biochem week 2

p K_{\mathrm{a}}

The pH at which the acid is half dissociated, meaning the concentrations of the conjugate base ([\mathrm{A}^-]) and acid ([\mathrm{HA}]) are equal.

Henderson-Hasselbalch equation

The equation relating pH, p K{\mathrm{a}} and the ratio of base to acid concentrations: \mathrm{pH} = \mathrm{p}K{\mathrm{a}} + \log \left( \frac{[\mathrm{A}^-]}{[\mathrm{HA}]} \right)

Peptide Bond

A covalent linkage formed via a dehydration reaction (loss of \mathrm{H}_2 \mathrm{O}) between the carboxyl group of one amino acid and the amino group of another. Once formed, the bond is uncharged and possesses resonance.

Q/A: How does the ionization state of an amino acid group relate to the pH and its p K_{\mathrm{a}}?

If \mathrm{pH} < \mathrm{p}K{\mathrm{a}}, the group is protonated; if \mathrm{pH} > \mathrm{p}K{\mathrm{a}}, it is deprotonated.

N-terminus

The beginning of a polypeptide chain characterized by a free amino group.

Primary Structure of Proteins

The linear sequence of amino acids connected by peptide bonds, read from the N-terminus to the C-terminus.

Q/A: Why is the uncharged nature of the peptide bond important?

It is crucial for the proper folding of proteins into their stable three-dimensional structures.

Zwitterion

A dipolar ion form of an amino acid, typically found at physiological pH (pH 7.4), where it carries both a positive and a negative charge resulting in a net neutral charge.

Nonpolar amino acid side chains

Side chains that lack ionization at any pH.

What is the typical charge of a deprotonated amino acid group?

Usually a negative charge, but exceptions exist, especially in nitrogen-containing amine groups.

What is the charge state of the acidic (protonated) form of Oxygen in an amino acid side chain?

Uncharged.

What happens to Sulfur (e.g., Cysteine) when it moves from its acidic to its basic form?

The acidic form retains hydrogen; the basic form loses hydrogen (deprotonated).

How does Nitrogen generally behave in ionization compared to Oxygen and Sulfur?

It generally behaves oppositely; it can accept an additional hydrogen ion leading to a positive charge under certain conditions.

Peptide Bond

Covalent linkages formed during translation between amino acids through carboxyl and amino groups.

Dehydration Reaction

The chemical process involving the loss of a water molecule (\text{H}_2\text{O}) when amino acids bond through carboxyl and amino groups.

Characteristics of a peptide bond once formed

They are uncharged and possess resonance characteristics.

PKa Relevance

Understanding typical pK_a values (Alpha carboxyl group, Alpha amino group, and Side chains) is necessary for the MCAT and overall understanding of amino acid behavior.

How are Nonpolar amino acid side chains classified regarding ionization?

They lack pK_a values and show no ionization at any pH.

What is the critical relationship between pH and pK_a in understanding amino acid behavior?

It dictates whether a group is protonated (and typically uncharged) or deprotonated (and usually negatively charged).

What is the typical charge status of a protonated form of an amino acid group?

Typically considered uncharged (unless specified otherwise).

Describe the ionization pattern of an oxygen-containing group (like a carboxyl group).

Acidic form (protonated) is uncharged; Basic form (deprotonated) is negatively charged.

Peptide Bonds

Covalent linkages formed during translation via a dehydration reaction (loss of a water molecule: \text{H}_2\text{O}) between the carboxyl and amino groups of amino acids.

What are two key characteristics of a peptide bond once it is formed?

They are uncharged and possess resonance characteristics.

Primary Structure of Proteins

The linear sequence of amino acids connected by peptide bonds, determined by genetic information.

N-terminus (Amino End)

The end of a protein or peptide chain characterized by a free amino group.

C-terminus (Carboxyl End)

The end of a protein or peptide chain characterized by a free carboxyl group.

pK_a

The pH at which the acid is half-dissociated.

What is the charge state of an amino acid at physiological pH (pH 7.4)?

Zwitterion (or dipolar ion).

What is the Henderson-Hasselbalch equation?

pH = pK_a + \log \left(\frac{ [A^-] }{ [HA] }\right)

Acid

A proton donor.

Conjugate Base

The chemical formed upon ionization of an acid.

How is a peptide bond formed?

Through a dehydration reaction involving the loss of a water molecule.

Amino acid residue

The portion of each amino acid remaining in the chain after peptide bond formation.

What are the typical pKa values for the \alpha -carboxyl group and the \alpha -amino group?

\alpha -carboxyl group: 2.2; \alpha -amino group: 10.6

Where is the N-terminus located on a polypeptide?

At the Amino end, which has a free amino group.

What is the typical pKa value for the side chain of Histidine?

6.0

What is the pKa value for the side chain of Lysine?

10.4

What characteristic is true of the peptide bond once it is formed?

It is uncharged.

Entropy

A measure of disorder or randomness in a system.

Hydrophobic Effect

The phenomenon where nonpolar molecules aggregate in an aqueous environment to minimize their exposure to water, which influences the entropy of the system.

Clathrate

A crystal structure where water molecules form cage-like lattices that physically trap "guest" molecules.

Zwitterion

A dipolar ion form of an amino acid where the amino group is positively charged and the carboxyl group is negatively charged, typically occurring at physiological pH (~7).

pK_a

The pH at which a weak acid is half dissociated, meaning the concentrations of the protonated form ([HA]) and deprotonated form ([A^-]) are equal.

What drives the formation of micelles in water?

Micelle formation is driven by an increase in water entropy (\Delta S > 0) rather than enthalpy.

How does the aggregation of nonpolar molecules affect the entropy of surrounding water?

When nonpolar molecules aggregate, the entropy of water increases because it releases the organized "cages" of water molecules back into a more disordered state.

What is the Henderson-Hasselbalch Equation?

pH = pK_a + \log \left( \frac{[A^-]}{[HA]} \right)

If the pH is lower than the pK_a, which form of an amino acid dominates?

The protonated (acid) form dominates (pH < pK_a).

If the pH is higher than the pK_a, which form of an amino acid dominates?

The deprotonated (base) form dominates (pH > pK_a).

How do nonpolar amino acids differ from polar amino acids in terms of functional groups?

Nonpolar amino acids typically contain hydrocarbon chains, while polar amino acids often feature functional groups like alcohol groups (-OH) that enhance hydrogen bonding and solubility.

What does a larger K_a value indicate about an acid?

A larger K_a indicates a stronger acid with a higher tendency to ionize.

What is the ratio of base to acid if the pH is 4 and the pK_a is 2?

The ratio of base ([A^-]) to acid ([HA]) is 100:1, as calculated by 10^{(4-2)} = 10^2 = 100.