Proteins

Question 1

What are proteins?

Answer 1

Are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. A term used to describe amino acid chains in the complete, functional form of molecule. Have unparalleled diversity of size, shape, and chemical properties of amino acid residues.

Question 2

What is an enzyme?

Answer 2

Are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) it acts on. The enzyme may help in breakdown, rearrangement, or synthesis reactions. All enzymes increase the rate of reaction and, therefore, are considered to be organic catalysts. Protein shape is critical to its function, and this shape is maintained by many different types of chemical bonds.

Question 3

What are catabolic enzymes?

Answer 3

Enzymes that break down their substrates.

Question 4

What are anabolic enzymes?

Answer 4

Enzymes that build more complex molecules from their substrates.

Question 5

What are catalytic enzymes?

Answer 5

Enzymes that affect the rate of reaction

Question 6

What is denaturation?

Answer 6

Permanent changes in the shape of a protein & the loss of function due to changes in temperature, pH, and exposure to chemicals.

Question 7

What are Amino acids?

Answer 7

Monomers that make up proteins. Only 20 types of amino acids make up a protein.

Question 8

What are the 3 functional groups attached to a central (α) Carbon molecule?

Answer 8

1. Amino group (NH2)
2. Carboxyl group (C O O H)
3. R group—“side chain”

Question 9

Which of the 3 functional groups is different depending on the amino acid?

Answer 9

The R group is the only one that varies between Amino acids.

Question 10

Why is the R-group or side chain important?

Answer 10

Represent part of amino acid core structure that makes each of 20 amino acids unique. Properties of amino acids vary because R-groups vary.
Side chains contain functional groups that can participate in chemical reactions. & some side chains have no functional groups that solely consist of carbon and hydrogen atoms.

Question 11

Do amino acids always have a neutral charge? If not, what are a few things that may change the charge of an amino acid?

Answer 11

No b/c it depends on the ionization of Amino Acids. In water (pH 7), the amino and carboxyl groups ionize to NH3+ (Positive Charge [Gained Hydrogen])and COO– (Negative charge [lost Hydrogen]), which helps amino acids stay in solution and makes them more reactive.

Question 12

What characteristics of an R-group may make it unique? How do R-groups affect solubility in water?

Answer 12

Its charge & polarity make it unique.

Polar and charged R-groups interact with water—are hydrophilic (water loving)
Nonpolar R-groups are hydrophobic (water fearing)—do not form hydrogen bonds with water.

Question 13

How do amino acids link together? What type of bond forms and what compound is released?

Answer 13

Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water. The resulting bond is the peptide bond.

Question 14

What is a peptide chain called when it polymerizes?

Answer 14

A polypeptide

Question 15

When do Amino acids polymerize?

Answer 15

When a peptide bond forms between carboxyl group of one amino acid and an amino group of another

Question 16

What is a dipeptide?

Answer 16

2 Amino acids

Question 17

What is a oligopeptide?

Answer 17

< 50 Amino acids

Question 18

What is a polypeptide?

Answer 18

> 50 Amino acids

Question 19

How do you number a polypeptide chain?

Answer 19

For the purpose of numbering the amino acid links, always start at the N-terminus (Amino end) & end at C-terminus (Carboxyl end).

Question 20

Why do Amino acids polymerize?

Answer 20

To form polypeptide chains.

Question 21

Could amino acids have joined into proteins during the formation of early earth? What hurdles could have prevented this from happening?

Answer 21

Unclear for proteins to be formed, BUT were able to generate stable polymers in lab using free amino acids. Observed amino acids being formed and even polymerized under hot, metal-rich conditions.
Join amino acids into polymers in cooler water with energy-rich carbon and sulfur gases.
To achieve attributes of life, proteins would need to replicate, evolve, and possess information. Nucleic acids do however.

Question 22

What are the 4 levels of protein structures?

Answer 22

1. Primary
2. Secondary
3. Tertiary
4. Quaternary

Question 23

In the Primary structure:
What is it and what do proteins look like after this structure is complete?
What types of bonds/interactions are primarily responsible for creating this structure?

Answer 23

It is the unique sequence of amino acids in a polypeptide chain. They look like beads. Each unique sequence for every protein is ultimately determined by the gene encoding the protein.
They are stabilized by peptide bonds.

Question 24

In the Secondary structure:
What is it and what do proteins look like after this structure is complete?
What types of bonds/interactions are primarily responsible for creating this structure?

Answer 24

The local folding of the polypeptide in some regions to form α-helix (alpha-helix) or β-pleated sheet (beta-pleated sheets).
It is formed by hydrogen bonds between a Carbonyl group of one amino acid & an Amino group of another amino acid. Occurs a long the peptide- bonded backbone

Question 25

In the Tertiary structure:
What is it and what do proteins look like after this structure is complete?
What types of bonds/interactions are primarily responsible for creating this structure?

Answer 25

Bending and folding contribute to distinctive three-dimensional shape of polypeptide.
Results from interactions between R-groups, or b/w R-groups & polypeptide-bonded backbone. These interactions cause the backbone to bend and fold. :
​1. Hydrogen bonding—form between polar side chains and opposite partial charges
2. ​Hydrophobic interactions—water forces hydrophobic side chains together
​3. van der Waals interactions—weak electrical interactions between hydrophobic side chains
4. ​Covalent bonding—covalent bonds between side chains of sulfhydryl groups (disulfide bonds)
​5. Ionic bonding—form between groups with full and opposing charges

Question 26

In the Quaternary structure:
What is it and what do proteins look like after this structure is complete?
What types of bonds/interactions are primarily responsible for creating this structure?

Answer 26

Bonding of two or more distinct polypeptides together. Shape produced by a combination of polypeptides (thus combinations of tertiary structures). Some cells contain molecular machines:
Complex of multiple proteins that carry out a particular function.
Bonds & other interactions b/w R-groups, & b/w peptide- backbones of diff. polypeptides

Question 27

What disease is caused as a result of a small change to the primary structure of a polypeptide chain? Why is primary structure absolutely critical?

Answer 27

Sickle Cell Anemia. Change in only ONE AMINO ACID produces hemoglobin molecules that stick to one another. Hemoglobin molecules form long fibers that distort the biconcave, or disc-shaped, red blood cells and assume a crescent or “sickle” shape, which clogs arteries
A Single amino acid change can radically alter protein function.

Question 28

What are the two main secondary structures of proteins? (be able to recognize and/or draw each)

Answer 28

1. α-helix (alpha-helix)
2. β-pleated sheet (beta-pleated sheets

Question 29

What is a subunit? Which level of structure is comprised of subunits?

Answer 29

Each distinct polypeptide. The Quaternary structure is composed of subunits.

Question 30

What is denaturation and why does it happen? What are 4 causes of denaturation?

Answer 30

Denatured (unfolded) proteins unable to function normally due to protein structure change:
1. Temp. Increase or decrease will possibly cause bonds to be disrupted.
2. pH. Disrupt the pattern of ionic attractions & repulsions that contribute to tertiary structures.
3. Salt concentration. Disrupt the pattern of ionic attractions & repulsions.
4. Solvents (liquids that dissolve)

Question 30

How does protein folding occur? Why don’t proteins just stay unfolded?

Answer 30

Normal protein folding is crucial and often spontaneous. They are a result of chemical bonds and interactions.
B/c folded molecules are more energetically stable than unfolded molecules.

Question 31

What are prions and why are they harmful? What are some diseases caused by prions?

Answer 31

They are proteins that have folded incorrectly. Normal proteins can be induced to fold into infectious, disease-causing agents called prions. Prions can induce normal protein molecules to change their shape to the altered form
Prion protein (PrP)- responsible for ”mad cow disease”
Huntington’s Disease, Parkinson’s Disease & Alzheimer’s Disease

Question 32

What are molecular chaperones and why are they important?

Answer 32

They facilitate protein folding.
EX: TRiC, a molecular chaperone which folds Htt proteins. When these proteins aren’t folded properly, Huntington’s Disease develops.

Question 33

What are 7 important functions of folded proteins?

Answer 33

1. Structural proteins- hold us together
2. Enzymes- catalyze specific reactions
3. Immune proteins- antibodies and complements
4. Hormones- messengers
5. Motor proteins – muscles
6. Receptor proteins– receive and deliver signals
7. Transport proteins – gatekeepers of the cell membrane

Question 34

Exergonic reactions…

Answer 34

release energy. This reaction will proceed.

Question 35

Endergonic reactions…

Answer 35

absorb energy. This reaction will not proceed.

Question 36

What is activation energy?

Answer 36

The energy needed to START a chemical reaction. The energy needed to get past the transition state

Question 36

What is a catalyst?

Answer 36

They are compounds that make a reaction go faster by lowering the activation energy of the reaction. Enzymes are an example. Catalysis can also be inorganic molecules. Catalysts do NOT get used up in a reaction.

Question 37

What is the lock-&-key model?

Answer 37

Substrate(s) fits like a lock-and-key because active site exactly matches the shape of the substrate(s).
Reaction takes place when enzyme and substrate(s) are bound 🡪 products are released.
Enzymes are usually specific to one reaction.

Question 38

What are the regulators of enzyme rates

Answer 38

1. Concentration of reactants
2. Environmental factors –temp, pH. Enzymes function best at some particular temperature and pH. The ideal temperature and pH for an enzyme usually reflects the environment in which an enzyme is expected to function.
3. Competitive inhibitors. Occurs when a molecule similar in size and shape to the substrate competes with the substrate for active site binding. “If it fits, it sits”
4. Allosteric regulators or noncompetitive inhibitors. Occurs when a molecule causes a change in enzyme shape by binding to the enzyme at a location other than the active site. Either increases or decreases enzyme activity depending on the way in which enzyme shape changes.

Question 39

What are cofactors?

Answer 39

Metal ions. Usually are in the active site and are involved in transition state stabilization.

Question 40

What are coenzymes?

Answer 40

Small organic molecules. Vitamins or minerals