Protein Structure and Function

Question 1

Amino Acid

Answer 1

An amino acids is simply a Carbon attached to a Hydrogen, a Carboxyl, an Amino group, and a “R-group”/Side chain.

This happens because Carbon can form 4 bonds.

It is called amino acid because:
Amino Group (a Base)
Carboxyl (an acid)

It can be ionized or non-ionized.
When Ionized, the Carboxyl loses the Proton from (COOH) to (COO-)
and the amino group GAINS a proton from (NH2) to (NH3+)

Question 2

Why are some amino acids polar and some are non-polar?

Answer 2

The R-group/Side chain affects the polarity of the amino acid. The polarity will alter its behavior in water (hydrophobic or hydrophilic)

Question 3

What are the four groups of atom(s) that bond to Carbon in an amino acid?

Answer 3

1. NH2 - the amino functional group
2. COOH - the carboxyl functional group
3. H - a hydrogen atom
4. “R-group” - an atom or group of atoms called a side chain

Question 4

How do amino acids link to form proteins?

Answer 4

Amino acids link through polymerization that occurs as a result of condensation. In this process, two hydrogens and oxygen form water and are replaced by another monomer.

Question 5

What is the role of the R-Group?

Answer 5

The R-groups vary in each amino acid from a single hydrogen atom to large structures containing carbon atoms linked into rings. All amino acids have a carbon atom bonded to an amino group, a hydrogen atom and a carboxyl group, but each R-group is unique.

The properties of amino acids vary because their R-groups vary.

Question 6

What affect does the polarity of the side chain have on solubility?

Answer 6

The nature of the R-group affects how soluble the amino acid is in water.

Amino acids with nonpolar side chains lack charged or electronegative atoms capable of forming hydrogen bonds with water - making them hydrophobic

Amino Acids with polar or charged side chains interact readily with water and are hydrophilic - dissolving easily in water!

Question 7

What is a peptide bond?

Answer 7

A peptide bond forms when the carboxyl group of one amino acid reacts with the amino group of another amino acid. This bonding creates polypeptide molecules.

Question 8

What are the three major characteristics of a polypeptide molecule?

Answer 8

1. The polypeptide chain has a peptide-bonded backbone. The R-group orientation extends from the backbone, which allows these side chains to interact with each other and with water.
2. Directionality is always
   N-Terminous/amino-terminus to C-terminous/carboxyl-terminus

Question 9

What is an oligopeptide?

Answer 9

When fewer than 50 amino acids are liked together. At this point they may also be called just peptides.

Question 10

When does a polypeptide become a protein?

Answer 10

When the polypeptide contains more than 50 amino acids. This can consist of single polypeptides or multiple polypeptides bonded to one another.

Question 11

What are the primary tasks of the protein?

Answer 11

1. Catalysis (enzymes)
2. Defense (anitbodies)
3. Movement (motor proteins)
4. Signaling (Carrying and receiving signals)
5. Structure (fingernails, hair, blood cells)
6. Transport (hemoglobin)

Question 12

Catalysis

Answer 12

Acceleration of the rate of a chemical reaction due to a decrease in the free energy of the transition state (activation energy)

Question 13

Four basic structures of all proteins:

Answer 13

1. Primary: Sequence of amino acids
2. Secondary: Hydrogen bonding between peptide chains and the helix and pleated sheets form when it coils and folds in on itself
3. Tertiary: interactions between the backbone and the side chains, and between side chains form a three-dimensional shape of a polypeptide. *hydrogen bonds, van der wallas, interactions, and covalent bonds, ionic bonds)
4. Quaternary: Many protines contain several distict polypeptides that interact to form a single complex protein

Question 14

What is ribonuclease?

Answer 14

An enzyme that breaks ribonucleic acid polymers apart.

Question 15

What is a prion?

Answer 15

Prions are improperly folded proteins. All prion illnesses are fatal.

Question 16

What is a substrate

Answer 16

A reactant that interacts with an enzyme in a chemical reaction.

Question 17

What is an optical isomer?

Answer 17

Each of two ore more forms of a compound that has the same structure but are mirror images of each other and differ in optical activity

Question 18

active site

Answer 18

Where substrates bind and react and catalysis occurs

Question 19

activation energy

Answer 19

The amount of free energy required to reach the transition state

Question 20

transition energy

Answer 20

The intermediate condition between the combination of old and new bonds

Question 21

denatured

Answer 21

unfolded secondary and tertiary structure

Question 22

molecular chaperone

Answer 22

A protein that facilitates the three-demensional folding of newly synthesized proteins (usually by an ATP-dependent mechanism)

Question 23

induced fit

Answer 23

The change in the shape of the active site of an enzyme as the result of the initial weak binding of the substrate, so that it binds substrate more tightly

Question 24

What is the three step process of enzyme catalysis

Answer 24

1. Initiation
2. Transition state facilitation
3. Termination

Question 25

do enzymes act alone?

Answer 25

no, there are enzyme cofactors or coenzymes that play a role in stabilizing the transition state at the active site.

Question 26

competitive inhibition

Answer 26

PART OF ENZYME REGULATION
A molecule that is similar in size and shape to a substrate may bind to the active site and inhibit the binding of the substrate - this is called competitive inhibition (Cock block?) because they compete with the substrate for access to the enzymes actives site

Question 27

allosteric regulation

Answer 27

PART OF ENZYME REGULATION
regulatory molecules may bind at a location other than the active site to change the shape of the enzyme in a way that makes the active site accessible (allosteric activation) or inaccessible (allosteric deactivation)
Like traffic cops?