Biochemistry: Amino Acids and Protein Structure Flashcards

Question 1

Define Amino Acid.

Accepted Answer

An organic molecule built around a central alpha carbon bonded to an amino group, a carboxyl group, a hydrogen atom and a variable side chain; twenty kinds are the building blocks of proteins.

Question 2

Define Alpha Carbon.

Accepted Answer

The central carbon of an amino acid, bonded to the amino group, the carboxyl group, a hydrogen atom and the side chain; it is a stereocenter in every standard amino acid except glycine.

Question 3

Define R Group (Side Chain).

Accepted Answer

The variable group attached to the alpha carbon that gives each amino acid its identity, size, charge and polarity, and therefore decides how it behaves inside a folded protein.

Question 4

What is Zwitterion?

Accepted Answer

A molecule carrying both a positive and a negative charge so that its net charge is zero; free amino acids exist this way near neutral pH, with a protonated amino group and a deprotonated carboxyl group.

Question 5

Define Isoelectric Point (pI).

Accepted Answer

The pH at which a molecule carries no net electrical charge, so it does not migrate in an electric field; for amino acids it is set by the pKa values of their ionizable groups.

Question 6

Define L-Amino Acid.

Accepted Answer

The mirror-image form of an amino acid that cells use to build proteins, defined by the arrangement of groups around the alpha carbon; the D forms are rare in nature and absent from ribosomal proteins.

Question 7

What is Glycine?

Accepted Answer

The smallest amino acid, whose side chain is a single hydrogen atom; it is the only standard amino acid without a chiral alpha carbon and gives a polypeptide unusual flexibility.

Question 8

What is Proline?

Accepted Answer

An amino acid whose side chain loops back to bond with its own backbone nitrogen, forming a rigid ring that restricts rotation and removes the hydrogen the backbone usually donates to hydrogen bonds.

Question 9

What is Cysteine?

Accepted Answer

A polar amino acid with a thiol (-SH) side chain; two cysteine thiols can be oxidized to join as a covalent disulfide bridge that locks parts of a protein together.

Question 10

Define Nonpolar Amino Acids.

Accepted Answer

Amino acids with hydrocarbon or otherwise uncharged, water-avoiding side chains, such as alanine, valine, leucine, isoleucine and methionine, which tend to be buried inside folded proteins.

Question 11

Define Polar Uncharged Amino Acids.

Accepted Answer

Amino acids whose side chains carry hydroxyl, amide or thiol groups that form hydrogen bonds with water but stay uncharged at physiological pH, such as serine, threonine, asparagine and glutamine.

Question 12

Define Acidic Amino Acids.

Accepted Answer

Aspartate and glutamate, whose side chains end in a carboxyl group that loses its proton at physiological pH, giving each residue a negative charge.

Question 13

Define Basic Amino Acids.

Accepted Answer

Lysine, arginine and histidine, whose nitrogen-containing side chains can accept a proton; lysine and arginine are positively charged at physiological pH, while histidine is only partly protonated.

Question 14

Define Aromatic Amino Acids.

Accepted Answer

Phenylalanine, tyrosine and tryptophan, whose side chains contain flat ring systems; tryptophan and tyrosine absorb ultraviolet light at 280 nanometres, which is used to measure protein concentration.

Question 15

Define Essential Amino Acids.

Accepted Answer

The nine amino acids the human body cannot synthesize in sufficient amounts and must obtain from food: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine.

Question 16

Define Peptide Bond.

Accepted Answer

The covalent amide link formed between the carboxyl group of one amino acid and the amino group of the next in a condensation reaction that releases one molecule of water.

Question 17

Define Partial Double-Bond Character.

Accepted Answer

The resonance sharing of electrons between the carbonyl and nitrogen of a peptide bond, which makes the C-N bond rigid and planar so the backbone can only rotate around the alpha carbon.

Question 18

What is N-Terminus?

Accepted Answer

The end of a polypeptide chain that carries a free alpha-amino group; by convention sequences are written starting here, and ribosomes add amino acids starting from this end.

Question 19

What is C-Terminus?

Accepted Answer

The end of a polypeptide chain that carries a free alpha-carboxyl group; it is the last residue added during translation and is written at the right-hand end of a sequence.

Question 20

What is Polypeptide?

Accepted Answer

A single unbranched chain of many amino acids joined by peptide bonds; one or more polypeptides fold into a functional protein.

Question 21

Define Primary Structure.

Accepted Answer

The linear order of amino acids in a polypeptide, held together only by peptide bonds and written from the N-terminus to the C-terminus; it ultimately determines how the chain folds.

Question 22

Define Secondary Structure.

Accepted Answer

Regular local shapes such as alpha helices and beta sheets, held in place by hydrogen bonds between backbone carbonyl oxygens and amide hydrogens rather than by side chains.

Question 23

Define Alpha Helix.

Accepted Answer

A right-handed coil of the backbone with 3.6 amino acids per turn, stabilized by hydrogen bonds from each carbonyl oxygen to the amide hydrogen four residues further along, with side chains pointing outward.

Question 24

Define Beta Pleated Sheet.

Accepted Answer

A secondary structure in which extended stretches of backbone lie side by side and are hydrogen bonded to neighbouring strands, running either parallel or antiparallel, with side chains alternating above and below.

Question 25

Define Beta Turn.

Accepted Answer

A tight bend of four amino acids that reverses the direction of a polypeptide chain, often connecting the strands of an antiparallel beta sheet and frequently containing glycine or proline.

Question 26

Define Tertiary Structure.

Accepted Answer

The complete three-dimensional fold of a single polypeptide chain, stabilized mainly by interactions between side chains: the hydrophobic effect, hydrogen bonds, ionic attractions and disulfide bonds.

Question 27

Define Quaternary Structure.

Accepted Answer

The arrangement of two or more separate polypeptide subunits into one functional protein complex, held together by the same kinds of noncovalent and covalent interactions that stabilize tertiary structure.

Question 28

Define Disulfide Bond.

Accepted Answer

A covalent sulfur-sulfur bond formed when the thiol groups of two cysteine residues are oxidized; it cross-links distant parts of one chain or different chains and resists denaturation by heat.

Question 29

Define Hydrophobic Effect.

Accepted Answer

The tendency of nonpolar side chains to cluster away from water inside a protein, driven mainly by the gain in entropy of water molecules released from ordered cages around them; it is the main force behind folding.

Question 30

Define Salt Bridge.

Accepted Answer

An ionic attraction between a positively charged side chain such as lysine or arginine and a negatively charged one such as aspartate or glutamate that helps hold a folded protein together.

Question 31

What is Denaturation?

Accepted Answer

The loss of a protein's secondary, tertiary and quaternary structure, and usually its function, while its peptide bonds and amino acid sequence stay intact; heat, extreme pH, urea and detergents can cause it.

Question 32

Define Native Conformation.

Accepted Answer

The specific folded three-dimensional shape in which a protein is biologically active, usually the lowest free-energy arrangement its amino acid sequence can adopt under cellular conditions.

Question 33

Define Anfinsen's Experiment.

Accepted Answer

Christian Anfinsen's 1950s-60s work showing that ribonuclease, unfolded with urea and a reducing agent, refolded into its active shape once those were removed, proving the amino acid sequence encodes the fold.

Question 34

Define Chaperone Protein.

Accepted Answer

A protein that helps other proteins fold correctly, or refold after stress, by preventing their exposed hydrophobic surfaces from sticking together, without becoming part of the final structure.

Question 35

Define Protein Domain.

Accepted Answer

A compact region of a polypeptide that folds independently into a stable structure and often performs a distinct job, so one protein can combine several domains with different functions.

Question 36

Define Globular Protein.

Accepted Answer

A protein whose chain folds into a compact, roughly spherical shape with hydrophobic residues inside and polar ones outside, making it water-soluble; most enzymes, transport proteins and antibodies are globular.

Question 37

Define Fibrous Protein.

Accepted Answer

A protein with an elongated, repetitive structure, often built from long helices or sheets, that is usually insoluble in water and serves a structural or mechanical role.