Biochemistry Exam 1 Study Guide: Amino Acids and Protein Structure

Flashcards covering key concepts related to amino acids and protein structure critical for biochemistry exam preparation.

What are amino acids?

Building blocks of proteins.

What is the general structure of an amino acid?

α-carbon bonded to an amino group (–NH₃⁺), carboxyl group (–COO⁻), hydrogen, and an R group.

Are all amino acids chiral?

Except for glycine, amino acids are chiral.

How are proteins formed?

Proteins are chains of amino acids linked by peptide bonds.

What features do all amino acids share?

Amino group, carboxyl group, α-carbon, and a unique R group.

Name a negatively charged (acidic) amino acid.

Aspartic acid (Asp, D) or Glutamic acid (Glu, E).

What is the charge and polarity of aspartic acid?

Charge: Negative, Polarity: Polar.

Name a polar, uncharged amino acid.

Serine (Ser, S) or Threonine (Thr, T) or Asparagine (Asn, N) or Glutamine (Gln, Q).

What is unique about cysteine?

Contains sulfur (–SH) and can form disulfide bonds.

Describe the difference between polar and nonpolar amino acids.

Polar amino acids can form hydrogen bonds; nonpolar amino acids drive hydrophobic interactions.

What is a peptide bond?

A covalent bond formed between the carboxyl group of one amino acid and the amino group of another.

How are peptide bonds formed?

By a condensation reaction, releasing water.

What is the directionality of peptides?

Peptides are written from N-terminus to C-terminus.

What is a dipeptide?

A peptide composed of 2 amino acids.

What is the primary structure of a protein?

The linear sequence of amino acids in a polypeptide chain.

What determines the higher levels of protein structure?

The primary structure determines all higher levels of structure.

What bonds stabilize primary structure?

Peptide bonds (covalent bonds).

What stabilizes secondary structure?

Hydrogen bonds between backbone atoms.

What is an α-helix?

A right-handed helical coil with 3.6 amino acids per turn.

What amino acids disrupt α-helices?

Proline and Glycine.

What is a β-sheet?

Extended polypeptide chains arranged in a zigzag pattern.

What types of β-sheets exist?

Antiparallel and parallel.

What are β-turns?

Tight turns that connect two adjacent β-strands.

What type of interactions stabilize tertiary structure?

Hydrophobic interactions, hydrogen bonds, ionic interactions, and disulfide bonds.

What is the quaternary structure of a protein?

The association of multiple folded polypeptide chains.

What stabilizing forces are present in quaternary structure?

Hydrophobic interactions, hydrogen bonds, ionic interactions, and sometimes disulfide bonds.

What is the role of disulfide bonds in proteins?

They stabilize tertiary and quaternary structure.

What defines enzymes?

Enzymes are catalysts that speed up reactions without being consumed.

What is the role of the active site in enzymes?

It's the region where the substrate binds.

What are the properties of water?

Water is polar, enabling hydrogen bonding and resulting in high boiling point and heat capacity.

What are common hydrogen bond donors and acceptors?

O–H and N–H.

How is pH defined?

pH is a measure of [H⁺] and is calculated as pH = –log[H⁺].

What is pKa?

The pH at which a molecule is 50% protonated and 50% deprotonated.

What are buffers?

Weak acids and their conjugate bases that resist changes in pH.

What is the hydrophobic effect?

Nonpolar molecules cluster in water, minimizing disruption of hydrogen bonding.

What is the difference between polar, nonpolar, and amphipathic molecules?

Polar: water-soluble; Nonpolar: avoid water; Amphipathic: both polar and nonpolar regions.

How many amino acids make a protein?

Typically at least 10 kDa in size, consisting of many amino acids.

How does temperature affect enzyme activity?

Increased temperature can speed up reactions to a point; too high can denature the enzyme.

What is the role of molecular chaperones?

They assist in the proper folding of proteins.

What is the significance of glycine in protein structure?

Its flexibility allows for tight turns and can destabilize structures.

What are examples of multimeric proteins?

Hemoglobin and some enzymes made of multiple subunits.

What is the role of hydrogen bonds in protein structure?

They stabilize secondary, tertiary, and quaternary structures.

What is the importance of the pH of blood?

It maintains a critical physiological environment for biochemical reactions.

Explain the concept of enzyme specificity.

Enzymes act on specific substrates due to their unique active sites.

What term describes amino acids with both positive and negative charges?

Zwitterionic form.

What bond character distinguishes peptide bonds?

Partial double-bond character, preventing free rotation.

How does dehydration synthesis relate to peptide bonds?

It is the process that forms peptide bonds by releasing water.

In protein structure, what does 'N-terminus' refer to?

The end of the polypeptide chain with a free amino group.

What amino acid sequence is known for its importance in defining structure?

The primary structure's linear amino acid sequence.

What type of amino acids are more common in enzyme active sites?

Polar or charged amino acids facilitate substrate binding.

Describe the function of the carboxyl group in amino acids.

Contributes to the acid nature and charge of the amino acid.

What property makes disulfide bonds particularly strong?

They are covalent bonds between cysteine residues.

How do ionic interactions affect protein structure?

They stabilize the tertiary and quaternary structures through salt bridges.

What factor primarily drives the folding of proteins?

Hydrophobic interactions of nonpolar side chains.

What is aldose?

A sugar that contains an aldehyde group.

What is a ketose?

A sugar that contains a ketone group.