Nutritional Biochemistry: Amino Acids and Proteins

Nutritional Biochemistry - Amino Acids and Proteins

• This lecture covers amino acids and proteins, specifically focusing on their structure and function.
• The study material details amino acids, their general structure, and side chain variations.
• It discusses the formation of primary, secondary, tertiary, and quaternary protein structures.
• The document also includes a brief look at why amino acids fold in a specific way to form proteins.
• Learning outcomes are listed for the topic.

Quiz Questions - Last Time

• The quiz from a previous session covered properties of carbon bonding.
• Students need to know how many bonds carbon atoms commonly form.
• The quiz also covered isomers and the orientations of atoms when carbon forms bonds with other carbon atoms.
• The 7 functional groups prevalent in biological molecules are part of the quiz.
• Students need to identify examples of isomers.

Previously (1)

• Matter compositions, chemical elements and compounds in life (carbon, oxygen, hydrogen and nitrogen make up 96% of living organisms).
• The number of protons defines an atomic number.
• Isotopes of an element can have different masses, and some are unstable.
• Strong covalent (electron sharing) and ionic (electron donating) bonds are described, in addition to weak chemical bonds such as van der Waals interactions and hydrogen bonding.
• Chemistry plays an integral role in understanding biology.

Previously (2)

• Water molecules' polarity results in hydrogen bonding.
• Water plays roles in cohesion, temperature moderation, and solvent in life processes.
• Water molecules transfer H+ to form H3O+ and OH−.
• pH is used to measure H+ concentration.
• Buffers resist pH changes in biological systems like blood.

Previously (3)

• Carbon's valence allows bonding with up to four other elements/atoms, which determines the versatility of molecules in nature.
• Carbon forms the backbone of most organic molecules, contributing to the complexity of life.
• Isomers have the same formula but different spatial orientations (structural, geometric).
• Enantiomers are mirror-images of each other.
• Molecular components contribute to the overall shape and function.

Learning Outcomes

• Students must describe the general structure of amino acids and their varying side chains.
• Students need to understand the formation of primary, secondary, tertiary, and quaternary protein structures, and why amino acids fold in a specific way.

Role of Proteins

• The document asks about the role of proteins.

Proteins Main Functions (detailed)

• Illustrations and diagrams of different protein structures, and their functions.
• The lecture explains amino acids and different protein structures in detail.

What Can You Tell Me About This Structure?

• A chemical structure is presented, requiring students to analyse its components.

The 20 Amino Acids

• Amino acids are the basic building blocks of proteins.
• A central carbon atom (alpha carbon) is covalently bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).
• The R groups give amino acids their unique properties.
• Amino acids exist as either L or D isomers.

L Amino Acids

• Only L amino acids are used in proteins.
• Subtle solubility differences contributed to the selection of L amino acids.
• Steric hindrance for RNA inclusion in primordial soup.

Amino Acid Ionisation

• Amino acids exist predominantly as dipolar ions at neutral pH.
• The amino group is protonated (-NH3+) and the carboxyl group is deprotonated (-COO−).

Activity

• Students are prompted to explain a graph about amino acid ionisation.

Amino Acids

• Explains the 20 amino acids in detail, including their properties, side chains, and function.

Clinical Relevance - Disorders

• The relationship between defects in amino acid metabolism and various diseases is explained.
• Inborn errors in metabolism, like phenylketonuria, are discussed.

R Groups

• Amino acids are grouped by the properties of their R groups.
• R group categories include hydrophobic, polar neutral, positively charged, and negatively charged.

Structures

• The overview of amino acids' side chain structures.
• Activities that ask students to locate the α-carbon in each amino acid.
• Activities asking about the chiral carbons of amino acids.
• Side chain properties.

Hydrophobic Amino Acids

• Glycine, alanine, valine, leucine, isoleucine, and methionine are described, highlighting their hydrophobic characteristics.
• These amino acids tend to cluster together in proteins to minimize contact with water.

Hydrophobic Amino Acids(2)

• Phenylalanine and tryptophan are described, emphasizing their hydrophobic aromatic side chains.
• The influence of the side chains on the protein's overall shape and function is discussed.

Polar Amino Acids

• Serine, threonine, tyrosine, asparagine, and glutamine are presented as polar but uncharged amino acids.
• Hydroxyl and amide groups are among their specific characteristics.
• The characteristics of these side chains are discussed, notably how they align with hydrophobic side chains.

Polar Amino Acids (2)

• The structure and properties of cysteine are highlighted.
• Pairs of cysteine residues can form disulfide bonds, stabilizing protein structure.

Positively Charged Amino Acids

• Lysine, arginine, and histidine are the positively charged amino acids.
• The properties of lysine's primary amino group and arginine's guanidinium group are highlighted.

Positively Charged Amino Acids (2)

• Histidine's role as an active side chain in proteins is emphasized.
• pKa helps to determine the charge of histidine in different surroundings.

Histidine's Involvement in Fat Metabolism

• The role of histidine in fat metabolism is briefly described.

Negatively Charged Amino Acids

• Aspartic acid and glutamic acid are presented as negatively charged, acidic amino acids.
• Their properties and significance in protein function are explained.

Ionizable Groups

• Key amino acids with readily ionizable side chains and their roles in protein function are listed.
• The pKa values relate to the ionization state under different conditions.

Amino Acid Abbreviations

• Standard abbreviations used to represent amino acids in scientific texts and papers are listed.

Amino Acid Fold

• The folding of polypeptide chains is discussed along with the concept that the amino acid sequence determines the protein's three-dimensional shape.
• Key considerations for the folding process (hydrogen bonds between main chain and side chains, hydrophobic effect, van der Waals forces etc.,.)

Polypeptide versus Protein

• The differences between peptides and proteins (based on the number of amino acids).

Size Comparison

• The average molecular weight of an amino acid residue in a protein.
• Molecular weights of common proteins vary considerably.

Polypeptide Chains

• Polypeptide chains are flexible yet conformationally restricted because certain bonds' rotations are limited by steric clashes.

Bond Rotation

• Bonds between amino groups and α carbons are single bonds.
• Rotation about these bonds allows for various protein confirmations.

Secondary Structure

• How polypeptides fold into regular structures (alpha helix and beta sheets).
• Hydrogen bonds between amino acid segments facilitate their folding process.

The Alpha Helix

• The structure and stability of alpha helices (coil within a protein).
• The relation between amino acid residues are described.
• The presence of branching side chains potentially destabilise the helix.

The Alpha Helix (2)

• Additional details are provided on the chemical properties that determine optimal positioning in an alpha helix structure.
• Variations resulting from branching side chains described.

Beta Sheets

• Structure and stability of beta sheets (flattened or pleated sections within a protein).
• Characteristics of the hydrogen bonding are highlighted.
• The differences between antiparallel and parallel beta sheets are presented.

Beta Sheets (2)

• Elaboration on the directionality and adjacent amino acid arrangement in beta sheets (parallel or anti-parallel).

Tertiary Structure

• The compact structures of water-soluble proteins are formed within a nonpolar core.
• The atomic structure of myoglobin, an oxygen-carrying protein, is examined.
• The role of haemoglobin as an oxygen transport protein is described.
• Important aspects of the overall folding of the chain are highlighted.

Myoglobin

• Myoglobin's structure is described.
• The key components of its structure and folding are emphasised.

Hydrophobic in, Hydrophilic out

• Hydrophobic residues are clustered towards the protein's interior in water-soluble proteins.
• The hydrophilic residues are oriented outward.

Main Chain Fate

• How important the fate of the main chain is in its interactions with hydrophobic side chains.
• The significance of hydrogen bonding for the burial of amino acid segments within proteins.

Main Chain Fate (2)

• The role of van der Waals interactions in stabilizing protein confirmations is outlined.
• The significance of the different sizes and shapes within a variety of amino acids is discussed.

Quaternary Structure

• Proteins consisting of more than one polypeptide chain.
• How the arrangement of subunits within the protein structure contributes to function are explored.
• Examples such as haemoglobin, consisting of four subunits (2 alpha and 2 beta), are given.

Amino Acid Sequence

• How the primary amino acid sequence is significant in forming the 3-D structure of proteins.
• Steps for denaturing and reforming a protein are listed.

Summary

• The lecture summarized protein structure and function levels.
• The order is primary-secondary-tertiary-quaternary.
• Emphasis on different functional groups in proteins and their location inside or outside the core of the protein.

Questions

• A set of questions covering the lecture content is presented.
• Basic inquiries about amino acid groups, amino-acid classifications, dipeptide formation, and protein structure are included.

Before Next Time

• Relevant textbook readings to prepare for future lectures.
• Key biological concepts required are listed, including stereoisomers, carbohydrates, and other related topics.

Practical (Tomorrow) - Formative Assessment

• Information about the assessment schedule and preparation for the practical involving workbooks and materials is presented.

This quiz covers essential concepts in nutritional biochemistry, focusing on amino acids and their role in protein structure and function. It includes topics such as the general structure of amino acids, various protein folding mechanisms, and the complexity of protein levels from primary to quaternary structures. Test your understanding of these biochemical fundamentals.