Amino Acids and Protein Structures Quiz

Chemistry of Amino Acids and Proteins - I

• The presentation covers the chemistry of amino acids and proteins, including their structure, classification, function, and properties.

Outline of the Topic

• General structure of Amino Acids
• Classification of amino acids
• Function of Amino Acids
• Acid-Base property of amino acids
• Peptide bond structure and functional peptides
• Protein structure
• Biological functions of proteins
• Protein classification

Objectives of the Topic

• Describe the general structure of amino acids
• List the biochemical functions of amino acids
• Categorize amino acids by different classification methods
• Explain the acid-base properties of amino acids
• Explain the peptide bond and its characteristics
• Identify functional peptides
• Detail protein structure
• Elucidate the biological functions of proteins
• Classify proteins

What are Proteins?

• Unbranched polymers of amino acids linked head-to-tail
• Major constituents of most cells
• Typically form multi-molecular complexes
• Folded into specific conformations
• Conformation and functional group chemistry control protein function
• Responsible for our phenotype (organism characteristics)
• Composed of almost 20 different types of standard amino acids
• Selenocysteine is incorporated during co-translation in humans (special case)

Amino Acids

• Structure: Central carbon atom, amino group, carboxyl group, and a variable side chain (R-group)
• Variable R-group: Confer unique chemical functionality to each amino acid
• Chiral/Optically active: Amino acids exist as mirror-image isomers
• Acid-base properties: Amino acids can act as both acids and bases, and their properties depend on the R-group
• Capacity to polymerize: Amino acids can link together to form chains, eventually creating proteins

Classification of Amino Acids

• Side chain character: Nonpolar, aliphatic, aromatic, polar uncharged, acidic, basic
• Nutritional value: Essential (must be obtained from diet), non-essential (synthesized by the body), conditionally essential
• Metabolic fate: Ketogenic, glucogenic, mixed
• Presence/absence in proteins: Some amino acids are found in proteins, while others are not

Amino Acid Classification by Side Chain Character

• Nonpolar, aliphatic R groups: Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Methionine
• Aromatic R groups: Phenylalanine, Tyrosine, Tryptophan
• Polar, uncharged R groups: Serine, Threonine, Cysteine, Asparagine, Glutamine
• Acidic R groups: Aspartate, Glutamate
• Basic R groups: Lysine, Arginine, Histidine

Classification by Nutritional Value

• Essential: The body cannot produce these amino acids in sufficient quantities for optimal function, and they must be obtained from the diet (Valine, Isoleucine, Threonine, Tryptophan, Leucine, Lysine, Methionine, Phenylalanine, Histidine).
• Non-essential: Can be synthesized by the body (others).
• Conditionally essential: These are typically non-essential, but may become essential under certain conditions like illness or stress (Tyrosine, Cysteine, Arginine, Glutamine, Glycine, Proline, and Serine).

Classification Based on Metabolic Fate

• Ketogenic: Break down to form ketone bodies
• Glucogenic: Break down to form glucose
• Mixed: Can yield both

Some Common Biological Functions of Amino Acids

• Formation of peptides and proteins
• Stabilize the 3D structure of proteins through multiple bonds.
• Vital for enzyme catalysis (specific AAs at active site).
• Source of glucose from certain amino acids
• Source of sulfur (for example, Fe-S clusters) in the body
• Components of nucleic acid synthesis (carbon skeleton and nitrogen utilized)
• Detoxification mechanisms
• Methyl donors in methylation reactions

Amino Acids as Precursors of Biologically Important Derivatives

• Glycine: Precursor for heme and creatine
• Tyrosine: Precursor for hormones (thyroxine, triiodothyronine, epinephrine, norepinephrine), and the skin pigment melanin
• Tryptophan: Precursor for niacin and serotonin
• Histidine: Precursor for histamine

Uncommon Amino Acids

• Hydroxylysine and hydroxyproline: Primarily in collagen and connective tissues
• Tyroxine and Triiodothyronine: Hormones for growth and development
• N-methylarginine and N-acetyllysine: Found in histone proteins
• Methylhistidine, N-methyllysine, N,N,N-trimethyllysine: Methylated in myosin
• γ-Carboxyglutamic acid: In blood clotting proteins and calcium-binding proteins (e.g., prothrombin)
• Desmosine: A derivative of four lysine residues, found in elastic protein
• Selenocysteine: Derived from serine, involved in protein synthesis and antioxidant activity (e.g., glutathione peroxidase)

Amino Acids Not Found in Proteins

• GABA (gamma-aminobutyric acid): A neurotransmitter
• Histamine: Involved in smooth muscle contraction and vascular permeability
• Serotonin: Neurotransmitter
• β-Alanine: Precursor for carnosine, involved in muscle endurance
• Dopamine: Precursor of melanin
• Epinephrine: Hormone
• Ornithine and Citrulline: Urea cycle intermediates
• S-adenosyl methionine (SAM): A methyl donor in transmethylation reactions

Acid-Base Properties of Amino Acids

• At low pH, the amino group is protonated (NH3+), acting as an acid
• At high pH, the carboxyl group is deprotonated (COO-), acting as a base
• At neutral pH, the amino acid exists as a zwitterion (dipolar ion), with both a positive and negative charge

pI of Neutral Amino Acids

• The pI (isoelectric point) is the pH at which the amino acid exists as a zwitterion
• Calculation involves averaging the pKa values for the amino and carboxyl groups

pI of Amino Acids-with Acidic, Neutral and Basic Side Chains

• pI values are calculated differently based on the characteristics of the side chain

Peptide Bonds (Amide Bonds), & Functional Peptides

• Formation of peptides involves a condensation reaction
• Characterized by N-terminal and C-terminal groups
• Acid-base behavior predicated on amino and carboxyl groups
• The pKa of ionizable R-groups may change in a peptide
• Functional examples include serylglycyltyrosylalanylleucine and aspartame (artificial sweetener)

Planar Peptide Groups in a Polypeptide Chain

• Amide nitrogens are non-basic
• Rotation around the C-N bond is restricted by double bond nature
• Peptide groups are planar

Biologically Active Peptides

• Examples include glutathione (important for cell defense), Insulin (hormone), and corticotropin

Protein Classification Based on Shape and Architecture

• Fibrous proteins: Long and thin, insoluble in water (e.g., collagen, keratin)
• Globular proteins: Roughly spherical, soluble in water (e.g., enzymes, hemoglobin, antibodies, insulin)

Membrane Proteins

• Hydrophobic amino acids are oriented towards the membrane
• Usually insoluble in water but soluble in detergents

Common Fibrous and Globular Proteins: Occurrence and Use

• Lists selected fibrous and globular proteins categorized by occurrence and function

Example of Fibrous Proteins: α-Keratin

• Major component of hair and nails
• A fibrous structural protein with a right-handed helix (α-helix)

Examples of Fibrous Proteins: Collagen

• Important fibrous structural protein
• Composed as a triple helix
• Plays crucial roles in tissues like ligaments, bones, and skin
• Repeating amino acid sequence has important structural implications

Summary of Levels of Protein Structure

• A summary of the different levels of protein structure (primary, secondary, tertiary, and quaternary)

Protein Classification Based on Function

• Enzymes: Catalyze biochemical reactions (e.g., glucokinase)
• Regulatory proteins: Regulate other proteins (e.g., insulin) or gene expression (e.g., transcription activators)
• Transport proteins: Transport molecules across cellular barriers (e.g., hemoglobin, serum albumin)
• Storage proteins: Store important molecules (e.g., casein)
• Contractile and Motile proteins: Involved in movement and contraction (e.g., Actin & Myosin, Dynein & Kinesin)
• Structural Proteins: Provide support and shape to tissues (e.g., keratin, collagen)
• Protective proteins: Defend the body from pathogens (e.g., immunoglobulins, thrombin & fibrinogen)

Protein Classification Based on Nutritional Value

• Complete proteins: Contain all essential amino acids
• Incomplete proteins: Lack one or more essential amino acids

Protein Classification Based on Composition

• Simple proteins: only amino acids
• Conjugated proteins: amino acids + non-amino acid component (prosthetic group)

Types of Conjugated Proteins

• Glycoproteins: proteins with carbohydrate groups (e.g., fibronectin, immunoglobulins)
• Lipoproteins: proteins with lipid groups (lipid transport)
• Nucleoproteins: proteins with nucleic acid groups (e.g., ribosomes, chromosomes)
• Phosphoproteins: proteins with phosphate groups (e.g., casein)
• Metalloproteins: proteins with metal ions (e.g., ferritin, SOD)
• Hemoproteins: metalloproteins containing heme (e.g., hemoglobin, myoglobin)
• Flavoproteins: proteins containing flavin groups (e.g., oxidoreductases)

Protein Classification Based on Shape

• Fibrous proteins: elongated, insoluble in water, structural role.

• Globular proteins: spherical, soluble, functional roles

• Membrane proteins: hydrophobic components oriented outward to interact with the membrane

Test your knowledge on the structural features of amino acids and their role in protein biology. This quiz covers various classifications, interactions, and the significance of specific amino acids in human health. Challenge yourself to understand the complexities of proteins and their building blocks!