WEEK 2 (1.7)

Question 1

What are the components of an amino acid?

Answer 1

1. Alpha C connected by covalent bonds to:

• Amino group gains a proton → becomes NH3+
• Carboxyl group: loses a proton → becomes COO-
• H atom
• Side chain: differ from one amino acid to the next and makes each one of them different from the other (chemical and physical properties)

Grouped according to their properties (hydrophilic or hydrophobic; special characteristics that may affect protein’s structure)

Question 2

What are the characteristics of hydrophobic amino acids?

Answer 2

Don’t form H bonds with water → have nonpolar R groups (hydrocarbon chains or uncharged C rings)
→ Since water molecules in the cell form H bonds with each other instead of the hydrophobic R group = R groups tend to aggregate with each other (stabilized by VDW)
→ Most hydrophobic amino acids tend to be buried in the interior of folded proteins

Question 3

What are the characteristics of hydrophilic amino acids?

Answer 3

Amino acids with polar R groups have a permanent charge separation (one end is slightly more negatively charged than the other)
- Tend to form H bonds with each other or water
- R groups of basic and acidic amino acids are typically charged

At pH of cell
- R group of basic amino acids gain a proton: positively charged
- R group of acidic amino acids lose a proton: negatively charged
→ Due to charge, they are located on the outside surface of protein
→ Charged groups can also form ionic bonds with each other and other charged molecules in the environment (important for proteins to associate with each other and other molecules - DNA)

Question 4

What are the special properties of glycine?

Answer 4

Glycine: R group is a H → not asymmetric (all others have a 4 different groups attached to the alpha-C)
Nonpolar and small enough to tuck into spaces where other R groups wouldn’t fit
Small size of R group: freer rotation around the C-N bond since the R group doesn’t get in the way of other R groups of neighbouring amino acids = increases flexibility of polypeptide backbone → important for protein folding

Question 5

What are the special characteristics of proline?

Answer 5

Proline: R group is linked back to the amino group → creates a kink in polipeptide chain and restricts rotation of C-N bond → constraints on protein folding

Question 6

What are the special characteristics of cysteine?

Answer 6

Cysteine: when 2 cysteine side chains of the same of different polypeptides come into proximity → create S-S (covalently joins the side chains)
Form cross-bridges that can connect different parts of the same protein or different proteins → contributes to the overall structure

Question 7

What are the characteristics of a peptide bond?

Answer 7

→ Amino acids are linked together to form proteins through peptide bonds

Carboxyl group of one amino acid reacts with the amino group of the next amino acid → water is released and the resulting molecule, the R groups of each amino acid point in different directions

C=O → carbonyl group and N-H → amine group (electrons of the peptide bond are more attracted towards the carbonyl group due to the greater electronegativity of O)

Question 8

What does primary structure refer to?

Answer 8

Primary structure: sequence of amino acids that makes up a protein (ultimately determines how a protein folds)
Primary dictates the secondary and tertiary structures

Question 9

What does secondary structure refer to?

Answer 9

Secondary structure: interaction between stretches of amino acids in a protein
H bonds can form between the carbonyl group in one peptide bond and the amine group in another = localized regions for the protein to fold (major contribution of this structure)

Question 10

What are the 2 types of secondary structure?

Answer 10

2 types of secondary structure found in many proteins: alpha and beta → both stabilized by H bond along polypeptide

Alpha helices: polypeptide backbone is twisted tightly in a right-handed coli
- Stabilized by H bond between the amino acid’s carbonyl group and the amide group four residues ahead
- R groups project outward the helix (chemical properties of the R group determines where the helix is positioned in the folded protein and how it interacts with other molecules)

Beta sheet: polypeptide folds back and forth on itself → pleated sheet that is stabilized by H bonds between carbonyl groups in one chain and amide groups in the other across
-R groups project alternately above and below
- Polypeptide chains are said to be antiparallel (one chain goes from left to right and the one across from right to left)
- B sheet can occur in parallel chains, but antiparallel is more favourable since the amide and carbonyl groups are more aligned for h bonding
Rely mainly on interactions in the polypeptide backbone (relatively independent from the R group)

Question 11

What does tertiary structure refer to?

Answer 11

Tertiary structure: longer-range interactions between secondary structures support the overall 3D shape of the polypeptide
- Regardless of the many functions that a protein can carry out, the ability to perform its function depends on the 3D shape of the protein
- 3D conformation of a single polypeptide chain made up of several secondary structure elements
- Largely defined by interactions between the amino acids R groups
- Determined by spatial distribution of hydrophilic and hydrophobic R groups along the molecule + chemical bonds and interactions between R groups
- R groups may be far apart in the chain, but end up near each other in a folded protein (loops or turns)

Question 12

What does quaternary structure refer to?

Answer 12

Quaternary structure: several individual polypeptides that interact with each other
→ When fully folded:
-Some contain pockets with positively or negatively charged side chains at the right position to trap molecules
-Others have surfaces that can bond to another protein or sequence of nucleotides
-Some form structural rids for structural support
-Others keep hydrophobic side chains away from water by inserting into the cell membrane
-Even though some proteins are fully functional as single polypeptide chains, others are composed of 2 or more polypeptide chains that come together in their tertiary form (subunits could be identical or different)
→ Amino acids in a protein are listed from left to right (start from amino end and proceeding to the carboxyl end)

Question 13

What does denatured mean in a protein?

Answer 13

Denatured: unfolded proteins due to chemical treatment or high temperature that disrupts the H and ionic bonds holding the tertiary structure together → lose function
Mutant proteins (amino acids that prevent proper folding) often inactive or don’t function properly

Question 14

What are chaperones?

Answer 14

→ The longer polypeptides remain in denatured state, the longer their hydrophobic groups are exposed to other macromolecules
Hydrophobic effect + VDW interactions tends to bring exposed hydrophobic groups together → inappropriate aggregation may prevent proper folding

Chaperones: helps protect slow-folding or denatured proteins until they can attain proper three-dimensional structure
Bind with hydrophobic groups and nonpolar R groups to shield them from inappropriate aggregation → cycles of binding and release give polypeptide time to find correct shape

Question 15

What is a catalyst?

Answer 15

Catalysts: substances that increase the rate of chemical reactions without themselves being consumed → in biological systems, these are enzymes (proteins)

• Enzymes are highly specific → act only on certain reactants and catalyze only some reactions; hence, they determine the reactions that take place in the cell
• Enzymes recognize a unique substrate or a class of substrates that share a common chemical structure (only one reaction)

Question 16

What is the difference between endergonic and exergonic reactions?

Answer 16

Endergonic reaction: require free energy
Exergonic reaction: release free energy (energy released is more than the initial input, so there is a net release)

Question 17

What energies drive a spontaneous reaction?

Answer 17

→ Regardless, all chemical reactions require an initial input of energy to proceed (activation energy → transition state → reaction can proceed)

• As chemical reactions proceed, existing chemical bonds break and new form → brief period of time, a compound is formed where old bonds are breaking and new ones are forming (transition state: intermediate between reactants and products → highly unstable; thus, has a large amount of energy)
• All chemical reactions, reactants adopt at least one transition state before their conversion into products

Spontaneous → free energy of reactant is higher than free energy of product and delta G is negative
Highest free energy value corresponds to transition state
In order to reach “transition state” → reactant must absorb energy from surroundings = all rations require energy in order to reach the transition state (activation energy)
Once transition state is reached → reaction proceeds

Question 18

What is the correlation between the energy barrier and the rate of reaction?

Answer 18

Lower the energy barrier, the faster the reaction
Higher the energy barrier, the slower the reaction

Question 19

How do enzymes work?

Answer 19

→ Reduce activation energy by stabilizing transition state and decreasing free energy
- Even through enzymes reduce the activation energy, the difference in free energy between reactants and products doesn’t change
Complex: enzyme + reactants and products
Substrate: reactant of a reaction and this is converted into a product
→ Presence of an enzyme
Substrate first forms a complex with the enzyme, while the substrate is converted to product
Complex dissociates: releases enzyme and product
S+E ESEPE +P

Answer 20

Folded into three-dimensional shapes that bring amino acids into close proximity to form an active site

Active site: part of the enzyme that binds substrate and catalyzes its conversion to the product
- Here, enzyme and substrate form transient covalent bonds, weak noncovalent interactions, or both (these interactions stabilize the transition state and decrease activation energy)

• Enzymes also reduce activation energy by positioning 2 substrates to react
• Enzymes area large in size to bring the catalytic amino acids into very specific positions in the active site of folded enzyme

Question 21

What are allostretic enzymes?

Answer 21

Allostretic enzymes: enzymes that are regulated by molecules that bind at sites other than active sites → play key role in the regulation of metabolic pathways
When a reaction has reached the desired production of a product and there is no need to maintain the production going, the inhibitor binds to the first enzyme to cease the pathway and stop production of products

Question 22

What are inhibitor and activators?

Answer 22

Inhibitors: decrease activity of enzymes
Irreversible: form covalent bonds with enzymes and irreversibly inactivate them
Reversible: weak bonds with enzymes and can dissociate from them
→ Some cases, inhibitors has a similar structure to the substrate = able to bind to the active site
Binding of inhibitor prevent binding of substrate (competitive inhibition) → solved by increasing amount of substrate
→ Others bind to a site other than the active site and inhibit the activity of the enzyme → binding of inhibitor changes shape and activity of the enzyme (different shape than substrate)

Activators: increase activity of enzymes

Question 23

How are amino acids numbered?

Answer 23

Numerically, starting from the N-terminus

Question 24

What does the backbone of an amino acid refer to?

Answer 24

Consisting of the peptide bonds (all except for the side chains)
- The side chains stick out from the backbone (their chemical properties are the ones responsible for folding a protein)