Introduction to Amino Acids and Sugars

Introduction to Amino Acids and Sugars

• The subject is biochemistry, specifically introduction to amino acids and sugars.
• The presentation is by Dr Sarah K. Coleman.
• Learning outcomes include defining structural features of amino acids and sugars, classifying amino acids and sugars, defining isoelectric point (pI), explaining bonding in biopolymers, and explaining chirality.
• A functional group is a specific combination of atoms making up part of a larger molecule.
• Functional groups determine the activity and polarity of larger molecules.
• Examples of biologically important functional groups are carbonyl, aldehyde, ketone, carboxyl, hydroxyl, amino, phosphate, and sulfhydryl.

Basic Amino Acid Structure

• Amino acids have a general structure with two carbon atoms.
• One carbon is in the carboxylic acid group, the other in the amine group.
• The side chain (R group) typically contains carbon atoms.
• The central carbon is the alpha-carbon.

Functions of Amino Acids

• Amino acids function in building proteins.
• They are energy sources from nutrients.
• They are precursors to other molecules like L-DOPA and GABA.
• They are important signaling molecules (e.g., glutamate, GABA, histidine).
• There are many other roles than just protein synthesis.

Amino Acids and Basic Molecular Geometry

• Amino acids have a central carbon atom (α-carbon).
• The α-carbon has tetrahedral molecular geometry.

Amino Acids and Side Chains

• Human proteins are constructed from 20 α-amino acids.
• Different side chains (R groups) determine the identity and properties of amino acids.
• The Greek alphabet is used to name the atoms involved.

Acid/Base Properties of Amino Acids

• Amino acids have a basic amine group and an acidic carboxyl group.
• At physiological pH (7.4), the carboxyl group is negatively charged (COO⁻) and the amino group is positively charged (NH₃⁺).
• This forms a zwitterion (hybrid ion).

Zwitterions

• The degree of ionization of an amino acid depends on surrounding pH values.
• Each amino acid has a specific pH value (pI) where the positive and negative charges are equal, called the isoelectric point.
• At this pI, the amino acid has no net charge.

Isoelectric Point (pI)

• pI is the pH at which the majority of molecules in a solution have no net charge.
• All amino acids have a pI influenced by their side chains.
• Thus, all proteins also have a pI.
• Specific pI values are provided for various amino acid side chains.

Amino Acid Side Chains (R groups)

• Varying side chains (R groups) cause different chemical properties among amino acids.
• Subclassifications are based on R group properties (size, shape, polarity, charge, hydrophobicity, ability to hydrogen bond).
• These properties influence protein structure, shape, and functionality.

Nonpolar Side Chains

• These side chains are typically hydrocarbon chains or rings.
• Vary in size from small (glycine) to large (methionine).
• Do not participate in ionic or hydrogen bonding.
• Alanine, Valine, Leucine, and Isoleucine have saturated hydrocarbon R groups.
• Tryptophan and Phenylalanine have ring systems.
• Methionine contains sulfur.
• Glycine has a single hydrogen atom as its R-group and is the only non-chiral amino acid.
• Proline is structurally restrictive because it forms a cyclic ring.
• Often clustered in the interior of proteins, avoiding aqueous environments.
• Often found in hydrophobic regions on the outside of membrane proteins.

Non-charged Polar Side Chains

• These chains include serine, threonine, asparagine, glutamine, cysteine, and tyrosine.
• Serine and threonine have hydroxyl groups, enabling phosphorylation.
• Asparagine and glutamine have carbonyl and amide groups, allowing hydrogen bonding.
• Cysteine has a sulfhydryl group, contributing to disulfide bond formation.
• Tyrosine has a ring structure and a hydroxyl group.

Acidic Side Chains

• These include aspartic acid and glutamic acid.
• At physiological pH (7.4), the carboxyl groups are negatively charged (aspartate and glutamate).
• These side chains frequently act as proton donors.

Basic Side Chains

• These include lysine, arginine, histidine.
• At physiological pH, they are positively charged.
• Histidine is weakly basic.
• Lysine and arginine are fully ionised.

Aromatic Side Chains

• Tryptophan, phenylalanine, and tyrosine have ring systems.
• Large and bulky structures.
• Tyrosine's hydroxyl group participates in hydrogen bonding and phosphorylation.

Polypeptides Formed by Linking Amino Acids

• Amino acids are linked by peptide bonds (formed by reaction between amine and carboxyl groups).
• The reaction releases water (condensation reaction).

Polypeptide Chains Cannot Branch

• Polypeptide chains are formed by the linking of amino acids, forming linear structures, non-branched.

Biological Roles of Amino Acids

• Amino acids have diverse biological roles beyond protein structure, including roles as precursors to many complex nitrogenous compounds (nucleotides), as messenger molecules, and as intermediates in metabolic processes.
• Over 1000 non-standard amino acids are created for roles in various organisms (fungi, plants, etc.).

Basic Structure of Carbohydrates

• The general formula for carbohydrates is (CH₂O)ₙ, where n ≥ 3.
• Monosaccharides are classified based on the number of carbon atoms.

Other Aspects of Simple Carbohydrate Structure

• (n-1) carbons have a hydroxyl group.
• A carbon has either an aldehyde or ketone group.
• Aldoses have aldehyde groups, and ketoses have ketone groups.
• The location of the functional group differentiates aldoses (located on C1) from ketoses (located on C2).

Simple Mono-Saccharide Structures

• Simple sugars are either mono- or di-saccharides.
• Haworth and Fischer projections illustrate the structures.

Glycosidic Bond Formation: Linking Saccharides

• Condensation reactions form glycosidic bonds, involving the removal of a water molecule.
• Sucrose is a disaccharide example.

Glycosidic bond formation: linking saccharides

• Disaccharides have two monosaccharides (e.g., sucrose, maltose, lactose).
• Oligosaccharides have several monosaccharides (e.g., raffinose, stachyose).
• Polysaccharides have many monosaccharides (e.g., cellulose, starch, glycogen).
• Polysaccharides can have branched or linear structures.
• Glycosidic bonds can form with multiple carbons on a monomer.
• Glycosidic bonds can form with non-saccharide molecules.

Cellulose and Glycogen

• Cellulose is a linear chain of glucose monomers (β-1,4 linkage).
• Glycogen is a branched chain of glucose monomers (α-1,4 and α-1,6 linkages).

Polysaccharides on Proteins

• Many proteins have carbohydrate components (glycoproteins).
• O-linked saccharides attach via the hydroxyl group on serine or threonine.
• N-linked saccharides attach via the amide nitrogen on asparagine.

Glycosylation of Proteins

• Glycosylation is often crucial for targeting proteins to specific locations within cells and for controlling protein-protein interactions.
• Incorrect glycosylation is associated with various diseases and cancers.

Human Blood Antigens

• Human blood antigens are the result of complex glycans attached to proteins.

Biological Roles of Carbohydrates (Sugars)

• Simple sugars are crucial energy sources.
• Complex sugars serve as energy stores and have structural roles (e.g., cellulose, bacterial cell wall).
• Complex and branched glycans are involved in cell signaling and quality control.
• Other roles include precursors, metabolic intermediates, and inclusion in plant toxins (e.g., oleandrin).

Isomerism and Chirality

• Isomers have the same atomic composition but different structures.
• Stereo-isomers have the same groups and bonding but differ in spatial arrangement (handedness).
• Chirality arises from tetrahedral molecular geometry around carbon atoms, impacting biological activity.
• Chiral molecules occur in amino acids and sugars, and have biological significance.

Chirality

• Chiral molecules cannot be superimposed on their mirror images.
• All amino acids, except glycine, are chiral.
• Most biological molecules are chiral, impacting interactions and reactions.
• Enantiomers have different effects on biological systems. An example of this is Thalidomide.

MCQs for Lecture 6

• There is a multiple-choice quiz provided to help students prepare for seminars.
• Students should attempt the quiz prior to each seminar.

This quiz covers the fundamentals of amino acids and sugars in biochemistry, highlighting their structural features and functional groups. Participants will learn to classify these molecules and understand concepts like isoelectric point and chirality. Dive into the essential building blocks of life and their roles in biopolymers!