Biochem Exam 2

Draw glycine

Draw alanine

Draw valine

Draw leucine

Draw isoleucine

Draw methionine

Draw proline

Draw phenylalanine

Draw tyrosine

Draw tryptophan

Draw lysine

Draw arginine

Draw histidine

Draw serine

Draw threonine

Draw asparagine

Draw glutamine

Draw cysteine

Draw aspartate

Draw glutamate

Which amino acid has no chiral center?

Glycine

Which amino acids have alkyl side chains?

Alanine, valine, leucine, isoleucine, and methionine

Which amino acids have alcohol side chains?

Serine, threonine, and tyrosine

Which amino acids have carboxylate side chains?

Aspartate and glutamate

Which amino acids have aromatic side chains?

Phenylalanine, tyrosine, and tryptophan

Which amino acids have amine side chains?

Lysine and arginine

Which amino acids have amide side chains?

Asparagine and glutamine

Which amino acid has a thiol side chain?

Cysteine

Which amino acid has a thioether side chain?

methionine

Which amino acid contains an indole ring?

Tryptophan

Which amino acid contains an imidazole ring?

histidine

Which amino acids are negatively charged at pH 7?

aspartate and glutamate

Which amino acids are positively charged at pH 7?

Lysine, arginine, histidine

Which amino acids are neutral polar at pH 7?

Serine, threonine, cysteine, tyrosine, asparagine, glutamine

What are aliphatic amino acids?

Amino acids with non-aromatic, carbon-based side chains

Which amino acids are aliphatic?

alanine, valine, leucine, isoleucine, methionine, proline

What amino acids have aromatic rings

Phenylalanine, Tyrosine, and Tryptophan

Draw aspartate at pH 7

Which amino acids are found on a protein surface?

Arg, lys, his, asp, glu, asn, gln, ser, thr

Which amino acids are most likely found inside a protein?

Val, leu, ile, met, phe, trp, pro, ala

What happens to amino acid carboxyl groups at physiological pH?

deprotonated as COO⁻

What happens to amino acid amino groups at physiological pH?

protonated as NH₃⁺

What is a zwitterion?

A molecule containing both a positive and negative charge but with an overall net charge of zero

At pH 1, what is the net charge of a typical polypeptide?

+

Which amino acid side chain has a pKa in the physiological pH range and is involved in proton transfer during enzymatic catalysis?

Histidine

What is the N-terminus of a peptide?

The end containing the free α-amino group

What is the C-terminus of a peptide?

The end containing the free α-carboxyl group

What is a peptide bond?

An amide bond between the α-carboxyl group of one amino acid and the α-amino group of another

Draw a dipeptide, tripeptide, and a tetrapeptide.

Which two amino acids are modified during translation?

Selenocysteine and pyrrolysine

Draw selenocysteine and pyrrolysine

Which 4 amino acids are modified post-translationally

Glutamate, lysine, proline, serine

What are the resonance structures of a peptide bond important for?

They give the peptide bond partial double-bond character and restrict rotation

What are proteases?

Enzymes that hydrolyze peptide bonds in proteins

What are three digestive proteases?

Trypsin, chymotrypsin, and pepsin

Where does trypsin cleave the protein sequence?

Lysine or arginine

Where does chymotrypsin cleave the protein sequence?

Tyrosine, tryptophan, phenylalanine, leucine

Where does thrombin cleave the protein sequence?

arginine

Where does V8-protease cleave the protein sequence?

Aspartic acid, glutamate

How can the local environment affect an amino acid side-chain pKa?

Nearby charges, hydrogen bonds, polarity, and the protein environment can shift its pKa

What is the primary structure of a protein?

The linear amino acid sequence of a polypeptide

What is a conservative mutation?

A mutation that does not alter the structure of an amino acid and rarely changes the stability of function of a protein

What is a nonconservative mutation?

A mutation that replaces an amino acid and changes the structure and properties of the protein

What is transcription?

The process of copying DNA information into mRNA

What is translation?

The process of using mRNA information to synthesize a protein

Define ribosomal translation

The process where a ribosome performs protein synthesis using mRNA templates

What is a codon?

A triplet of nucleotides used to code an amino acid

How many combinations are there for the 20 amino acids?

64

What are the three stop codons?

UAA, UAG, and UGA

What is the start codon?

AUG

Which codon can encode selenocysteine?

UGA

Which codon can encode pyrrolysine?

UAG

What codon encodes methionine?

AUG

What is preproinsulin?

The initial single-chain insulin precursor containing a signal peptide

What is the function of the preproinsulin signal peptide?

It directs the protein into the appropriate secretory pathway

What happens when the signal peptide is removed?

Preproinsulin becomes proinsulin

What happens during proinsulin maturation?

The protein folds, disulfide bonds form, and a connecting peptide is later removed

What is mature insulin composed of?

Two chains, A and B, held together by disulfide bonds

What connects insulin's A and B chains?

Disulfide bonds between cysteine residues

What is the difference between identical and similar protein sequences?

Identical sequences have the same amino acids; similar sequences differ but share related residues/properties

What does homologous mean when describing protein sequences?

Sequences related by common evolutionary ancestry

What is a GLP-1

An incretin hormone secreted by intestinal L-cells that stimulate insulin secretion, suppresses glucagon release, and slows gastric emptying

What is enkephalin?

An endogenous opioid peptide involved in pain regulation and analgesia

What is neuropeptide Y?

A neurotransmitter peptide that regulates appetite, energy, balance, and anxiety

What is neurotensin?

A peptide that regulates dopamine pathways, gut motility, and nociception

What is orexin?

A neuropeptide that regulates wakefulness, arousal, and appetite

What is the 3-letter and 1-letter code for alanine

Ala, A

What is the 3-letter and 1-letter code for arginine

Arg, R

What is the 3-letter and 1-letter code for asparagine

Asn, N

What is the 3-letter and 1-letter code for aspartate

Asp, D

What is the 3-letter and 1-letter code for cysteine

Cys, C

What is the 3-letter and 1-letter code for glutamine

Gln, Q

What is the 3-letter and 1-letter code for glutamate

Glu, E

What is the 3-letter and 1-letter code for glycine

Gly, G

What is the 3-letter and 1-letter code for histidine

His, H

What is the 3-letter and 1-letter code for isoleucine

Ile, I

What is the 3-letter and 1-letter code for leucine

Leu, L

What is the 3-letter and 1-letter code for lysine

Lys, K

What is the 3-letter and 1-letter code for methionine

Met, M

What is the 3-letter and 1-letter code for phenylalanine

Phe, F