Biology Chapter on Amino Acids and Proteins

Cell Structure and Function - Cell Biology

• The presentation covers cell biology, including cell structure, function, and the cell doctrine.
• The presenter (Reem Dakhil) has expertise in biochemistry (M1) and physiology (M2), epigenetics, differentiation, and cancer.
• The presentation is from the Lebanese University and the Université Grenoble Alpes.

Chapter 1 – Cell Biology Birth

• This chapter introduces fundamental definitions in cell biology, specifically relating to the cell doctrine.

Cell Biology vs Cytology

• Cell biology studies cells and their components functionally and structurally.
• Cytology solely focuses on the structural aspects of cells and their components.

The Cell Doctrine

• The fundamental unit of structure and function is the cell.
• Cells divide and are the building blocks of organisms.
• Cells perpetuate life through processes like mitosis, meiosis, and fertilization.
• Cells have a double life; one life for each cell and one for the organism.

Chapter 2 – Molecular Components of Cells

• Chapter 2 focuses on the inorganic and organic compounds that compose cells at the molecular level.

What Atoms and Molecules Are Found in Our Cells?

• The most abundant atoms in cells are carbon (C), hydrogen (H), nitrogen (N), and oxygen (O), comprising 96% of the total.
• Other atoms, including sodium (Na), potassium (K), chlorine (Cl), and phosphorus (P), make up about 4% in cells.
• Trace elements like boron (B), fluorine (F), manganese (Mn), iron (Fe), cobalt (Co), copper (Cu), zinc (Zn), selenium (Se), and iodine (I) are present in very low concentrations

Molecular Level

• Organic molecules (biomolecules): Proteins, carbohydrates, lipids, and nucleic acids.
• Inorganic Molecules: Water and mineral salts.

1. Water

• Essential for life's functions, being the most abundant substance in cells.
• Water's polarity allows it to form hydrogen bonds, dissolving salts and interacting with other molecules.

2. Mineral Salts

• Found dissolved and ionized in water.
• Essential for cellular processes such as nerve impulse transmission, membrane permeability, muscle contraction, and cell division.
• Crucial for the activity of certain proteins.

3. Organic Compounds

• Molecules such as amino acids, fatty acids, nucleotides, as well as, the macromolecules formed from them.
• Vitamins are also noted as needed in small amounts, which may be part of carbohydrates or lipids.

1. Proteins

• Abundant organic molecules with diverse functions.
• Their functions encompass cell structure, morphology, communication, organ function, and other functions for cell and organism life, including genes expression, DNA replication, storage, transport, tissue building, immune system response, sense perception and muscle activity.
• However, they are not major sources of energy for the cell.
• Chemically, they are a homogeneous class of unbranched amino acid polymers.
• Proteins differ by the number and sequence of their amino acids.

4. The Amino Acids

• Proteins are composed of carbon (C), hydrogen (H), nitrogen (N), oxygen (O), and sometimes sulfur (S).
• Amino acids vary depending on the side chain.
• There are 20 different types of amino acids.
• Nine are considered essential, needed through dietary intake.

5. Polypeptide

• Polypeptides are linear chains of covalently bonded amino acids.
• The formation is through the ribosome and are digested by proteases.
• The sequence of amino acids determines a unique protein’s final conformation, including its 3D shape.
• The structure is primarily due to hydrogen bonds and other interactions between amino acid chains.

6. Polypeptide Flexibility

• Flexibility in protein structure allows for diverse 3D conformations essential for function.

7. Structures of Proteins

• Primary: Linear sequence of amino acids. Determined by DNA and stabilized by covalent bonds between amino acids. Altering it can affect protein function. All copies of the same protein have matching primary structure.
• Secondary: Further folding of amino acid chains into alpha-helices and beta-sheets. Stabilized by hydrogen bonds, except in specific instances.
• Tertiary: Precise folding of helical and non-helical regions into a specific 3D structure; important for function. Driven by various interactions including hydrogen bonds, ionic interactions, hydrophobic interactions, and disulfide bridges.
• Quaternary: Multiple polypeptide chains associate through non-covalent interactions to form a functional proteins with multiple subunits

8. Classification of Proteins

• By composition: Holoproteins (only amino acids) vs. heteroproteins (amino acids and other molecules). Examples include lipoproteins, glycoproteins, and hemoproteins.
• By structure: Fibrous (insoluble in water) vs. globular (soluble in water).
• By function: Structural, defense, regulatory, transport, catalytic, and contractile proteins are among the many protein classifications.

FS.I Partial 2020 and 2019 Questions

• Covers various aspects of cell components and their properties—amino acids, proteins, carbohydrates, lipids and their functions/characteristics.
• Questions tested multiple knowledge areas including: definitions, correct terms, structure and interactions in organic molecules, in addition, their classifications and functions.

II. Carbohydrates

• Carbohydrates have energetic, structural, and identity roles.
• Monosaccharides: Simple sugars like glucose, fructose, and galactose. These types do not combine much.
• Disaccharides: Two monosaccharides linked together, like sucrose, lactose, and maltose. Formed by releasing water molecules.
• Oligosaccharides: A few linked monosaccharides. They can be branched or unbranched; these are often attached to proteins or lipids.
• Polysaccharides: Long chains of monosaccharides used for energy storage (e.g., glycogen, starch) or structure (e.g., cellulose. These are branched or unbranched.

2. Cyclic Oses

• Cyclic forms of monosaccharides are more stable than linear forms in the body.
• Isomers like α and β, differ in the orientation of the OH group.

4. Modification of Carbohydrates

• Modifications like adding an amine group to osamines or an acetyl group to N-acetyl osamines are important for certain functions.
• Uronic acids result from the acidification of CH2OH.

III. Lipids

• Lipids are non-polar, insoluble in water but soluble in other nonpolar solvents.
• Functions: Structural (phospholipids in cell membranes), energetic (triglycerides), and communication (steroid hormones).
• Types: Saponifiable (contain fatty acids) and nonsaponifiable (do not contain fatty acids).
  • Saturated fatty acids: No double bonds; solid at room temperature
  • Unsaturated fatty acids: Contain double bonds; liquid at room temperature

1. Saponifiable Lipids

• a. Fatty Acids: Have a hydrophilic head (COOH) and a hydrophobic tail (hydrocarbon chain).
• b. Triglycerides: Glycerol + 3 fatty acids; important for energy storage.
• c. Phospholipids: Important cell membrane components; amphipathic with a hydrophilic phosphate head and hydrophobic fatty acid tails. Different types are found in differing parts of cell membranes; some are derived from glycerol, others from sphingosine.
• d. Glycolipids: Cell identity markers found on cell membranes; have a carbohydrate group attached to a lipid backbone

1. Saponifiable Lipids - e. Cerides

• Esters of a fatty acid and a fatty alcohol.
• Examples include components of waxes.

2. Non-Saponifiable Lipids - a. Terpenes

• Polymers of isoprene, with varied structures and functions. Example: vitamins A, E, K.

2. Non-Saponifiable Lipids - b. Steroids

• Cyclic molecules with diverse functions. Example: cholesterol, and steroid hormones. Includes vitamins like Vitamin D, which has structural and communication roles.

3. Hydrophobic Interactions

• Lipids, due to their amphipathic nature, form monolayers, bilayers, micelles, and liposomes in water-based environments.

IV. Nucleic Acids

• Nucleic acids are polymers of nucleotides, including DNA and RNA.
• Composition: Nucleosides are comprised of nitrogenous base + a pentose sugar and a phosphate group, forming the nucleotide structure. Nitrogenous bases include purines and pyrimidines.
• Different RNA types include messenger, transfer, and ribosomal RNA.
• DNA structure: Double helix formed from two polynucleotide chains, pairing between purines and pyrimidines via hydrogen bonds. DNA structure has grooves and differing helices.
• DNA replication: Copying DNA molecule during the S-phase of interphase using specific enzymes. The process is semi-conservative, with each new DNA molecule containing one original strand and one newly synthesised.
• Nuclease activity: Enzymes that degrade DNA extremities.
• Transcription: Creating RNA molecules using DNA as a template.
• RNA types: messenger (mRNA), transfer (tRNA), ribosomal (rRNA), and others to facilitate protein translation, mRNA transport and structural functions.