Proteins and Amino Acids Quiz

Introduction to MEDF 1012A

• Course title: MEDF 1012A Foundation Course for Health Sciences II
• Instructor: Dr. Yeung Hang Mee, Po
• Email: [email protected]
• Office: 6/F Room 610P, Choh-Ming Li Basic Medical Sciences Building

Learning Objectives

• Describe the chemical properties and classifications of amino acids found in the human body.
• Define the four levels of protein structure.
• Explain the importance of correct protein folding to a protein's biological activity.
• Understand blood disorders caused by abnormal protein folding.

Biomolecules

• Biomolecules include hydrocarbons, carbohydrates, lipids, amino acids, proteins, nucleic acids (DNAs and RNAs), and lipids (fatty acids).
• Components depicted visually with their respective categories.

Protein Structure and Function

• Protein is a linear polymer of amino acids.
• Proteins carry out cellular functions, including enzymes, membrane transport, motor functions, cell signaling, and hormones (like insulin).
• A diagram illustrating a protein's structure with labels for parts like substrate, active site, enzyme, plasma membrane, cell-surface receptor protein, p-type pump.
• A detailed illustration and description of the structure of a human insulin molecule.

More About Insulin

• Insulin is a peptide hormone produced by the pancreas (β-cells).
• It regulates blood glucose levels after meals.
• This hormone has 51 amino acids arranged in two subunits connected by disulfide bonds.

General Structure of Amino Acids

• Every amino acid has four components attached to a central carbon atom (α-carbon):
  • An amino group (NH2 or +NH3)
  • A carboxyl group (COOH or COO-)
  • A hydrogen atom (H)
  • An R-group (side chain) that varies among different amino acids

Different Configurations of Amino Acids

• Except for glycine, all amino acids contain at least one asymmetric carbon atom (α-carbon), making them chiral molecules.
• All amino acids used by the human body are L-isomers; the amino group is located on the left side of the central carbon atom.

Classifications of Amino Acids

• Amino acids are classified based on their side chain properties:
  • Hydrophobic (nonpolar)
  • Hydrophilic (polar & uncharged)
  • Charged (polar)

Nonpolar (Hydrophobic) Amino Acids

• Nonpolar amino acids have hydrocarbon side chains with very few or no oxygen and nitrogen atoms.
• They typically reside within the interior of cell membranes.
• Examples include glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, and proline.

Polar & Uncharged (Hydrophilic) Amino Acids

• Polar amino acids have polar or charged side chains.
• They are commonly found on the surface of proteins, interacting with water and/or other polar molecules.
• Examples include serine, threonine, cysteine, tyrosine, asparagine, and glutamine.

Polar & Charged (Hydrophilic) Amino Acids

• The side chains of these amino acids carry a net charge at cellular pH and display electrostatic properties.
• They are involved in electrostatic interactions within proteins and with other polar or charged substances in the surrounding environment.
• Examples include aspartate, glutamate, lysine, arginine, and histidine.

The R Groups of Usual Amino Acid

• A table listing the various amino acids found in the human body, their three-letter and one-letter abbreviations, and the structure of their R-group side chain.

Chemical Properties of Amino Acids

• Properties of amino acids are influenced by factors such as surrounding pH, which impacts the charge and interactions between amino acids. The net charge of an amino acid becomes zero at its isoelectric point (pl).

Effects of Surrounding pH Value on Amino Acids

• Amino acids exist in different forms depending on the pH of their surrounding environment.
• At the isoelectric point (pl), the net charge of the amino acid is zero.
• The amino acid assumes a zwitterionic state, or a hybrid ion with both positive and negative charges simultaneously.

Different pI Values of Total 20 Amino Acids

• A table providing pI values for all 20 standard amino acids.
• Different pI values reflect different behaviors of amino acids in varying environments.

Importance of pI Value in Protein

• pI values of therapeutic antibodies (proteins) are usually higher than the physiological pH of blood (around 7.4).
• Antibody interactions with the negatively charged outer layer of cell membranes are promoted when antibodies are positively charged (after intravenous administration).

Special Property of Aromatic Amino Acids

• Aromatic amino acids (tyrosine and tryptophan) strongly absorb ultraviolet (UV) light at a wavelength of 280 nm due to their aromatic ring structures.
• Phenylalanine absorbs UV light at 260 nm.
• Absorbance of unknown samples of proteins can be measured by comparing their value with the absorbance values of known protein concentrations

Different Levels of Protein Structure

• Describes the four levels of protein structural organization (primary, secondary, tertiary, quaternary) and gives diagrams for each level.
• The levels of structure are nested; the primary structure (sequence of amino acids) determines the higher levels of structure— secondary, tertiary, and quaternary.

The Primary (1st) Level of Protein Structure

• The primary structure of a protein is the linear sequence of amino acids linked together by peptide bonds.
• The polypeptide chain is directional, starting with the N-terminus and ending with the C-terminus.

Importance of Primary (1st) Structure

• The order of amino acids in a polypeptide is dictated by the genetic code within our DNA (gene).
• This order determines the protein's specific sequence and, in turn, its function and other properties

The Secondary (2nd) Level of Protein Structure

• The polypeptide chain can fold into secondary structures, namely alpha-helices and beta-sheets, via hydrogen bonds.

What Is Alpha (α) Helix?

• The C=O group of one amino acid's side chain forms a hydrogen bond with the -NH group of a subsequent amino acid four positions away (n+4th).
• Hydrogen bonds run along the backbone structure of the polypeptide chain, stabilizing the alpha-helix conformation.
• Explains how this structured is maintained by hydrogen bonding between the components.

Factors Affecting Stability of a-Helix

• Proline is a helix breaker due to its unique ring structure.
• Glycine, tryptophan, tyrosine, and phenylalanine can disrupt the regular hydrogen bonding pattern or favor other secondary structures within a-helices.
• Electrostatic repulsion between nearby charged amino acids can destabilize the alpha-helix.

What Is Beta (β) Conformation?

• In beta-sheets, the hydrogen bonds form between different polypeptide segments, not from components running along one same chain structure.
• The polypeptide chains run parallel or antiparallel to each other. R-groups of amino acids extend above and below the sheet's plane.

Preferences of Different Amino Acids on a-Helix or B-Conformation

• Certain amino acids have a strong preference to form alpha-helices, while others prefer beta-sheets or turns.

Overview of a-Helix & B-Conformation

• Detailed, labeled diagrams of the two configurations.

What Is Beta (β) Conformation?

• A single polypeptide folds into beta-sheets, a secondary structure stabilized by hydrogen bonds among different polypeptide chains.

The Tertiary (3rd) Level of Protein Structure

• The folding of secondary structures into a three-dimensional conformation.
• Various types of interactions stabilize tertiary structures, including disulfide bonds, hydrogen bonds, ionic bonds, and hydrophobic interactions among amino acids' side chains.

Overview of Stabilities in Protein Structure by Side-chain Interactions

• Illustrates how various types of interactions between side chains of different amino acids influence the tertiary structure of proteins.

Importance of Tertiary (3rd) Level of Protein Structure

• Describes how the folded conformation of proteins creates hydrophobic interiors, promoting interaction between polar chains on the exterior of a protein, and how such interactions promote important function, such as enzyme catalytic mechanisms.

The Quaternary (4th) Level of Protein Structure

• This level of protein structure arises when multiple polypeptide chains (subunits) assemble and interact to form a larger complex.
• Interactions among subunits are critical in determining the function of multimeric proteins such as Hemoglobin.

Disorders of Protein Misfolding

• Some diseases result from improperly folded proteins, such as sickle cell anemia and spongiform encephalopathy.

Sickle Cell Anemia

• A genetic disorder caused by abnormal beta-globin subunits in hemoglobin.
• The abnormal hemoglobin (HbS) forms sickle-shaped structures, lowering oxygen-carrying capacity and blocking blood vessels.

Spongiform Encephalopathy

• Diseases, like mad cow disease, resulting from misfolded proteins called prions.
• Prion proteins trigger a chain reaction of misfolding, causing spongiform damage to the brain tissue.

Test your knowledge on the structure and function of proteins and amino acids. This quiz covers key concepts such as protein folding, amino acid components, and the role of proteins in cellular biology. Perfect for students studying biochemistry or molecular biology.