UWorld Amino Acids and Proteins

Carboxyl and Amino groups of Amino Acids

All amino acids contain carboxyl and amino groups. The carboxyl groups have a pKa of approximately 2 and acts a proton donor, the amino group has a pKa of 9 and acts as the proton acceptor

Zwitterions

At 7.4 physiological pH this is how amino acids exists as and is both positive and negative. The carboxyl group is deporotonated (COO-) and carries a negative charge, and the amino group is fully protonated (NH3+) and has a positive charge.

Nucleophilic Amino Acids

KYTCS (Kites) Lysine, Tyrosine, Threonine, Cysteine, and Serine. R groups contain atoms that donate electrons when deprotonated

Stereocenter

Molecules with one atom bonded to four different chemical groups are chiral. Chiral molecules can be L or D but most are L.

Rotation of plane polarized light

Only solutions of chiral molecules rotate plane polarized light, and chiral molecules with opposite arrangements ate every stereocenter (enantiomers) rotate light by the same amount but in opposite directions.

Alpha Carbon

The alkyl carbon that links an amino and carboxylate group. The alpha carbon is also bonded to a hydrogen atom and to one other chemical group, called the R group or the side chain.

Glycine (Chirality)

It is achiral and will not rotate plane polarized light

Peptide Hormones

Hydrophilic signal molecules interact poorly with the hydrophobic tails of phospholipid bilayers, so they cannot easily cross across the cell membrane.

G Protein — Coupled Receptors (GPCRs)

Cells surface receptors that peptide hormones bind to. Relay the signal from extracellular ligands by causing the production of the new molecules called second messengers. Second messengers interact with proteins in the cytosol and nucleus which lead to a response.

Steroid Hormones

Hydrophobic molecules can cross the cell membrane and interact directly with effector proteins. Derived from cholesterol and are three five membered rings and one six membered ring fused together.

Protein Folding

Proteins naturally fold into their lowest energy conformations as amino acid side chains to optimize their interactions with each other.

Hydrophilic Side Chains

For portions of proteins exposed to aqueous environments, hydrophilic side chains interact with polar molecules through hydrogen bonding and electrostatic interactions.

Hydrophobic Residues

Interact poorly with water. Because they cannot form hydrogen bonds, they force nearby water molecules to interact to interact with each other to form a solvation layer which are thermodynamically unfavorable.

Nonpolar Residues

Found buried within the protein or in the hydrophobic environment of the molecules where they can avoid water

Positively Charged Residues

Can interact with the partial negative charge of the oxygen in water molecules. These residues are found on the surface of globular proteins.

Polar Uncharged Residues

Can hydrogen bond with water and are often found at the surface of proteins.

Negatively Charged Residues

Can interact with the partial positive charge of the oxygen in water molecules. These residues are found on the surface of globular proteins.

Tertiary Structure

Stabilized by noncovalent side chain interactions by amino acids including hydrogen bonding and electrostatic interactions.

Disulfide Bonds

Covalent bonds between two sulfur atoms that may form between cysteine residues in oxidizing environments such as the lumen of a vesicle or the extracellular space.

Peptide Bonds

Covalent bonds that form between amino acids to make proteins and peptides. They contribute only to a protein’s primary structure.

Electrostatic Interactions

Frequently involved in tertiary protein structure but do not involve shared electrons and therefore are not covalent bonds

Thioester Bonds

Form between a sulfur atom and a carbonyl carbon. Important for coenzymes and metabolites like acetyl CoA and Succinyl CoA

A protein’s secondary and tertiary structure are determined by its:

Amino acid sequence. Proteins with similar amino acid sequences fold similarly and those with distinct sequences fold differently.

Post Translational Modifications

Non amino acid additions to proteins, such as phosphorylation and glycosylation.

Kd (Ligand Affinity Dissociation Constant)

The affinity of a protein for its ligand is described by the dissociation constant Kd.

Low Kd (Ligand Affinity Dissociation Constant)

Few ligands required for binding and high affinity for its ligand

High Kd (Ligand Affinity Dissociation Constant)

Many ligands required for binding and low affinity for its ligand

Amino Acids that are similar in some ways and different for others can:

Be substituted for each other to preserves some protein properties and change other

Stationary Phase

Separation techniques that take advantage of molecular properties to cause some molecules to move faster than others through a separation phase.

Column Chromatography

A set of techniques to separate a protein by charge, molecular weight/size, or binding partner/affinity

Isoelectric Point

The pH at which the protein has a net charge of zero

When pH is lower than the pl:

The protein gains a proton and becomes positively charged.

When pH is greater than the pl:

The proton loses a proton and becomes negatively charged

All amino acid titration curves have:

Two buffering regions/pKas

Amino acids with three buffering regions/pKas in titration curves:

R, K, Y, C, , H, E, and D

Holoprotein

A correctly folded protein that contains all cofactors

Apoproteins

Proteins that lack cofactors

Heme

A common cofactor found in many proteins and is required for oxygen binding in hemoglobin and myoglobin. The characteristic structure of _____ is a porphyrin ring with a central iron atom.

Tertiary Structure of a protein is stabilized by:

Ionic bonds, hydrogen bonds between hydrophilic side chains, and hydrophobic interactions between side chains in the proteins core.

Protein Denaturation (Unfolding)

Driven by amphipathic molecules (hydrophilic and hydrophobic) that disrupt the energetically favorable hydrophobic interactions between the amino acids in the interior of the protein.

Hydrophobic Effect

In the absence of denaturant molecules, the hiding of hydrophobic residues in the interior of the protein allows water molecules surrounding the protein to adopt a much higher entropy state, resulting in a large, negative gibbs free energy of folding.

Standard Gibbs Free Energy Equation

Delta G = -RT ln(K)

A negative DG in the Delta G = -RT ln(K) equation means:

Indicates an equilibrium constant greater than 1

A positive DG in the Delta G = -RT ln(K) equation means:

Indicates an equilibrium constant between 0 and 1

The only amino acid without an identical backbone to the others is:

Proline

The Branched Chain Amino Acids

(Valine, Alanine, Isoleucine, and Leucine) VAIL share the structural feature of having branched alkyl side groups.

Zwitterions contain the compounds:

COO- and NH3+

Stereoisomers

Molecules that have the same composition and connectedness of atoms but with different spatial orientations of atoms around at least one stereocenter

Chiral Center

A stereocenter that has a nonsuperimposable mirror image and is commonly formed when an sp3 hybridized carbon attached to four different substituents

Enantiomers

Molecules that differ from each other at all chiral centers and share the same chemical and physical properties

L and D Enantiomers

All amino acids except (glycine) are chiral and exist as L enantiomers. Peptides composed of the D enantiomer are less common in nature and less likely to be recognized by enzymes.

Hydrophilic Amino Acids (Polar/Charged)

Found on the outside of proteins. When these molecules are exposed to water they form hydrogen bonds with water molecules.

Hydrophobic (Nonpolar/Uncharged)

Found in the protein interior

R56K

How substitutions for amino acids are made, in this substitution R is substituted with K at position 56

Amino Acid substitutions that alter charge:

are likely to destabalize protein interactions, particularly if they result in repulsive forces between similarly charged amino acids

B-Sheets and a-Helices

Common secondary structures found in proteins. Alphas helices contain 3.6 amino acids per turn and are stabilized by hydrogen bonds between carbonyl (C=O) and amide (N-H)

Linker Regions

Regions between beta sheets and alpha helices particularly at sharp turns/beta turns where proline and glycine are found. Proline is not in alpha helix because it is rigid and introduces a king that disrupts a-helices. Glycine disrupts a helices structure because it is small and flexible.

Structure and sequence of a peptide (Ala-Ser_

N terminal residue on the left (Connected to N terminus NH3+ and C terminal residue on the right (Connected to C terminus C=O)

Hydrophilic Amino Acids

Acidic, basic, and polar

Hydrophobic Amino Acids

Aliphatic, nonpolar, and aromatic

Condensation Reactions

How peptide bonds form are by condensation in which water is released

Hydrolysis Reactions

How peptide bonds are broken in which water is consumed

Side chains of the amino acids in a peptide interact with each other:

Through electrostatic interactions including: ionic attractions and repulsions, hydrogen bonding, london dispersion forces, and steric interference. Amino acids with similar charges repel and decrease probability that they will collide in a way that results in a reaction

Reading peptide sequences

Peptide Sequence: RKKRKPQPQPKRPQQ Read from N terminus on the left and C terminus on the right. The first three amino acids on the left are N terminus and last three on the right are the C terminus

Disulfide Bonds

Cysteine residues in proteins and peptides form disulfide bonds. These bonds are in dimers and multimers and help hold protein subunits together.

Formation of a disulfide bonds:

Forms through oxidation reduction reactions in which the sulfur atoms of cysteine residues in reduced form are oxidized. An oxidizing agent is needed for this to occur.

The negative charge of DNA causes it to migrate towards the:

anode of an electrophoretic cell

How to decrease DNA gel mobility

Neutralizing the negative charge with positively charged residues and increasing the size of the complex

Side chains of amino acids at pH of 7:

K and R are positively charged while D and E are negatively charged. Everything else is neutral.

Removing a negatively charged amino acid D or E from a polypeptide or adding a positively charged one R or K will:

Change the net charge by +1

Removing a positively charged amino acid R or K from a polypeptide or adding a negatively charged one D or E will:

Changes the net charge by -1

A decrease in pH yields:

Increased H+ concentration which favors protonation

An increase in pH yields:

Decrease H+ concentration which favors deprotonation

Ratio of Protonated to Deprotonated Side Chains

At pKa 8.4 the ratio of protonated to deprotonated in the side chain is 1:1. Protonated increases by 10 when pKa increases by 1 (from 8.4) and decreases by 10 when pKa decreases by 1 (from 8.4)

Histones and Proteins

Histones are proteins that bind DNA through electrostatic interactions between negatively charged DNA backbone and positively charged histone residues. Modifications that remove the positiive charge loosen the DNA histone interaction and lead to an upregulation of gene expression.

Blotting Techniques

(Southern, Northern, and Western) Involve the separation of biomolecules by electrophoresis and the detection of a specific molecules using a specific probe.

Epitope

The specific region in a protein where an antibody binds to. Some ______ contain amino acids that are far apart from each other in the primary structure but are close together when protein folds in tertiary structure. For these epitopes, unfolding them prevent the antibody from binding.

SDS causes:

Proteins to unfold and should not be used in western blots where the epitope consists of amino acids that are far apart in their primary structure.

Phosphorylation

Occurs when the hydroxyl group of an amino acid acts as a nucleophile to attack a phosphate group on ATP. Found on amino acids that contain hydroxyl groups (Serine, Threonine, and Tyrosine)

Transcription Factors

PROTEinS that bind to specific DNA sequences to regulate transcription of the corresponding gene. Can upregulate or downregulate transcription.

Peptide Bonds

Link amino acids together and form proteins

Primary Structure

Linear amino acid sequence and peptide bonds.

Secondary Structure

Results from hydrogen bonding in polypeptide backbone

Tertiary Structure

Results from amino acid side chain R group interactions. Protein does not bind DNA at higher temperature so transcription occurs.

Quatenary Structure

Protein binds DNA at lower temperature, blocking DNA transcription

Amino Acid Da

The average molecular weight of an amino acid is 110 Da. The molecular weight of the polypeptide can be estimated by multiplying the number of amino acids in the polypeptide by 110.

Ex: 591 AA x 110 Da/AA = 65 kDa

For short peptides that do not adopt higher levels of structure:

Properties such as isoelectric point and hydrophobicity depend on which amino acids are present and not the order in which the amino acids are arranged (primary structure)

n! for a peptide of known competition

In which each amino acid is different from every other amino acid, the number of possible arrangements is n! where n is the number of amino acids in the peptide

Ex: A tripeptide can be expressed in 3! = 6 different ways

Antagonists

Molecules that bind to receptor proteins to inhibit a response.

P values less than ___ are statistically significant

0.05

Isoelectric Focusing (IEF)

A powerful analytic technique that can detect and distinguish proteins with mutations that affect their ionizability. Proteins migrate through a gel until they reach an isoelectric point (pl value) where the protein is neutral. To neutralize the pH OH- or H+ will be added.

Covalent Catalysis

When a temporary covalent bond is made between an enzyme and substrate

Nucleophile

a chemical species that forms bonds by donating an electron pair. Hydroxyls, thiols, and amines (S, T, Y), (C), (K, R, H) can serve as nucleophiles to form covalent bonds in nucleophilic substitutions or addition reactions during covalent catalysis. Other residues in the enzyme active site can deprotonate these groups to enhance their nucleophility.

Amino Acid with a Thioether (Side Chain) (C-S-C)

Methionine M

Amino Acid with a Hydroxyl Group (-OH)

Threonine (T) and Serine (S)

Amino Acid with a Amine Group (Side Chain) (-NH2)

Lysine, Argininge, and Histidine (K, R, H

Native PAGE

Separates proteins by charge and molecular weight without affecting their structure.

SDS-PAGE

Separates proteins only on the basis of molecular weight.

Reducing Agents

May be added to SDS gels to break any disulfide bonds that are present

Detergents

Such as SDS disrupt noncovalent interactions and cause proteins to unfold so proteins can only exist in their primary structure and do not perform their biological function