chains due to steric repulsion.

Kcat

Kcat, a constant related to Vmax, is the rate constant of the RDS. Kcat= Vmax/[Et] Kcat is the turnover number that reflects relative catalytic effectiveness.

Competitive inhibition: Lineweaver Burk

L-B analysis in the presence of an inhibitor suggests that Km (x-intercept) changes (by a factor of alpha) and Vmax does not. **Km doesn't actually change, just apparent Km!**

Elastin Cross-links

Lysine cross-links ensure the molecule returns to its original state after stretching.

How to determine Km and Vmax

Measure Vo for variable [S] and constant [E], preferably using spectrophotometric measurements. The rate can be expressed as disappearance of substrate or appearance of product. The Michaelis Mensen equation can be solved either directly or by linear transformation (i.e. Lineweaver-Burk double reciprocal plot)

Kcat/Km

Measure of the overall effectiveness of a given catalytic enzyme: it accounts for both binding (Km) and catalysis (Kcat). The bigger the better: we want high Kcat (more catalytic turnover) and less Km (less substrate needed to reach maximum reaction levels).

Metabolism (catabolism and anabolism)

Metabolism: sum of total chemical reactions in an organism, also the method by which cells extract and use energy from their environment. Catabolism: The process by which stored nutrients and ingested foods are converted to a usable form of energy. It produces simple products CO2, H2O, NH3, and building blocks such as sugars and fats that are used in anabolism. Anabolism: the process by which simple products and building blocks of catabolism are used to create complex biological products that contribute to organismal growth and development. It also uses the energy produced in catabolism to do biological work.

Properties of cells

Metabolism: undergoing catabolic and anabolic processes. Reproduction: cell populations grow via asexual reproduction. Mutation: during growth and reproduction, cells sometimes make mistakes, leading to mutations and evolution. Respond to environment: metabolic pathways respond to signals, including light, touch, hormones, and nutrients, that can turn the pathways on or off. Speed and efficiency: cell operations are highly specific to maximize targeting and efficiency. Similar building blocks: most species are very similar at the cellular level.

Hemoglobinopathies

Mutations in one of the polypeptide chains of hemoglobin. They are not uncommon, and range from harmless to severe.

Myoglobin vs. hemoglobin: structures

Myoglobin (Mb) and the two chains of hemoglobin (Hb) are homologous proteins, meaning they had a common ancestor, with random mutations over evolutionary time resulting in key changes. Homologous proteins often have similar sequences, and similar 3-D structures, as is the case here. They have similar secondary and tertiary structures, both having about 78% alpha helix makeup (8 alpha helixes). They both have one heme group, with a non-polar interior. However, they differ in their quaternary structure: Myoglobin has none, while hemoglobin has 2 alpha chains and 2 beta chains combined into one structure with heme at the center of each, attached to iron.

Protein makeup

One or more polypeptide chains, and optional prosthetic groups that make a conjugated protein. The folding of the chains is what delineates function of the protein itself.

What type of bond characterizes the secondary structure of proteins?

Peptide Bonds. They are planar, and exist between the C=O of one amino acid and the N-H of the other (the C binds to the N). The trans structure is preferred by nature due to the steric hinderance of the cis form.

4 protein structure levels, and their components

Primary structure: amino acid reside sequences Secondary structure: alpha helix and beta sheet folded segments Tertiary structure: polypeptide chains in 3-D shapes Quaternary structure: Assembled subunits comprised of multiple chains

The Bohr Effect: H+

Production of CO2 during metabolism leads to increased H+ in the bloodstream, shifting the curve to the right and enhancing oxygen delivery. Increased H+ results in protonation of His 146 B, which helps stabilize the deoxy form of hemoglobin (pKa of His is about 8), creating a stabilizing salt bridge. In oxygenated Hb, pKa of His 146 B is about 6, this salt bridge does not exist!

Determining primary structure of proteins (steps)

1) Determine how many chains are present 2) Cleave one chain into small pieces using an enzyme with a known preferred cleavage site 3) Characterize each piece 4) Perform a second round of cleavage and characterization 5) Determine how the pieces fit together

Enzyme classes

1) Oxidoreductases: catalyze the transfer of electrons in reactions (redox reactions). 2) transferases: catalyze group transfer reactions 3) hydrolyses: catalyze hydrolysis reactions (transfer of functional groups to water) 4) Lyases: catalyze addition of groups to double bonds, or formation of double bonds by removal of groups. 5) Isomerases: catalyze transfer of groups within molecules to give isomeric forms. 6) Ligases (aka synthase): catalyze formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to ATP cleavage.

The unique properties of water (specific heat, heat of vaporization, solubility)

1) high specific heat, or heat required to raise the temperature of the unit mass of a given substance by one degree. For water to increase in temperature, water molecules must be made to move faster, or get higher KE, and doing this requires breaking hydrogen bonds, which absorbs heat. So, as heat is applied, most of it goes to breaking the bonds not upregulating KE, thus making water harder to heat than substances where no bonds need to be broken. 2) High heat of vaporization, or the amount of heat needed to turn one g of a liquid into vapor, without a temperature rise in the liquid. Important for sweat because it ensures that when the liquid evaporates from our skin, the heat required for the transition is kept in the gas, causing a net cooling effect on the skin. 3) Unique solubility properties: "like dissolves like". Water dissolves polar molecules and ions, and can act as an H-bond donor or receptor 4) Amphoteric, it can act as an acid (donating electrons) or a base (accepting electrons). The conjugate acid of water is the hydronium ion, H3O+, and the conjugate base of water is the hydroxide ion, OH-.

Two sources of enzyme-substrate specificity

1) shape complementarity 2) chemical complementarity

BPG

2,3 bisphosphoglycerate, produced by RBC, decrease O2 binding affinity of Hb by binding to deoxy Hb and stabilizing it. It again shifts the curve to the right, making it harder to bind O2.

What wavelength is indicative of aromatic amino acids?

280 nm, with tryptophan absorbing more, tyrosine absorbing a bit less, and phenylalanine absorbing a lot less.

Rules for secondary protein structure (proposed by Linus Pauling, Robert Corey, and Herman Branson)

3 principles: 1) planar peptide bonds gave allowed torsion angles 2) Hydrogen bonds are maximized in favorable structures 3) Linear hydrogen bonds are most effective

Enzyme commission number

4 numbers, separated by periods. 1: class 2: subclass 3: sub-subclass 4: specific enzyme

Normal blood pH range

7.35-7.45

Thalassemia

A hemoglobinopathy in which a mutation leads to reduced production of one hemoglobin chain, giving unusual quaternary structure. Alpha thalassemia gives no alpha chain, just beta chain, and Beta thalassemia gives no beta chain, just alpha and gamma (fetal) chains.

Sickle-cell anemia

A hemoglobinopathy that results from a surface mutation promoting an aggregation of hemoglobin molecules. This gives the RBC a sickled shape that lends itself to clotting and other blood flow complications.

Collagen (what it is, where it is found)

A key type of fibrous protein found in the body. The most abundant protein in mammals, found in ligaments, cartilage, tendons, bones, skin, and teeth. It is a family of 26 genetically distinct proteins.

Competitive Inhibition, and methanol/ethanol example

A type of reversible enzyme inhibition in which the substrate and inhibitor compete head to head for binding to the active site. Methanol and ethanol compete for alcohol dehydrogenase enzyme, that converts methanol to formaldehyde, which is toxic, and ethanol to acetaldehyde, which is not. Treatment for methanol poisoning is administration of large quantities of ethanol to act as a competitive inhibitor.

Connecting Elements for both alpha helixes and beta sheets

Random coils: polymer conformation where the monomer subunits are oriented randomly while still being bonded to adjacent units. Turns, bends, and loops: connect α helices and β strands. The most common types cause a change in direction of the polypeptide chain allowing it to fold back on itself to create a more compact structure. (Ex: type-1 beta bends typically include cis-Pro) Flexible, disordered segments: no one defined structure, it can change circumstantially

What fibrous protein makes up skin, and why?

Skin requires elasticity, resilience, strength, and protection- so keratin is key, along with elastin and collagen.

Allosteric Enzymatic Regulation and Michaelis-Menten kinetics

Some enzymes do not display Michaelis-Menten kinetics, an example being allosteric effectors. When they are plotted as [Substrate] vs. Reaction velocity they show a sinusoidal curve rather than a linear or hyperbolic one. When an allosteric effector binds, the binding of one ligand (non-covalently) influences the binding of another ligand (substrate) to a different protein site. This helps the enzyme prepare a better active site and thus react with more substrate more efficiently. Hemoglobin is an allosteric effector: the binding of oxygen to one of the subunits is affected by its interactions with the other subunits.

What fibrous protein makes up spider webs, and why?

Spider webs require high tensile strength and low-density (rates of strength to density exceed that of steel). As a result, the protein fibroin makes up the majority of spider webs: it is flexible, light, and high-strength. In spider webs, it combines with the gummy protein sericin to cement it together.

Origin of Hemoglobin's Cooperativity

Structures of oxygenated (R state) and de-oxygenated (T state) hemoglobin differ. The T state, or the de-oxygenated form of hemoglobin, is more stable in the absence of O2 because of several key interactions (including ion pairs) that do not exist in the R state. However, when deoxy-hemoglobin binds O2, it undergoes a conformational change that breaks many of these interactions. O2 pulls iron into the heme plane, which drags His-F8, and the rest of the molecule, with it, giving the R state, or the oxygenated form of hemoglobin that has a higher affinity for other O2 molecules. After the initial bind, the second, third, and fourth O2 molecules bind at lower partial pressure increments! **The fact that the two alpha and two beta chains only have two stable positions makes the T to R transition binary**

Koshland (Sequential) Model

Subunits can either be T or R. The binding of a substrate induces T--> R transition in that subunit, which induces neighboring subunits to convert.

What fibrous protein are tendons made up of, and why?

Tendons require strength, resilience, and elasticity. They serve as biological springs, until they are stretched past their breaking point. They are primarily made up of collagen, as a result (80% collagen when dried). Collagen is a tough yet flexible fiber that is able to recover quickly after stretching (unless the stretch passes its breaking point). It is simultaneously long-lasting and incredibly flexible, making it the perfect material for connective tissue.

Amino Acids with ionizable side chains

Terminal carboxyl group: pKa of 3.1 Aspartic Acid/Glutamic Acid: pKa of 4.1 Histidine: pKa of 6.0 Terminal amino group: pKa of 8.0 Cysteine: pKa of 8.3 Tyrosine: pKa of 10.9 Lysine: pKa of 10.8 Arginine: pKa of 12.5

How to measure cooperativity

The degree of cooperativity is measured by the Hill coefficient, or n. When n>1, positive cooperativity (each successive loss or reaction makes following ones easier to conduct). When n<1, negative cooperativity (each successive loss or reaction makes following ones harder to conduct). When n=1, there is no cooperativity (each successive loss or reaction has no impact on further conduction).

Tropocollagen, and its key amino acids

The fundamental unit of collagen (Mr=300,000). Its sequence is GLY-X-Y, where X and Y are often OH-Pro or Pro, or sometimes OH-Lys and His.

Protein Denaturation

The loss of protein structure due to unfolding. It can happen as a result of heat or chemicals breaking hydrogen bonds and other weak non-covalent bonds that hold the proteins together.

Protein Native conformation

The low-energy structure a given protein will fold into.

Myoglobin

The oxygen carrying protein of red muscle.

Hemoglobin

The oxygen carrying protein of the blood. An average human has 2L hemoglobin, has 5-6L of blood, and uses 600L O2 per day.

What determines the amount of oxygen bound to hemoglobin (saturation)?

The partial pressure of oxygen, or PO2. Normal arterial O2 pressures, typically around 100 mmHg, give 97% hemoglobin saturation. However, when blood travels to tissues, PO2 is much lower than in the lungs, typically around 20-40mmHg. This cues hemoglobin to release oxygen to the tissues, leaving it about 50% saturated (2 oxygen molecules have been released).

What fibrous protein are blood vessels made out of, and why?

They are mostly elastin. They require the ability to expand and contract with each heart beat- they must be extensible but also resilient. So, elastin is the perfect material. It is common for tissues requiring flexibility to have a network of elastic fibers interwoven with collagen (the elastic fibers being 50% elastin by mass).

Reversible inhibitor mechanism of action, and three kinds

They bind non-covalently to target enzymes. There are three major types: competitive, uncompetitive, and non-competitive.

Trojan horse irreversible inhibitor: Penicillin

They react with the essential serine residue to transpeptidase, an enzyme that cross-links the peptidoglycan chains of bacterial cell walls. Like other Trojan horse inhibitors, they do this by resembling the substrate of transpeptidase, only to bind irreversibly to it and compromise its function.

Essential Amino Acids

Those that cannot be made in the body and thus must be obtained via the diet. Some can be made from others, so it isn't a hard line, but: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, and Valine are all essential. **Cysteine can be made from methionine, tyrosine can be made from phenylalanine, etc.**

MWC (symmetry) model

Two forms of the enzyme: T and R. All subunits are either T or R (binary). The R form binds the substrate better, and the T form is more stable in the absence of substrate. The substrate binds the R form, trapping the enzyme in that form. Any molecules with substrate bound are more likely to bind additional substrate molecules. Larger amounts of substrate trap more enzyme molecules in the R form, making more substrate molecules even more likely to bind. Any Allosteric effectors added stabilize either the T or R state: positive effectors (activators) stabilize the R state, shift the curve left, and induce binding, while negative effectors (inhibitors) stabilize the T state, shift the curve right, and block binding. **HOW HEMOGLOBIN WORKS**

Alpha Helix (what they are, and how they are de-stabilized)

Type of secondary protein structure. They are typically right-handed, with stabilizing hydrogen bonds between each -NH and -CO of peptide bonds four residues apart. They are de-stabilized by runs of similarly charged amino acids and too many bulky amino acids, such as proline and glycine.

Beta Sheets

Type of secondary protein structure. They have multiple strands (typically 2-15) that interact via inter-chain hydrogen bonds between -NH and -CO of peptide bonds. Successive R groups on opposite sites of the sheets project into the surrounding space. There are two sub-types: 1) Anti-parallel: characterized by two peptide strands running in opposite directions held together by hydrogen bonding between the strands 2) Parallel: characterized by two peptide strands running in the same direction held together by hydrogen bonding between the strands **Anti-parallel sheets are stronger because the hydrogen bonds are linear, which means better orbital overlap**

Competitive inhibitor: Vmax (app), Km (app), Ebind, ESbind, and equation

Vmax= vmax Km= Km*alpha (Where alpha is 1+[I]/Ki, and Ki is the binding constant for the EI complex over the ES complex). Binds to E and ES. Equation: v0= vmax[S]/Km(1+[I]/Ki) +[S]

When are buffers optimal? What equation can we use for this?

When [HA]= [A-], occurring when pH=pKa Henderson- Hasselbalch allows use to calculate pH at given pKa, and vice versa:

The Hydrophobic Effect

When non-polar molecules aggregate in the presence of water, minimizing the entropy decrease water must go through to order themselves around the border of the non-polar molecule. Reducing the surface area water must organize around increases entropy, which is favorable. The aggregation is responsible for the formation of a variety of lipid structures in the body, including cell membranes.

Oligomers

a polymer whose molecules consist of relatively few repeating units. Allosteric enzymes are always Oligomers.

Enzyme Kinetics Equation

k= A*e^(-Ea/R*T) Where k= rate constant, A= pre-exponential factor, e= base of natural logarithms, R= gas constant, T= temperature in K, and Ea is the activation energy.

Calculation for pH and pKa

pH= -log[H3O+] pKa= -log(Ka)

Amino acid name post-peptide bond

residues

Amino Acids, peptides, and polypeptides

the building blocks of proteins, a chain of which is called a peptide. There are 20 standard amino acids that act as the monomers to make protein polymers! A long peptide is called a polypeptide! Proteins are composed of one or more polypeptide chain.

PI

the isoelectric point, or the pH at which an amino acid or peptide has no net charge. - At pH= PI, the predominant species is the zwitterion - At pH<PI, the predominant species is net positive - At pH>PI, the predominant species is net negative **At PI, amino acid or peptide cannot migrate through an electric field, so this is a way we can separate amino acids (by PI via electric field!)**

Michaelis- Menten Equation

v0 = (vmax [S])/(Km + [S]) Where: -vmax is the reaction rate when the enzyme is fully saturated by substrate, indicating that all the binding sites are being constantly reoccupied. The maximum saturation reachable by the enzyme. - [S] is substrate concentration - Km is The Michaelis constant, and is defined as the substrate concentration at which the reaction rate is half of its maximal value (or in other words it defines the substrate concentration at which half of the active sites are occupied). **In general, a smaller Km suggests better enzyme-substrate binding, since it takes less substrate to get 1/2 of the maximal reaction rate!**