Proteins and Amino Acids Quiz

Proteins

• Proteins are polymers of amino acids.
• Proteins have diverse functions including:
  • Providing structure in membranes
  • Building cartilage and connective tissues
  • Transporting oxygen in blood and muscle
  • Directing biological reactions as enzymes
  • Defending the body against infection
  • Controlling metabolic processes as hormones

Amino Acids

• Amino acids are the building blocks of proteins.
• The general structure of an α-amino acid includes:
  • An α-carboxylate group
  • An α-amino group
  • A side-chain R group
• The α-carbon of amino acids is chiral, except for glycine.
• The amino acid configuration isolated from proteins is L.
• The most oxidized end of the molecule, carbonyl, is drawn at the top.

Amino Acid Classification

• Nonpolar, aliphatic R groups: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline

• Polar, uncharged R groups: Serine, Threonine, Cysteine, Asparagine, Glutamine

• Aromatic R groups: Phenylalanine, Tyrosine, Tryptophan

• Positively charged R groups: Lysine, Arginine, Histidine

• Negatively charged R groups: Aspartate, Glutamate

• Derived amino acids (nonstandard amino acids) are formed by enzyme-facilitated reactions. Examples include 4-hydroxyproline and 5-hydroxylysine.

• Y-carboxyglutamic acid is a constituent of several proteins involved in blood clotting.

• O-phosphoserine presence of P regulates the activity of proteins.

• Cystine is made up of two cysteine molecules or residues joined together by a disulfide bond.

• Ornithine and citrulline are metabolites of the urea cycle.

Essential Amino Acids

• PVT. TIM HALL
  • Phenylalanine
  • Valine
  • Tryptophan
  • Threonine
  • Isoleucine
  • Methionine
  • Histidine
  • Arginine
  • Leucine
  • Lysine

Complete and Incomplete Protein Sources

• Complete proteins provide all essential amino acids. Examples include eggs, milk, meat, and fish.
• Incomplete proteins lack one or more essential amino acids. Examples include grains, corn, rice, legumes, beans, nuts and walnuts.
• Combining incomplete proteins can create a complete protein source.

Properties of Amino Acids

• Nonionic and Zwitterionic forms: The zwitterion is the predominant form at neutral pH.
• Isoelectric Points (pI): The pH at which the + and charges are balanced. Values vary by amino acid.

pKa Values

• pKa values are provided for the ionising groups of each amino acid.

Titration of Amino Acids

• Titration curves depict the pH changes during the titration of an amino acid.

Peptide Formation

• Condensing or dehydrating two amino acids forms a dipeptide.
• The N-terminal amino acid is written on the left.

Peptide Bond

• Peptide bonds form between the carboxyl group of one amino acid and the amino group of another by a dehydration reaction.

Formation of Peptides

• Describes the formation of a dipeptide, as well as a tripeptide.

Peptide Bond Characteristics

• Rigid.
• Planar.
• Small electric dipole.

Polypeptide Structure & Trans Amide Bonds

• Various factors affect the shape of a protein.
• Some proteins have a-helices, some have B-sheets, some have both.
• There are regions that do not have an organized structure, these are considered to be disordered or as turns.

Some Biologically Important Peptides

• Glutathione
• Oxytocin
• Vasopressin
• Met-enkephalin
• Leu-enkephalin
• Atrial natriuretic factor
• Substance P
• Bradykinin

Levels of Protein Structure

• Primary: Order of amino acids.
• Secondary: Local structures like a-helices and B-sheets.
• Tertiary: Overall 3D shape of a polypeptide and its arrangements
• Quaternary: Organization of polypeptide subunits

The Primary Structure of Proteins

• The primary structure of a protein is the amino acid sequence.
• Differences in amino acid sequences and the location of amino acids in the sequence result in different protein structures and functions.
• The primary structure is a translation of information contained in genes.

Hemoglobin & Sickle-Cell Anemia

• A single amino acid substitution in the beta-chain of hemoglobin causes sickle-cell anemia.

Amino Acid Sequencing

• Acid hydrolysis
• Alkaline hydrolysis
• Enzymatic hydrolysis
• Sanger's method
• Edman degradation
• Determination of C-terminal amino acid

Ordering Peptide Fragments

• The overlapping segments allow piecing together the amino acid sequence.

Sample Problems

• Problems illustrating the analysis of protein sequences

Denaturation of Proteins

• A change in conditions disrupts the interactions between the R groups of amino acids in the protein, which affects the secondary, tertiary, and quaternary structure but not the primary structure.
  • Factors that denature proteins:
    • Temperature
    • Acids/bases
    • Organic solvents
    • Heavy metal ions (e.g. Ag+, Pb2+, Hg2+)
    • Agitation
    • Detergents
    • Mechanical Stress

Classification of Proteins

• By shape and solubility:

  • Fibrous proteins: Long, linear shape, mainly structural, low solubility in water.
  • Globular proteins: Compact, spherical shape, mainly functional, low solubility in water.
  • Membrane proteins: Found in membranes, generally insoluble in water, often polyhelical.

• By composition:

  • Simple proteins: Only amino acids.
  • Conjugated proteins: Amino acids + other components (e.g. lipids, carbohydrates, metals).

• By function:

  • Structural
  • Contractile
  • Transport
  • Hormonal
  • Catalytic
  • Antibodies
  • Storage