Chapter 19 2.0

Primary Structure

• Refers to the linear sequence of amino acids in a protein, which is determined by the corresponding gene. The primary structure dictates the protein's unique characteristics and ultimately influences its three-dimensional shape.

• Refers to the peptide bonds between the amino acids

Secondary Structure

• Describes the local folded structures that form within a protein due to interactions between nearby amino acids, typically including alpha helices and beta sheets.

• Achieved when hydrogen bonds form between the carboxyl group of one amino acid and the amino group of a different amino acid

• held by hydrogen bonds

Tertiary Structure

• Refers to the three-dimensional shape of a protein that results from interactions and bonds between the side chains (R groups) of the amino acids. This structure is critical for the protein's functionality.

Quaternary Structure

• Refers to the complex formed when two or more polypeptide chains aggregate and interact to form a functional protein. This structure is essential for the activity of many proteins.

• ex: Hemoglobin

Structural

characteristic of protein: Collagen in tendons, keratin in hair

Contractile

characteristic of protein: Myosin and actin make muscles move

Transport

characteristic of protein: Hemoglobin carries oxygen, lipoproteins transport lipids.

Storage

characteristic of protein: Casein in milk, ferritin stores iron in the body.

Hormonal

characteristic of protein: Insulin regulates blood glucose, growth hormone for body growth.

Enzymes

characteristic of protein: Sucrase, amylase and trypsin facilitate biochemical reactions

Protection

characteristic of protein: Antibodies defend against pathogens, and fibrinogen helps in blood clotting.

Amino acids

• building blocks of proteins that link together to form polypeptides and ultimately proteins, playing key roles in various biological functions.

• two functional groups: ammonium (+) and carboxylate (-)

Polar neutral

• amino acids contain hydroxyl, thiol, or amide R groups

• ex: Serine (Ser), Threonine (Thr), Tyrosine (Tyr), Cysteine (Cys), Asparagine (Asn), Glutamine (Gln)

Polar acidic

• amino acids contain a carboxylate R group

• ex: Aspartate (Asp), Glutamate (Glu)

Polar basic

• amino acids contain an ammonium R group

• ex: Histidine (His), Lysine (Lys), Arginine (Arg)

Essential amino acids

• are 9 amino acids that cannot be synthesized by the body and must be obtained through diet. These include lysine, methionine, and tryptophan.

• complete proteins

Hydrophobic Interactions

• are nonpolar interactions that occur when hydrophobic molecules aggregate together in aqueous environments to minimize their exposure to water.

• helps stabilize tertiary and quaternary structures

Hydrophilic interactions

• are polar interactions where hydrophilic molecules interact favorably with water, often forming hydrogen bonds.

• These interactions are crucial for maintaining the solubility and stability of proteins and other biomolecules in an aqueous environment.

Salt bridges

• are ionic interactions between charged side chains of amino acids (polar basic and polar acidic), stabilizing protein structure.

• can be seen in tertiary structures.

Hydrogen bonds

Bond formed between the H of a polar R group and the O or N of another polar amino acid

Disulfide Bonds

are covalent links formed between the SH groups of two cysteine residues in polypeptide chain, providing stability to protein structure.

Hemoglobin

• A protein in red blood cells that carries oxygen from the lungs to the body's tissues and returns carbon dioxide from the tissues back to the lungs.

• Consists of four polypeptide chains: two alpha chains and two beta chains

• example of quaternary structure

Myoglobin

carries oxygen in muscle tissue, similar to hemoglobin but with one polypeptide chain (one oxygen molecule).

Protein Denaturants

• high temp

• low or high pH

• addition of a heavy metal ion

• addition of certain organic compounds

• mechanical agitation

Proteins

• large molecules made up of amino acids, essential for various biological functions, including the structure, function, and regulation of tissues and organs.

• composed from a set of twenty amino acids, made more of 50 amino acids

• polyamides

Zwitterion

a molecule that has both positive and negative charges but is overall neutral. It typically occurs in amino acids and other compounds where the functional groups can ionize.

Serine

is a polar amino acid with a hydroxymethyl group, essential for protein synthesis and involved in the active sites of enzymes.

Tyrosine

an aromatic (phenol functional group) amino acid that contains a phenolic hydroxyl group, important for protein synthesis and the precursor of neurotransmitters such as dopamine.

Non polar

• amino acids that do not interact favorably with water, often found in the interior of proteins.

• ex: tyrosine

+2

charge of glutamic acid at pH 10 is

C-terminus

the end of a peptide or protein chain with a free carboxyl group (-COOH). It typically determines the directionality of protein synthesis.

Collagen structure

triple helix

Polar

• A type of molecule that has a partial positive charge on one end and a partial negative charge on the other, resulting in an ability to interact with water and other polar substances.

• ex: Cysteine and aspartic

Bite salts

Synthesized from cholesterol

Valine

An essential amino acid that is one of the three branched-chain amino acids (BCAAs) important for muscle metabolism.

Salt bridges AND hydrogen bonds

Acids and bases denature a protein by disrupting….

Hydrophobic and hydrogen bonds

Heat denatures a protein by disrupting….

Peptide (amide) bond

a covalent chemical bond linking two consecutive amino acid monomers along a peptide or protein chain.

Dipeptides

formed by two amino acids linked by a peptide bond.

Tripeptides

composed of three amino acids linked by 2 peptide bonds.

Tetrapeptides

formed by four amino acids linked by three peptide bonds.

Polypeptide

a long, continuous, and unbranched peptide chain of many amino acids linked by peptide bonds, typically composed of more than four.