Natural Sciences / Biochemistry

Wk 9

Amino Acids - The Building Blocks of Proteins [General Structure]

• Central α-carbon

• Amino group (-NH₂)

• Carboxyl group (-COOH)

• Hydrogen Atom

• Variable R-group (side chain)

• Exist as Zwitterions at physiological pH (both positive and negative charges)

Properties of Amino Acids

• Classified by Side Chains

• Nonpolar (Hydrophobic): Glycine, Alanine, Valine

• Polar (Hydrophilic): Serine, Cysteine

• Acidic (- charge): Aspartic acid, Glutamic acid

• Basic (+ charge): Lysine, Arginine

Peptide Bond Formation

• Peptide bonds form between amino acids via condensation reactions (water is released).

• N-terminus (free NH₂) & C-terminus (free COOH) define sequence direction.

  Example: Formation of a Dipeptide (Ala-Ser)

• Alanine + Serine → Ala-Ser + H₂O

Summary of Amino Acids & Peptides

Peptide bonds form between amino acids via condensation reactions (water is released) [REPEAT]

Isoelectric Point (pI): The pH at which an amino acid has no net charge.

Essential vs. Non-Essential Amino Acids

Essential: Must be obtained from food (e.g., Lysine, Histidine).

Non-Essential: Synthesized by the body (e.g., Glycine, Serine).

Protein Structure Levels

• Primary Structure: Sequence of amino acids in a polypeptide.

• Secondary Structure: Localized folding via hydrogen bonds → α-helices & β-sheets.

• Tertiary Structure: 3D folding due to disulfide bonds, hydrophobic interactions, & ionic bonds.

• Quaternary Structure: Multiple polypeptide chains interact (e.g., Hemoglobin, Collagen).

Protein Folding and Stability

Forces Stabilizing Protein Structure: Hydrogen bonds - Ionic interactions - Hydrophobic effects - Disulfide bonds (-S-S-) between cysteine residues

Denaturation and how?

When proteins lose their structure & function due to: heat, pH changes and chemical exposure.

Enzyme Function

Enzymes are biological catalysts that speed up reactions.

Lock & Key Model

Substrate fits perfectly into active site.

Factors Affecting Enzymes

Temperature, pH, inhibitors, and substrate concentration.

Isoelectric Point (pl) & Amino Acid Change

• pI = The pH at which an amino acid has no net charge
• Acidic amino acids → Lower pI
• Basic amino acids → Higher pI
• Used in electrophoresis for protein separation

Lipids - Introduction

• Lipids are hydrophobic molecules
• Major Classes of Lipids:
• Fats & oils (triglycerides) → Energy storage
• Phospholipids → Membranes
• Steroids → Hormones (cholesterol,
testosterone, estrogen)
• Prostaglandins → Cell signaling

Lipids

• Lipids serve as energy storage, insulation, and structural components in cells.
• Lipid Transport:
• Lipids travel in the bloodstream via lipoproteins
(HDL = good, LDL = bad).
• Excess lipids can lead to atherosclerosis
(clogged arteries).

Fatty Acids & Triglycerides | Saturated vs. Unsaturated

• Fatty acids = Long hydrocarbon chains with a carboxyl (-COOH) group
• Saturated (no double bonds) → Solid at room temp (butter, animal fats)
• Unsaturated (double bonds) → Liquid at room temp (oils, fish fat)
• Triglycerides = Glycerol + 3 fatty acids (major energy storage)

Fatty Acids & Triglycerides Continued

Fatty Acids Classification: Saturated: No double bonds (e.g., Butter, Lard
– solid at room temp). → Unsaturated: One or more double bonds (e.g.,
Olive oil, Avocado – liquid at room temp). → Polyunsaturated: Multiple double bonds (e.g.,Omega-3, Omega-6 fatty acids)

Omega-3 & Omega-6 Fatty Acids

Essential fatty acids - must be obtained from diet

Omega-3 (EPA, DHA) → Anti-inflammatory, heart health

Omega-6 (Linoleic acid) → Essential for growth

Hydrogenation

Converts unsaturated fats to saturated fats

Trans fats

Partial hydrogenation → Increases heart disease risk

Phospholipids & Membranes

• Amphipathic (hydrophilic head + hydrophobic tails)
• Forms lipid bilayers in cell membranes
• Membrane fluidity regulated by cholesterol

Steroids & Cholesterol

• Steroids = Four fused rings
• Steroids: Derived from cholesterol,
include:
• Hormones (Testosterone, Estrogen,
Cortisol).
• Vitamin D (for calcium metabolism).
• Bile Acids (for fat digestion).
• Cholesterol functions:
• Maintains membrane fluidity
• Precursor for hormones (estrogen, testosterone, cortisol)

Saponification & Soap Formation

• Saponification: The reaction of fat + strong base (NaOH or KOH) to form glycerol + soap.
• Soap molecules form micelles in water:
• Hydrophilic heads interact with water.
• Hydrophobic tails trap dirt & oil.
• Detergents vs. Soap:
• Soaps work in soft water, but form scum in hard water.
• Detergents contain surfactants that work in both soft & hard water.

Lipids contain…

esters

Esterification forms…

lipids

Alkaline hydrolysis of lipids occurs during…

decomposition

Saponification produces

soap

Adipocere is formed in…

hard water

Proteins are polypeptides of many…

amino acids

Amino acids are connected through:

peptide bonds

End products of oxidation of protein is:

CO2, H2O and nitrogenous waste

Coagulation is a product of:

converting soluble protein into insoluble

Imbition is the…

ability of proteins to absorb moisture

An enzyme is a protein that…

is also a catalyst