Biochemistry: Amino Acids and Proteins

Amino Acids/Proteins

• Proteins/polypeptides are chains formed by the condensation/combination of 20 different α-amino acids.
• Polypeptides can be di-, tri-, etc., up to 10 amino acids.
• Proteins are longer than 10 amino acid units, with molecular weights greater than 10,000.
• Amino acids have both a carboxyl group (-COOH) and an amino group (-NH₂).
• All amino acids in proteins have the -NH₂ group attached to the α-carbon of the -COOH group.
• All naturally occurring α-amino acids, except glycine, are chiral and the L-stereoisomer.
• There are 20 α-amino acids in naturally occurring proteins.
• Each amino acid has a common name often ending in "-ine".
• Approximately 150 other physiologically important amino acids exist, including GABA (a neurotransmitter).

Amino Acid Structure

• Amino acids are categorized based on the properties of their R groups.
• Nonpolar R groups (hydrophobic) include glycine, alanine, proline, valine, tryptophan, isoleucine, methionine, leucine, and phenylalanine.
• Polar R groups (hydrophilic) include serine, asparagine, glutamine, threonine, tyrosine, histidine, cysteine, aspartic acid, glutamic acid, lysine, and arginine.

Peptide Bonds

• Peptide bonds form when the carboxyl group of one amino acid reacts with the amino group of another amino acid, releasing a water molecule.
• This process is known as condensation.
• When peptide bonds are broken by hydrolysis, the hydroxyl and hydrogen from water are added to the amino acid.
• Dipeptides are formed by linking two amino acids.
• Tripeptides involve three amino acids.

pH Dependent Properties

• Zwitterionic structures in amino acids contain both N-H⁺ and COO⁻ groups.
• At low pH, the COO⁻ group is protonated.
• At higher pH, the N-H⁺ group loses a hydrogen ion.
• The isoelectric pH differs for each amino acid.

Protein Structure Levels

• Primary structure: the sequence of amino acids and the position of disulfide bridges in the polypeptide chain.
• Secondary structure: the conformation/shape of the backbone of the protein, which includes α-helices and β-sheets.
• Tertiary structure: the three-dimensional structure of the entire polypeptide chain.
• Quaternary structure: exists for proteins with more than one polypeptide chain, describing the arrangement of those chains.

Insulin

• Insulin is a protein with a specific amino acid sequence.

Hemoglobin and Myoglobin

• Hemoglobin has four polypeptide chains and possesses quaternary structure, carrying O₂, CO₂, and H⁺ in the blood.
• Myoglobin has a single amino acid chain (153) that carries O₂ from blood vessels to muscles.

Enzyme Structure

• Many enzymes are proteins.
• Their specific binding properties to a substrate depend on their overall molecular shape/conformation.

Protein Denaturation

• Denaturation is a process that changes protein structure, making it incapable of performing its normal function.
• Heating egg whites and permanent hair waving are examples of denaturation which can be irreversible or reversible.

Protein Classification

• Proteins are classified by structure into simple (fibrous and globular) and conjugated proteins (lipo-, glyco-, and hemo- proteins).
• Fibrous proteins (e.g., collagen, elastin, keratins, myosins) are insoluble and structural.
• Globular proteins (e.g., albumins, globulins, enzymes) are soluble and reactive.

Protein Functions

• Proteins perform diverse functions: enzymatic catalysis, muscle contraction, hormone transport (eg., insulin), neurotransmitter signaling , storing nutrients (eg., casein in milk), transporting other molecules (e.g., hemoglobin, transferring, ceruloplasmin), immunologic roles (eg., antibodies), hormones, enzymes, and as structural components.

(Non)Essential Amino Acids

• Essential amino acids (10) cannot be synthesized in the body and must be obtained from the diet (histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and arginine in infants).
• Non-essential amino acids (10) can be synthesized in the body from metabolic breakdown products.

Vegetarian Diets

• A key challenge in vegetarian diets is obtaining sufficient high-quality protein with a correct balance of essential amino acids.

Protein Content of Foods

• Different foods have varying protein contents (e.g., cheese has high, cassava has low).

Malnutrition

• Malnutrition is the inability to obtain sufficient complete proteins, specifically essential amino acids, hindering proper body function.
• Symptoms include emaciation, bloated abdomen, lack of pigmentation, and mental apathy, sometimes leading to eventual death.

Glycolipids

• Glycolipids are derived from ceramides with directly attached carbohydrates.
• Unlike sphingomyelin, they lack a phosphocholine group.

Glycoproteins

• Glycoproteins contain oligosaccharide (glycans) chains attached to polypeptide chains through glycosylation.
• Glycosylation occurs during co- and post-translational protein modification.

Functions of glycoproteins

• Glycoproteins have diverse functions including structural components (e.g., collagen), lubricants (e.g., mucins), transport molecules (e.g., transferrin), immunologic molecules (e.g., antibodies), hormones (e.g., thyroid stimulating hormone), enzymes, and cell-recognition sites.

Glycolipid structure

• Glycolipids such as cerebrosides contain a carbohydrate component linked to ceramide via an O-glycosidic bond.
• They are abundant in brain and myelin sheaths, containing a single or short chain of sugars.

Roles of Glycolipids

• Glycolipids play important roles in cell signaling, growth, development, and antigenic activity, acting as surface receptors and influencing cell transformation.

Test your knowledge on the fundamental aspects of amino acids and proteins in this biochemistry quiz. Explore questions about molecular weight, chirality exceptions, and the structural features common to all amino acids. Evaluate your understanding of their properties under various pH conditions.