Biochemistry Quiz: Amino Acids and Structures

Nutritional Biochemistry - Amino Acids and Proteins

• The course is DIET413/BHCS1019
• Dr Nathaniel Clark FHEA RNutr MRSB is the lecturer
• Contact details are provided

Last Time - Quiz Questions

• Carbon commonly forms 4 bonds with other atoms.
• When carbon forms a double bond with another carbon, the orientation of atoms changes.
• An isomer is a molecule with the same chemical formula but a different arrangement of atoms. There are three main types of isomers.
• Two examples of isomeric sugars were not specified.
• Seven functional groups give rise to biological molecules; the particular molecules rich in these groups were not listed.
• The term "amino acid" indicates a molecule with both an amino group and a carboxyl group.

Previously (1)

• Matter is composed of elements in pure form or in combinations (compounds).
• Essential elements of life include carbon, oxygen, hydrogen, and nitrogen, which account for 96% of these elements.
• Atomic number is the number of protons in an atom.
• Isotopes of an element differ in the number of neutrons.
• Electrons orbit the nucleus in specific energy levels.
• Strong chemical bonds include covalent (atoms share electrons) and ionic (atoms transfer electrons).
• Weak chemical bonds include van der Waals interactions and hydrogen bonding.
• Chemistry underlies the understanding of biology.

Previously (2)

• Water's polarity leads to hydrogen bonding.
• Water's properties (cohesion, temperature moderation, and solvent properties) are vital for life.
• Water molecules can transfer H+ to form hydronium (H3O+) and hydroxide (OH-) ions.
• pH measures the concentration of H+.
• Buffers maintain the pH of biological fluids.
• A buffer comprises an acid-base pair in reversible equilibrium with hydrogen ions.

Previously (3)

• Carbon's valence allows it to form up to four bonds.
• Double bonds alter molecular configuration.
• Carbon forms the structural backbone of most organic molecules, allowing for complexity and diversity of living matter.
• In hydrocarbons, only carbon and hydrogen atoms are present.
• Isomers have the same chemical formula but different spatial arrangements (structural, geometric, or enantiomers).
• The properties of organic molecules depend on their carbon skeleton and attached components.
• There are 7 functional groups.

Learning Outcomes

• Describe the general structure of amino acids.
• Explain variable amino acid side chains.
• Understand primary, secondary, tertiary, and quaternary protein structure.
• Understand the forces causing the folding of amino acids into proteins.

What is the Role of Protein?

• The role of protein was not detailed.

Proteins Main Functions

• Proteins have diverse functions based on their structure. Diagrams illustrating these functions were present.

What can you tell me about this structure?

• The structure shown is a general representation of an amino acid. Amino acids consist of an amino group, a carboxyl group, a central carbon atom (α-carbon), and a variable R group.

The 20 Amino Acids

• Amino acids, the building blocks of proteins, have a central chiral carbon atom.
• The R group varies between amino acids.
• They have L or D forms (different spatial arrangements).

L Amino Acids

• Only L-amino acids are used in proteins.
• L-amino acids are slightly more soluble than D-amino acids.
• This solubility difference might account for the predominance of L-amino acids in primordial soup.

Amino Acid Ionisation

• Amino acids exist as dipolar ions, or zwitterions in solutions at neutral pH.
• The amino group is protonated, while the carboxyl group is deprotonated.
• The ionization state varies depending on pH.

Activity (Page 13)

• The graph illustrated the varying ionization states of amino acids at different pH levels.

Amino Acids

• The 20 amino acids have varying side chains in size, shape, charge, hydrogen bonding, hydrophobic character, and chemical reactivity.
• All proteins are constructed from the same 20 amino acids.
• Nine of these are essential amino acids (obtained from diet).
• Five are non-essential (synthesized in the body).
• Six are conditional; these are essential at certain life stages or in disease states.

Clinical relevance - disorders

• Interference with normal amino acid metabolism can lead to various disorders.
• Errors in metabolic processes, such as tyrosine metabolism, can result in changes to biochemistry.
• Inborn errors of metabolism, such as phenylketonuria, are examples of genetic defects affecting metabolic pathways.

R Groups

• Amino acids are classified into 4 groups based on the characteristics of their R groups:
  • Hydrophobic non-polar
  • Polar neutral
  • Positively charged
  • Negatively charged

Structures

• An overview of amino acid side chain structures.
• Questions on identifying a-carbons, those without a-carbons, and amino acids with two chiral carbons.
• Questions to determine the properties of the side chains.
• Polar, non-polar, basic, and acidic are the categories for side chain properties.

Hydrophobic Amino Acids

• Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, and others are among the hydrophobic amino acids.
• Larger aliphatic side chains cluster together to avoid water.
• Aliphatic chain in proline differs from the others.

Hydrophobic Amino Acids (2)

• Phenylalanine and tryptophan have more simple aromatic side chains.
• Phenylalanine is purely hydrophobic, while tryptophan has aromatic characteristic with an NH group.

Polar Amino Acids

• Serine, threonine, tyrosine (contain hydroxyl -OH).
• Which of these 3 polar amino acids is closely aligned with hydrophobic side chains?
• Asparagine and glutamine contain carboxamide groups instead of carboxylic acid groups.
• Cysteine contains a sulfhydryl group, which is highly reactive compared to hydroxyl.
• Pairs of sulfhydryl groups may come together to form disulphide bonds, thus stabilizing some proteins.

Positively Charged Amino Acids

• Lysine and arginine have long chains with positively charged terminal groups at neutral pH.
• Lysine has a primary amino group.
• Arginine has a guanidinium group
• Histidine has an imidazole group which can be either charged or uncharged, depending on its local environment.

Histidine's Involvement in Fat Metabolism

• Histidine is involved in fat metabolism. Diagram shows its role.

Negatively Charged Amino Acids

• Aspartic acid and Glutamic acid have acidic side chains.
• Aspartate and glutamate are often called 'negatively charged' at physiological pH.

Ionizable Groups

• Seven amino acids have readily ionizable side chains.
• These side chains can donate or accept protons, facilitating reactions and ionic bonds.

Amino Acid Abbreviations

• Abbreviations are used in scientific papers. The abbreviations use the first 3 letters except for some (Asn, Gln, Ile, Trp).

Amino Acid Fold

• How amino acids fold into a protein.
• The factors important to protein folding.
• Considering the main chain hydrogen bonding capability of amino acids.

Polypeptide Versus Protein

• Definitions for polypeptides versus proteins.
• Large proteins (e.g., titin) contain large amounts of amino acids.
• Shorter chains (e.g., insulin) of amino acids are called oligopeptides
• Structure can determine if molecule is peptide or protein.

Size Comparison (by weight)

• Mean molecular weight of amino acid residues (100 Daltons).
• Most protein molecular weights fall between 5500 and 220,000.
• Proteins can be expressed in kilodaltons (kDa).
• Example sizes (titin, insulin, glucose).

Polypeptide Chains Flexibility

• Peptide bonds are planar and thus limit rotation.
• Rotation in other bonds (adjacent to peptide bonds) enables protein folding flexibility.

Secondary Structure

• Polypeptide chains fold into regular secondary structures like alpha helices and beta sheets.
• These structures result from hydrogen bonds between adjacent N-H and C=O groups.

The Alpha Helix

• This describes the structure of and forces involved in the formation of the α-helix.

The Alpha Helix (2)

• The rise and rotation per turn of a-helix structure was described and the factors stabilizing it.

Beta Sheets

• Different types of β-sheets are possible.

Beta Sheets (2)

• Alternative arrangements where amino acids point in opposite directions for hydrogen bonds. The various arrangements of β-sheets are described.

Quaternary Structure

• Polypeptide chains can assemble into quaternary structures like dimers and other forms, which contains multiple subunits (a dimer consists of two identical subunits).
• Explains human hemoglobin as example of more complex quaternary structure, with its alpha and beta subunits.

Amino Acid Sequence

• Explains how the structure of proteins is determined from amino acid sequence through a series of intermediates.

Summary

• Summary of amino acid structure and function.
• Key points about amino acid categories and their roles in protein structure.

Questions (Quiz)

• Questions on amino acid chemical groups.
• Questions on amino acid side chain classification.

Before Next Time

• List of topics for the next lecture (various structural components of biochemistry, such as isomer, chiral molecules, different types of carbohydrates).
• List of resources for additional reading on these topics in relevant textbooks.

Practical Assessment (Tomorrow)

• Practical scheduled, workbook is linked (to be reviewed prior to the session).