Amino Acids and Their Properties

A comprehensive set of flashcards summarizing key concepts related to the structure and function of amino acids as presented in the lecture.

What are the main components attached to the alpha-carbon of an amino acid?

A carboxylate group, a protonated amino group, and a side chain (R group).

What is a zwitterion?

A neutral molecule with equal numbers of positive and negative charges.

What is the significance of the amino acid glycine among the common amino acids?

Glycine is the only common amino acid that is not chiral.

What are the groups of amino acids based on their side chain polarity?

Hydrophobic, polar neutral, negatively charged, and positively charged.

Which amino acids have nonpolar side chains?

Glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, and methionine.

What is the difference between acidic and basic amino acids?

Acidic amino acids have negatively charged side chains and basic amino acids have positively charged side chains at physiological pH.

What is the isoelectric point (pI)?

The pH at which an amino acid is electrically neutral, with no net charge.

What biochemical roles do neurotransmitters play?

They carry signals from nerve cells to targets and can be either excitatory or inhibitory.

How do amino acids behave in terms of solubility?

They can form crystals, have high melting points, and are water soluble.

What happens to the structure of amino acids upon titration?

Titration curves show different states of ionization depending on pH, impacting charge and solubility.

What is a chiral center in an amino acid?

A carbon atom bonded to four different groups, making the molecule non-superimposable on its mirror image.

Which part of an amino acid determines its chirality?

The alpha-carbon, which is bonded to the amino group, carboxyl group, hydrogen atom, and a unique R-group (except for glycine).

What is an L-amino acid?

An amino acid in which the amino group is on the left side when the carboxyl group is oriented at the top in a Fischer projection.

What is a D-amino acid?

An amino acid in which the amino group is on the right side when the carboxyl group is oriented at the top in a Fischer projection.

Why are L-amino acids biologically significant?

All amino acids found in proteins synthesized by ribosomes are L-amino acids.

What is a peptide bond?

An amide bond formed between the carboxyl group of one amino acid and the amino group of another amino acid, releasing a molecule of water.

How is a peptide bond formed?

Through a dehydration (condensation) reaction between the alpha-carboxyl group of one amino acid and the alpha-amino group of another.

How can a peptide bond be broken?

By hydrolysis, typically catalyzed by enzymes (proteases) or strong acid/base under heat.

What are the key characteristics of a peptide bond?

It has partial double-bond character, making it rigid and planar, preventing rotation around the C-N bond.

What is the difference between an oligopeptide and a polypeptide?

An oligopeptide usually contains a few amino acid residues (typically less than 20-30), while a polypeptide contains many more and forms a protein.

What is the primary structure of a protein?

The unique linear sequence of amino acids linked by peptide bonds.

Why is the primary structure crucial for a protein's function?

It dictates all higher levels of protein structure, and thus ultimately determines the protein's three-dimensional shape and biological function.

What determines the primary structure of a protein?

The genetic information encoded in the DNA sequence.

What is the secondary structure of a protein?

The local folding patterns of the polypeptide backbone, primarily stabilized by hydrogen bonds between backbone atoms (e.g., alpha-helices and beta-sheets).

Describe an alpha-helix.

A spiral structure where the polypeptide backbone coils around an imaginary axis. It is stabilized by hydrogen bonds between the carbonyl oxygen of one peptide bond and the amide hydrogen of a peptide bond four residues away.

Describe a beta-sheet.

Composed of two or more polypeptide strands (beta-strands) arranged side-by-side, stabilized by hydrogen bonds between backbone atoms of adjacent strands. Can be parallel or antiparallel.

What contributes to the stability of secondary structures like alpha-helices and beta-sheets?

Primarily hydrogen bonds formed between the oxygen of a carbonyl group and the hydrogen of an amide group within the polypeptide backbone.

What is a 'random coil' in protein structure?

Regions of a polypeptide chain that do not possess a defined secondary structure, appearing flexible and irregular.

What is the tertiary structure of a protein?

The overall three-dimensional shape of a single polypeptide chain, including the spatial arrangement of all its atoms.

What types of interactions stabilize the tertiary structure?

Hydrophobic interactions, ionic bonds (salt bridges), hydrogen bonds, and disulfide bonds (covalent linkages).

What is the role of the hydrophobic effect in tertiary structure formation?

It drives nonpolar side chains to bury themselves in the interior of the protein, away from water, while polar and charged side chains remain on the surface.

What is a protein domain?

A distinct functional and/or structural unit within a protein, often capable of folding independently and associated with specific functions.

What is the 'molten globule' state in protein folding?

An intermediate state during protein folding characterized by compact structure, significant secondary structure, but a less organized tertiary structure than the native state.

What is the quaternary structure of a protein?

The arrangement of multiple polypeptide subunits (two or more) into a larger functional protein complex.

Give an example of a protein with quaternary structure.

Hemoglobin, which consists of four polypeptide subunits (two alpha and two beta chains).

What forces stabilize quaternary structure?

Similar to tertiary structure: hydrophobic interactions, ionic bonds, and hydrogen bonds between the surfaces of interacting subunits.

Which amino acid is capable of forming disulfide bonds?

Cysteine, through the oxidation of the thiol (-SH) groups of two cysteine residues to form a disulfide (-S-S-) bond.

What are the common aromatic amino acids?

Phenylalanine, tyrosine, and tryptophan.

Which amino acids absorb UV light, and why is this useful in biochemistry?

Tryptophan, tyrosine, and to a lesser extent phenylalanine absorb UV light (around 280 nm) due to their aromatic rings, allowing for protein concentration measurement.

What is the importance of the amino acid histidine in biological systems?

The side chain of histidine has a pK_a near physiological pH (6.0), allowing it to act as an effective buffer in many enzymatic reactions and proton transfer processes.

What defines an essential amino acid?

An amino acid that cannot be synthesized by the human body and must be obtained through diet.

What defines a non-essential amino acid?

An amino acid that can be synthesized by the human body from other molecules.

List three examples of essential amino acids.

Valine, Leucine, Isoleucine (others include Histidine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan).

What is a pK_a value?

The negative logarithm of the acid dissociation constant (K_a), representing the pH at which an ionizable group is half-protonated and half-deprotonated.

How many pK_a values does a typical free amino acid have?

At least two (pKa of the alpha-carboxyl group and pKa of the alpha-amino group). Some amino acids also have a third pK_a for their ionizable side chain.

What are the buffering regions on an amino acid titration curve?

The flat regions of the curve around each pK_a value, where the amino acid effectively resists changes in pH.

Which amino acids serve as precursors for important hormones?

Examples include tyrosine (for thyroid hormones and catecholamines like adrenaline) and tryptophan (for serotonin and melatonin).

What neurotransmitter is derived from glutamate?

Gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the central nervous system.

What role do certain amino acids play in gluconeogenesis?

Some amino acids (glucogenic amino acids) can be converted into glucose precursors (like pyruvate or oxaloacetate) and used to synthesize glucose.

How do amino acids contribute to the formation of coenzymes?

Various amino acids or their derivatives are components of crucial coenzymes, such as S-adenosylmethionine (SAM) derived from methionine, or NAD+/NADH formation involving tryptophan.