Protein chemistry

Question 1

Amino acid residue

Answer 1

Chemical groups left behind after two or more amino acids have undergone condensation reactions

Question 2

Amino terminus

Answer 2

End of a protein whose amino acid has not condensed with a carboxyl group (H3N+) (on the left)

Question 3

Carboxyl terminus

Answer 3

End of a protein whose carboxyl group has not undergone condensation (COO-) (on the right)

Question 4

Peptide

Answer 4

Short protein

Question 5

Peptide bond

Answer 5

Another name for the amide bond found in a protein

Question 6

Peptide backbone

Answer 6

All of the amide bonds and the alpha carbon atom in a peptide (everything except ‘R’ groups/sidechains)

Question 7

Sequence

Answer 7

Order of arrangement of amino acid residues in a protein, from amino to carboxyl terminal

Question 8

Primary structure

Answer 8

Order of amino acid residues (sequence)

Question 9

Amino acid structure

Answer 9

Carboxylic acid group, Amine group, Alpha carbon (attached to both the amine and carboxylic acid group- protein backbone), ‘R’ group- substituent that makes each amino acid different (eg. alanine has a methyl group, sidechain)

Question 10

Acid and base reaction of amino acids

Answer 10

Acid + base —> salt + water, Acting as an acid the H+ is taken from the COOH group making COO-, Some are diprotic meaning you need 2 moles of base to react, Acting as a base the H+ is added to the H2N group making H3N+ (put + on top of N), Some have more than one amine meaning you need 2 moles of acid to react

Question 11

Zwitterion (dipolar salt)

Answer 11

When both a positive and negative charge are present making the overall charge 0, Amino acids can be an acid and base at the same time as they groups involved are on different functional groups, Around pH of 7, High melting and boiling point

Question 12

Aliphatic side chain

Answer 12

Hydrophobic, CH3 group, non-polar, dispersion forces

Question 13

Basic side chain

Answer 13

NH2 group, ionic bonds, can accept a proton

Question 14

Neutral side chain

Answer 14

amide group, polar, dipole-dipole, hydrogen bonding and dispersion forces

Question 15

Acidic side chain

Answer 15

Can donate a proton, can make ionic bonds with a basic side chain

Question 16

Cysteine and sulfur side chains

Answer 16

Cysteine can make a covalent bond with another cysteine side chain, Sulfur makes the side chain polar

Question 17

Types of side chains

Answer 17

Aliphatic, basic, neutral, acidic, aromatic

Question 18

Forming proteins

Answer 18

Amino acids undergo a condensation reaction (endothermic reaction, water is a product) , n Amino acids —> 1 protein + n-1 H2O, Acid-base chemistry of resulting protein is determined by the amino terminus, carboxyl terminus and functional groups on the ‘R’ portions of its amino acid residues

Question 19

Primary structure

Answer 19

Sequence of amino acid residues coded by the DNA in living systems, Involves covalent bonds in the peptide (amide) bonds between amino acid residues

Question 20

Secondary structure

Answer 20

Caused solely by the hydrogen bonding between the oxygens and nitrogens in the amide bond (backbone), Nature of the R group (it its bulky and prevents movement of the peptide chain) affects the type of secondary structure present

Question 21

Types of secondary structure

Answer 21

Alpha helix, beta sheet (parallel), antiparallel beta-sheet, random coil

Question 22

Alpha helix

Answer 22

Formed when residues in the same region of a peptide undergo hydrogen bonding, Oxygen atoms from an amide bond form hydrogen bonds with a NH4 amino acid residues further along the chain

Question 23

Beta pleated sheet

Answer 23

Occurs when there is hydrogen bonding between =O and HN- on the peptide backbone of the protein, Hydrogens and oxygens on ‘R’ groups don’t participate in beta sheet formation as they are in the wrong geometric plan to do this, Two forms: Parallel- where the hydrogen bonds are zig-zag, Anti-parallel- where hydrogen bonds line up straight (more stable as there is less stress on the hydrogen bonds)

Question 24

Random coil

Answer 24

“No” secondary structure, No hydrogen bonds

Question 25

Tertiary structure (5 bonds)

Answer 25

Way the lower levels of structure (primary, helices and sheets) are organised , Determined by interactions between side chains of amino acid residues, Involves dispersion forces (hydrophobic interactions), dipole-dipole bonds, hydrogen bonds, ionic (salt bridges) and covalent bonding (disulfide bridges between cysteine residues)

Question 26

Hydrophobic interactions (dispersion forces)

Answer 26

non-polar side groups clump together (like oil in water), weak interaction

Question 27

Dipole-dipole bonds

Answer 27

polar side chains containing SH, OH, or NH

Question 28

Hydrogen bonds

Answer 28

Between basic amino acids (have an amine group in their side chains, eg. lysine) and those with an oxygen (eg. Serine)

Question 29

Salt bridges

Answer 29

between amino acids with carboxylate side chains and those with amine groups, consists of both electrostatic interactions and hydrogen bonding between oxygen and the hydrogen on the amine, stability is determined by pH which determines ionisation (ionic bond between acidic and basic)

Question 30

Disulfide bridges

Answer 30

formed by the oxidation of the thiol groups in two cysteine residues, strong covalent (primary) bond

Question 31

Enzymes

Answer 31

Types of proteins, Biological catalysts, Specific and depend on their 3-D structure (tertiary structure)

Question 32

Lock and key model

Answer 32

Active site- specific part of the enzyme with which a reactant can interact, Substrate- reactant molecule that binds with the active site

Question 33

Enzyme optimal conditions

Answer 33

Have an optimum pH range (usually around body range, 7.4) meaning extremely high or low pH values can cause an enzyme to denature as side chains accept or donate protons changing the tertiary structure, Eg- Normal Ph has an ionic salt bridge but when changed to low/high pH, the salt bridge picks up/donates a proton and becomes an ion-dipole interaction (secondary bond, unfolds), Have an optimum temperature between 30-40 degrees, As temperature increases, average kinetic energy increases and disrupts the tertiary structure as some interactions between side chains are held together by weak intermolecular forces (kinetic energy overcomes weak forces)

Question 34

Denaturation

Answer 34

Change in tertiary structure causes a change in the shape of the active site meaning the enzyme loses its catalytic activity, Irreversible

Question 35

Advantages of enzymes (4)

Answer 35

Specific meaning they only catalyse one particular reaction or type of reaction, Effective at biological temperatures and pH which saves energy and cost as high temperatures and pressures aren’t required, Not consumed in the reaction meaning they can be used for a long period of time, Biodegradable meaning less environmental pollution

Question 36

Disadvantages of enzymes (4)

Answer 36

Sensitive to changes in temperature and pH meaning reaction conditions must be tightly controlled, Certain chemicals can change the structure of enzymes and cause them to lose their function, Can be expensive to produce, Reactions generally take place in aqueous solutions meaning it can be difficult to separate the products from the reaction mixture