Biochemistry Amino Acids Quiz

Chemistry of Amino Acids and Proteins - I

• This topic covers the chemistry of amino acids and proteins.
• The outline of the topic includes general structure, classification, function, acid-base properties, peptide bonds, protein structure, biological functions, and protein classification.
• Objectives include describing amino acid structure, listing biochemical functions, categorizing amino acids, explaining acid-base properties, explaining peptide bonds, mentioning functional peptides, describing protein structure, elucidating protein functions, and classifying proteins.
• Proteins are unbranched polymers of amino acids linked head to tail.
• Proteins are major constituents of most cells.
• Proteins form multi-molecular complexes.
• Protein conformation and functional-group chemistry control function.
• Proteins are responsible for most of an organism’s phenotype.
• Proteins are made from almost 20 different types of standard amino acids.
• A special case exists where selenocysteine is incorporated during co-translation in humans.
• Amino acids have a central carbon, an amino group, a carboxyl group, and a variable side chain (R group).
• The side chain confers unique chemical functionality.
• Amino acids exhibit chiral/optically active properties.
• Amino acids have acid-base properties.
• Amino acids have the capacity to polymerize.

Amino Acid Classification

• Amino acids can be classified by side chain character, nutritional value, metabolic fate, and presence/absence in proteins.
• Examples include nonpolar, aliphatic R groups (e.g., glycine, alanine, valine, leucine, isoleucine, proline, methionine), aromatic R groups (e.g., phenylalanine, tyrosine, tryptophan), polar, uncharged R groups (e.g., serine, threonine, cysteine, asparagine, glutamine), acidic side chains (e.g., aspartate, glutamate), and basic side chains (e.g., lysine, arginine, histidine).
• The side chain determines whether an amino acid is hydrophobic or hydrophilic.
• Hydrophobic side chains stabilize protein structures via interactions.
• Tyrosine can form hydrogen bonding.
• Based on nutritional value, amino acids are classified as indispensable/essential amino acids, dispensable/non-essential amino acids, and conditionally essential amino acids.
• Indispensable amino acids cannot be synthesized by the human body in adequate amounts.
• Dispensable amino acids can be synthesized by the human body.
• Conditionally essential amino acids become essential under certain conditions like illness or stress.

Amino Acids Classification Based on Metabolic Fate

• Ketogenic amino acids catabolically yield intermediates convertible to acetyl-CoA or acetoacetyl-CoA.
• Glucogenic amino acids produce intermediates used in glycolysis and Krebs cycle.
• Mixed-type amino acids provide both intermediate routes during catabolism.

Common Biological Functions of Amino Acids

• Amino acids are used in the formation of peptides and proteins.
• Amino acids stabilize the 3D structure of proteins by forming bonds, which are essential for enzyme catalysis.
• Some amino acids act as a source of glucose.
• Cysteine and methionine are sources of sulfur in the body, crucial for the formation of iron-sulfur centers.
• Amino acid skeletons and nitrogen are used for nucleic acid synthesis.
• Glycine and methionine participate in detoxification mechanisms.
• Methionine acts as a methyl group donor in methylation reactions.
• Amino acids are precursors for biologically important derivatives.
  • Glycine is a precursor for heme and creatine.
  • Tyrosine is the precursor for thyroid hormones, epinephrine, nor-epinephrine, and melanin.
  • Tryptophan can be converted to niacin and serotonin.
  • Histidine can be converted to histamine.

Uncommon Amino Acids

• Hydroxylysine and hydroxyproline are mainly found in collagen and connective tissues.
• Tyrosine and triiodothyronine originate from thyroglobulin and act as hormones for growth and development.
• N-methylarginine and N-acetyllysine are found in histone proteins
• Methylhistidine, N-methyllysine, and N,N,N-trimethyllysine are methylated amino acids found in myosin.
• γ-Carboxyglutamic acid is found in blood clotting proteins and calcium-containing proteins like prothrombin.
• Desmosine is a derivative of four lysine residues present in elastin.
• Selenocysteine is derived from serine and plays a role in antioxidant activity as seen in glutathione peroxidase.

Amino Acids Not Found in Proteins

• GABA (gamma-aminobutyric acid) is a neurotransmitter.
• Histamine is involved in smooth muscle contraction, vascular permeability, and neurotransmission, derived from Histidine.
• Serotonin is a neurotransmitter derived from tryptophan.
• β-alanine is used in the synthesis of carnosine, important for muscle endurance.
• Epinephrine is a hormone.
• Ornithine and citrulline are involved in the urea cycle and arginine synthesis.
• Dopa (3,4-dihydroxyphenylalanine) is a precursor for melanin
• S-adenosyl methionine (SAM) is a methyl donor in transmethylation reactions

Acid-Base Properties of Amino Acids

• The ammonium form acts as an acid and the carboxylate form acts as a base
• The pI (isoelectric point) is a crucial property of amino acids and proteins.

Protein Structure And Classification

• Protein structure is determined by types, number, and sequence of amino acids.
• The primary structure describes the sequence and number of amino acids.
• The primary structure is determined by the DNA sequence.
• The primary structure contains the information necessary for folding into the native structure.
• Secondary structure describes the local folding pattern resulting from hydrogen bonding.
• Examples include alpha-helices and beta-sheets.
• Super secondary structures are common motifs in proteins. -Examples include helix-loop-helix, coiled coil, beta-alpha-beta unit, hairpin or beta meander.
• Tertiary structure describes the overall 3D structure of a polypeptide.
• It is determined by interactions between R groups, including hydrogen bonds, hydrophobic interactions, disulfide bridges, and ionic bonds.
• Quaternary structure describes the structure of proteins formed from multiple polypeptide chains. -Interactions between chains are similar in nature to interactions in tertiary structures, including hydrogen bonds, hydrophobic interactions, disulfide bridges, and ionic bonds
• Proteins with quaternary structure are often oligomers.
• Examples of proteins with Quaternary Structure include Alcohol dehydrogenase, Immunoglobulins, Malate dehydrogenase, Superoxide dismutase, Triose phosphate isomerase, Glycogen phosphorylase, Alkaline phosphatase, 6-Phosphogluconate dehydrogenase Phosphoglucoisomerase, Tyrosyl-tRNA synthetase, Glutathione reductase, and Aldolase.
• Advantages of quaternary association include stability due to a lower surface-to-volume ratio, increased stability from interactions, and shielding hydrophobic interactions from solvent water.
• Protein functions can be based on overall structure, shape, or size.
• Some proteins that have a fibrous structure are insoluble in water, while globular proteins are soluble, and membrane proteins are insoluble in water but interact with membranes and are present in membranes.

Classification of Proteins Based on Function

• Enzymes (e.g., glucokinase) catalyze reactions.
• Regulatory proteins (e.g., insulin) affect other proteins and processes, including gene expression.
• Transport proteins (e.g., hemoglobin) facilitate the transport of substances.
• Storage proteins (e.g., casein) store nutrients.
• Contractile and Motile proteins (e.g., actin and myosin) are involved in movement.
• Structural proteins (e.g., keratin and collagen) provide support and strength.
• Scaffold Proteins (Adapter Proteins) act as a scaffold onto which different proteins assemble.
• Protective proteins (e.g., immunoglobulins) are involved in the cell defense.

Classification of Proteins Based on Composition

• Simple proteins consist solely of amino acids.
• Conjugated proteins consist of amino acids plus other components. -Different types of conjugated proteins include Glycoproteins, Lipoproteins, Nucleoproteins, Phosphoproteins, Metalloproteins, Hemoproteins, and Flavoproteins.

Protein Classification Based on Shape (Architecture)

• Fibrous proteins are long and thin, insoluble in water, and often serve structural roles.
• Globular proteins are roughly spherical, soluble in water, and often have diverse functions.
• Membrane proteins have hydrophobic side chains, are insoluble in water, but are found in membranes.

Summary of Levels of Protein Structure

• The primary structure defines the linear sequence of amino acids in a polypeptide chain, determined by DNA.
• The secondary structure involves local folding patterns resulting from hydrogen bonds in the polypeptide chain, with examples being alpha-helices, beta-sheets, and beta-turns.
• The tertiary structure describes the overall three-dimensional arrangement and interactions within a polypeptide chain, involving the various bonds and interactions.
• At the quaternary structure, multiple polypeptide chains combine to form a protein complex, with various bonds and interactions at play.

Test your knowledge on amino acids with this quiz focusing on their classification, functions, and chemical properties. From essential to conditional and glucogenic amino acids, cover a range of essential concepts in biochemistry related to amino acids and their roles in the body.