Amino Acids & Peptides

Question 1

Proteins: Main Agents of Biological Function

Answer 1

• Proteins rely on the recognition of specific 3D molecular shapes to function correctly for DEFENSE, TRANSPORT, ENZYMES, STRUCTURE, STORAGE, and COMMUNICATION.
• Proteins are the most abundant biological macromolecules
• -> Proteins occur in all cells and all parts of cells.
• Proteins also occur in great variety
• Proteins Serve a Wide Range of Biological Functions

Question 2

Examples of proteins with different functions

Answer 2

The light produced by fireflies is the result of a reaction involving luciferin and ATP, catalyzed by the enzyme luciferase–> reaãço fotoluminescente

The protein keratin, formed by all vertebrates, is the main structural component of hair, scales, horn, wool, nails, and feathers

Erythrocytes contain large amounts of the oxygen-transporting and heme- containing protein hemoglobin.

Question 3

AA

Answer 3

All proteins are made out of 21 building blocks, called amino acids.

Amino acids are made of carbon, oxygen, nitrogen, and hydrogen, and some contain sulfur atoms. Selenocysteine is the only standard amino acid that contains a selenium atom.

Question 4

AA structure

Answer 4

Amino Acids Share Many Features, Differing Only at the R Substituent

• The α carbon always has four substituents and is tetrahedral.
• All (except proline) have:
-an acidic carboxyl group
connected to the α carbon
-a basic amino group
connected to the α carbon
-an α hydrogen connected to
the α carbon
-The fourth substituent (R) is unique in glycine, the simplest amino acid. The fourth substituent is also hydrogen.

Question 5

AA stereochemistry

Answer 5

All Amino Acids Are Chiral (Except Glycine) + Proteins only contain L amino acids!

The formation of stable, repeating substructures in proteins requires that their constituent amino acids be of one stereochemical series.
Cells are able to specifically synthesize the L isomers of amino acids.
This is possible because the active sites of enzymes are asymmetric, causing the reactions they catalyze to be stereospecific

Question 6

AA classification

Answer 6

Common amino acids can be placed in five basic groups depending on their R substituents:
• nonpolar, aliphatic (7)
• aromatic (3)
• polar, uncharged(5)
• positively charged(3)
• negatively charged(2)

Question 7

Proline

Answer 7

is an imino acid!
In chemistry, an imino acid is any molecule that contains both imine and carboxyl functional groups.

The distinctive cyclic structure of proline’s side chain gives proline an exceptional conformational rigidity compared to other amino acids. –> consequências na flexibilidade das zonas da proteina onde está inserida
It also affects the rate of peptide bond formation between proline and other amino acids.

Question 8

Aromatic AAs

Answer 8

The aromatic amino acid chains absorb UV light at 270-280 nm

This is a useful property to detect the presence of proteins by measuring the absorbance

Question 9

Polar, uncharged AAs

Answer 9

• Can form hydrogen bonds
• interact well with water.
• Cysteine can form disulfide bonds

Question 10

Charged AAs

Answer 10

Charged amino acids interact with oppositely charged amino acids or other molecules.

Question 11

Ionization of AAs

Answer 11

Amino acids contain at least two ionizable protons, each with its own pKa

The carboxylic acid has an acidic pKa and will be protonated at an acidic (low) pH
deprotonation:
−COOH ↔ COO− + H+

The amino group has a basic pKa and will be protonated until basic pH (high) is achieved:
deprotonation:
−NH3+ ↔ NH2 + H+

A pH neutro: forma zwitteriónica

Chemical Environment Affects pKa Values
alpha-carboxy group is much more acidic than in carboxylic acids.
alpha-amino group is slightly less basic than in amines.

Question 12

Titration of an AA

Answer 12

Ponto Isoelétrico: Carga da molécula= 0 (Quando titulamos com… equivalente(?))

Se AA tiver cadeia lateral ionizável (Como Histidina):
• Ionizable side chains influence the pI of the amino acid.
• Ionizable side chains can be
also titrated.
• Titration curves are now more
complex, as each pKa has a buffering zone of 2 pH units.
Há mais valores de pKa, 3 grupos a serem desprotonados;
Cadeia lateral corresponde ao ponto intermédio de pKa

Question 13

Peptides

Answer 13

Amino Acids Polymerize to Form Peptides
• Peptides are small condensation products of amino acids.
• They are “small” compared with proteins (Mw < 10 kDa).

Numbering (and naming) starts from the amino terminus (N-terminal) –> carboxyl-terminal end.

Question 14

Peptides: A variety of functions

Answer 14

Hormones and pheromones
• insulin (think sugar metabolism)
• oxytocin (think childbirth)
• sex-peptide (think fruit fly mating)

Neuropeptides
• substance P (pain mediator)
This pentapeptide, Leu- enkephalin, is an opioid peptide that modulates the perception of pain.

Antibiotics
• polymyxin B (for Gram – bacteria)
• bacitracin (for Gram + bacteria)

Protection/toxins
• amanitin (mushrooms)
• conotoxin (cone snails)
• chlorotoxin (scorpions)

Question 15

Disulfide bonds

Answer 15

A disulfide bond, also called an S-S bond, or disulfide bridge, is a covalent bond derived from two thiol groups (from Cys residues)
Depende do estado de oxidação: para quebrar= reduzir, adiciona-se um agente redutor como Ditiotritol (DTT)

Insulin contains disulfide bonds