Cell and Molec Lecture 3

How many amino acids are coded for by the standard genetic code?

20

What is the general structure of an amino acid?

• A central alpha (α) carbon

• A hydrogen atom

• An amino group

• A carboxyl group

• An R group, or side chain

What determines the identity and chemical properties of an amino acid?

The R group (side chain)

What is the alpha carbon?

the central carbon atom of an amino acid to which the hydrogen, amino group, carboxyl group, and R group are attached

What is an R group?

the variable portion of an amino acid, giving them different chemical properties

What happens to the amino and carboxyl groups at pH 7?

They are both ionized

Why are the side chains of amino acids important?

They determine if amino acids are:

• Polar or nonpolar

• Charged or uncharged

• Acidic or basic

• Capable of hydrogen bonding

• Capable of forming particular chemical bonds or undergoing modifications

What does it mean for an amino acid to be asymmetric?

its central alpha carbon has four different groups attached to it, making it chiral.

Which amino acid is the exception to having an asymmetric alpha carbon?

Glycine because its R group is simply a hydrogen atom.

What are enantiomers?

molecules that are mirror images of one another but cannot be superimposed.

What are the two possible forms of chiral amino acids?

L and D

Which form of amino acid is found in proteins?

L-amino acids are found in proteins synthesized by bacterial and eukaryotic cells.

Where are D-amino acids found?

in bacterial cell walls, but they are not incorporated into bacterial proteins.

Which amino acid has no enantiomers?

Glycine

What are the three- and one-letter abbreviations for alanine?

Ala and A

What are the three- and one-letter abbreviations for glycine?

Gly and G

What are the three- and one-letter abbreviations for phenylalanine?

Phe and F

How can polar amino acids be further classified?

Negatively charged/acidic

Positively charged/basic

Uncharged polar

What makes an amino acid polar?

its side chain contains chemical groups that have an uneven distribution of charge and can interact favorably with polar molecules such as water.

What characterizes a nonpolar amino acid?

Its side chain is generally uncharged and nonpolar and does not readily participate in hydrogen bonding.

Which three amino acids have basic side chains?

Lysine

Arginine

Histidine

What does it mean for an amino acid to have a basic side chain?

Its side chain can accept protons and tends to carry a positive charge

What makes arginine particularly basic?

Its positive charge is stabilized through resonance.

What is resonance?

the delocalization or spreading of electrons across a group or molecule.

Why is lysine particularly important beyond its role as an amino acid?

Lysine residues are frequently sites of post-translational modifications (PTMs)

What is a post-translational modification?

a chemical modification made to a protein after it has been synthesized.

Give two examples of modifications that can occur on lysine residues.

Acetylation

Ubiquitination

What happens during lysine acetylation?

An acetyl group is covalently attached to the lysine side chain.

What is an acetyl group?

a small chemical group containing two carbon atoms that can be covalently attached to molecules such as lysine

What happens during lysine ubiquitination?

A small protein called ubiquitin is attached to the lysine side chain.

How does ubiquitination differ from acetylation?

Acetylation adds a relatively small chemical group, whereas ubiquitination attaches an entire small protein molecule (ubiquitin).

What type of bond connects ubiquitin to lysine?

isopeptide bond.

Why are post-translational modifications important?

They alter a protein's properties, activity, interactions, localization, stability, or regulation.

Which two amino acids have acidic side chains?

Aspartic acid (aspartate)

Glutamic acid (glutamate)

What makes aspartic acid and glutamic acid acidic?

side chains contain carboxyl groups that can readily give up protons

What happens when an acidic side chain gives up a proton?

It becomes negatively charged.

What charge do acidic amino acid side chains generally have at physiological pH?

negatively charged

What is the difference between aspartic acid and glutamic acid?

Glutamic acid has one additional carbon in its side chain compared with aspartic acid

What characterizes nonpolar amino acid side chains?

They are generally uncharged and nonpolar.

Do nonpolar side chains readily participate in hydrogen bonding?

No

Where are nonpolar amino acids commonly found in a folded protein?

the hydrophobic core of a folded protein

Why are nonpolar amino acids commonly found in the protein's interior?

Their nonpolar side chains interact poorly with water, so proteins often bury them away from the aqueous environment in the hydrophobic interior.

Where are polar or charged amino acids more likely to be found?

on the surface of proteins, where they can interact with water.

What is the simplest amino acid?

Glycine

What is glycine's side chain?

Hydrogen

Why is glycine unique regarding chirality?

Because its side chain is hydrogen, glycine's alpha carbon has two hydrogen atoms attached to it. Therefore, it is not asymmetric or chiral.

Why can glycine be structurally different from other amino acids?

small side chain gives it greater flexibility than amino acids with larger side chains

Which two standard amino acids contain sulfur?

Methionine

Cysteine

What is significant about methionine's role in protein synthesis?

Methionine is encoded by the start codon AUG in mRNA

What is the corresponding start codon in DNA?

ATG

Is the initial methionine always present in the mature protein?

No. The initial methionine can be cleaved off during protein maturation.

Can methionine form disulfide bonds?

No

What is cysteine particularly important for?

forming disulfide bonds (disulfide bridges).

What is a disulfide bond?

a covalent bond formed between the sulfur atoms of two cysteine residues.

Where can disulfide bonds form?

Between cysteine residues within the same polypeptide

Between cysteine residues on different polypeptides

Can cysteine form disulfide bonds with another cysteine?

Yes

What makes proline structurally unusual?

Its side chain folds back and connects to the nitrogen, creating a five-membered ring.

Is proline technically a standard amino acid?

classified as an imino acid rather than a conventional amino acid because of its unusual nitrogen-containing ring structure.

How does proline affect protein secondary structure?

Proline cannot easily be incorporated into certain secondary structures, particularly alpha helices, because of its rigid structure

Why is proline called a "helix breaker"?

Proline can disrupt or prevent the formation of an alpha helix because its rigid ring structure restricts the backbone conformation

Where is proline commonly found relative to alpha helices?

It is often found at the start or end of alpha helices.

What can happen when proline occurs within an alpha helix?

It can introduce a slight bend or kink in the alpha helix.

What structural feature do phenylalanine and tyrosine share?

Both contain a benzene ring.

What is the major structural difference between phenylalanine and tyrosine?

Tyrosine has an additional hydroxyl (-OH) group attached to its benzene ring.

Why is tyrosine polar while phenylalanine is nonpolar?

Tyrosine contains a polar hydroxyl group, which allows it to participate in hydrogen bonding.

What are phenylalanine and tyrosine important for besides being incorporated into proteins?

They serve as precursors for:

Monoamine neurotransmitters

Melanin

What neurotransmitters can ultimately be synthesized from Phenylalanine and Tyrosine?

Dopamine

Norepinephrine

Epinephrine

What are norepinephrine and epinephrine also called?

Norepinephrine = noradrenaline

Epinephrine = adrenaline

Which three amino acids have hydroxyl groups in their side chains

Serine

Threonine

Tyrosine

Why are serine, threonine, and tyrosine polar?

Each contains a hydroxyl (-OH) group, which is polar and can participate in hydrogen bonding

Can serine, threonine, and tyrosine form hydrogen bonds?

Yes. Their hydroxyl groups allow their side chains to hydrogen bond with molecules such as water.

Are serine, threonine, and tyrosine charged or uncharged polar amino acids?

They are classified here as uncharged polar amino acids.

Which amino acids discussed in the lecture can be phosphorylated?

Serine

Threonine

Tyrosine

What is phosphorylation?

the addition of a phosphate group to a molecule, such as a protein.

Which enzymes add phosphate groups to proteins?

Kinases

Which enzymes remove phosphate groups from proteins?

Phosphotases

Why are the hydroxyl groups of serine, threonine, and tyrosine important for phosphorylation?

Their hydroxyl groups can react with phosphate groups to form phosphoester bonds, allowing phosphorylation to occur

What type of bond links the phosphate group to these amino acid side chains?

A phosphoester bond

Can amino acids other than serine, threonine, and tyrosine be phosphorylated?

Yes. Other amino acids can also undergo phosphorylation, although the lecture emphasizes serine, threonine, and tyrosine.

Arginine 3 letter abbreviation, 1 letter abbreviation and polarity

Arg, R, basic/positive

Asparagine 3 letter abbreviation, 1 letter abbreviation and polarity

ASN, N, uncharged polar

Aspartic acid 3 letter abbreviation, 1 letter abbreviation and polarity

ASP, D, acidic/negative

Cysteine 3 letter abbreviation, 1 letter abbreviation and polarity

Cys, C uncharged polar

Glutamic acid 3 letter abbreviation, 1 letter abbreviation and polarity

Glu, E, acidic/negative

Glutamine 3 letter abbreviation, 1 letter abbreviation and polarity

Gln, Q, uncharged polar

Glycine 3 letter abbreviation, 1 letter abbreviation and polarity

Gly, G, nonpolar

Histidine 3 letter abbreviation, 1 letter abbreviation and polarity

His, H, basic/positive

Isoleucine 3 letter abbreviation, 1 letter abbreviation and polarity

Ile, I Nonpolar

Leucine 3 letter abbreviation, 1 letter abbreviation and polarity

Leu, L, nonpolar

Lysine 3 letter abbreviation, 1 letter abbreviation and polarity

Lys, K, basic/positive

Methionine 3 letter abbreviation, 1 letter abbreviation and polarity

Met, M, nonpolar

Phenylalanine 3 letter abbreviation, 1 letter abbreviation and polarity

Phe, F, nonpolar

Proline 3 letter abbreviation, 1 letter abbreviation and polarity

Pro, P, nonpolar

Serine 3 letter abbreviation, 1 letter abbreviation and polarity

Ser, S, uncharged polar

Threonine 3 letter abbreviation, 1 letter abbreviation and polarity

Thr, T uncharged polar

Tryptophan 3 letter abbreviation, 1 letter abbreviation and polarity

Trp, W, nonpolar

Tyrosine 3 letter abbreviation, 1 letter abbreviation and polarity

Tyr, Y, uncharged polar

Valine 3 letter abbreviation, 1 letter abbreviation and polarity

Val, V, Nonpolar

What is a ligand?

a molecule that binds to a protein. Ligands can include substrates, signaling molecules, inhibitors, and other molecules that interact specifically with proteins.

What are two major examples of proteins that bind ligands?

Enzymes, which bind substrates.

Receptors, which bind signaling molecules or other ligands.