Slide 1: Biomolecules - Amino Acids

• Amino acids are organic compounds that contain both an amino group (-NH2) and a carboxyl group (-COOH)
• They are building blocks of proteins
• Amino acids are characterized by a central carbon atom called alpha carbon (α-carbon)
• There are 20 different amino acids commonly found in proteins
• Each amino acid is unique due to the side chain, also known as R-group

Slide 2: Classification of Amino Acids

Amino acids can be classified based on the nature of their side chain (R-group):

1. Non-Polar Amino Acids

   • Side chains are hydrophobic
   • Examples: Glycine, Alanine, Valine

2. Polar Amino Acids

   • Side chains are hydrophilic
   • Examples: Serine, Threonine, Glutamine

3. Acidic Amino Acids

   • Side chains are negatively charged at physiological pH
   • Examples: Aspartic acid, Glutamic acid

4. Basic Amino Acids

   • Side chains are positively charged at physiological pH
   • Examples: Lysine, Arginine, Histidine

Slide 3: Structure of Amino Acids

• Amino acids have a common structure consisting of an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (H), and an R-group
• The amino group and the carboxyl group are attached to the α-carbon
• The R-group varies between different amino acids, giving them distinct properties

Slide 4: Essential Amino Acids

• Essential amino acids cannot be synthesized by the human body and must be obtained from the diet
• There are 9 essential amino acids: Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Leucine, Lysine, and Histidine
• Insufficient intake of essential amino acids can lead to protein malnutrition

Slide 5: Peptide Bond Formation

• Amino acids are joined together through a peptide bond
• The reaction between the carboxyl group of one amino acid and the amino group of another amino acid forms a peptide bond
• The resulting molecule is called a dipeptide
• Water is released during the formation of peptide bond (condensation reaction)

Slide 6: Primary Structure of Proteins

• The primary structure of a protein is the linear sequence of amino acids
• It is determined by the order and number of amino acids in the polypeptide chain
• A change in just one amino acid can significantly affect the protein’s function

Slide 7: Secondary Structure of Proteins

• Secondary structure refers to the local folding patterns within a protein
• Two common secondary structures are alpha helix and beta sheet
• Alpha helix is a right-handed coiled structure stabilized by hydrogen bonding between amino acid residues
• Beta sheet consists of multiple strands of extended polypeptide chains held together by hydrogen bonds

Slide 8: Tertiary Structure of Proteins

• Tertiary structure refers to the overall three-dimensional folding of a protein
• It is stabilized by various interactions such as hydrogen bonds, disulfide bridges, ionic interactions, and hydrophobic interactions
• Tertiary structure determines the protein’s overall shape and function

Slide 9: Quaternary Structure of Proteins

• Quaternary structure refers to the arrangement of multiple polypeptide chains (subunits) in a protein complex
• Protein subunits can be identical or different
• Quaternary structure is stabilized by the same types of interactions as tertiary structure

Slide 10: Protein Denaturation

• Denaturation is the disruption of a protein’s structure, resulting in loss of its biological activity
• Denaturation can be caused by heat, pH extremes, exposure to certain chemicals, or mechanical agitation
• Denatured proteins usually lose their secondary, tertiary, and quaternary structures

Slide 11: Protein Folding

• Protein folding is the process by which a protein adopts its functional three-dimensional structure
• It occurs spontaneously, guided by the protein’s amino acid sequence and various interactions
• Misfolding of proteins can lead to diseases such as Alzheimer’s and Parkinson’s

Slide 12: Protein Functions

• Proteins have a wide range of functions in living organisms:
  1. Enzymes: Catalyze biochemical reactions
  2. Structural Proteins: Provide support and framework to cells and tissues
  3. Transport Proteins: Carry molecules across cell membranes
  4. Hormones: Regulate various physiological processes
  5. Antibodies: Defend against pathogens
  6. Receptors: Receive and transmit signals in cells

Slide 13: Carbohydrates

• Carbohydrates are organic compounds composed of carbon, hydrogen, and oxygen in a ratio of 1:2:1
• Main functions include energy storage and structural support
• Monosaccharides are the simplest carbohydrates (e.g., glucose, fructose)
• Disaccharides are formed by the condensation of two monosaccharides (e.g., sucrose, lactose)
• Polysaccharides are complex carbohydrates formed by the polymerization of monosaccharides (e.g., starch, cellulose)

Slide 14: Lipids

• Lipids are hydrophobic molecules that include fats, oils, waxes, and steroids
• Functions of lipids include long-term energy storage, insulation, and protection of organs
• Fatty acids are the building blocks of lipids
• Triglycerides are formed from glycerol and three fatty acid molecules
• Phospholipids have a hydrophilic head and hydrophobic tails, making them essential for cell membranes

Slide 15: Nucleic Acids

• Nucleic acids are macromolecules that store and transmit genetic information
• Two types of nucleic acids: DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid)
• DNA carries the genetic code and is responsible for inherited traits
• RNA plays a role in protein synthesis and gene expression
• Nucleotides are the building blocks of nucleic acids, consisting of a phosphate group, a sugar (ribose or deoxyribose), and a nitrogenous base (adenine, guanine, cytosine, thymine/uracil)

Slide 16: DNA Structure

• DNA is a double-stranded helix composed of two antiparallel strands held together by hydrogen bonds
• The complementary base pairing rule: Adenine (A) with Thymine (T) and Guanine (G) with Cytosine (C)
• The structure of DNA was determined by Watson and Crick in 1953
• The discovery of the DNA structure is one of the most significant findings in the history of biology

Slide 17: DNA Replication

• DNA replication is the process by which DNA is duplicated to produce identical copies
• It occurs during the S phase of the cell cycle
• The double helix is unwound, and each strand serves as a template for the synthesis of a new complementary strand
• DNA replication is a highly accurate process, with an error rate of approximately 1 in 10 billion nucleotides

Slide 18: RNA Structure

• RNA is a single-stranded nucleic acid that plays various roles in protein synthesis and gene regulation
• It contains ribose sugar instead of deoxyribose and the base uracil (U) instead of thymine (T)
• Types of RNA include messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)
• RNA molecules can fold into complex structures, allowing them to perform diverse functions

Slide 19: Transcription

• Transcription is the process by which DNA is “copied” into RNA
• It occurs in the nucleus of eukaryotic cells
• RNA polymerase binds to the promoter region of a gene, unwinds the DNA double helix, and synthesizes an RNA molecule using one strand of DNA as a template
• The resulting RNA molecule is called the primary transcript or pre-mRNA

Slide 20: Translation

• Translation is the process by which an mRNA molecule is translated into a sequence of amino acids to produce a protein
• It occurs in the cytoplasm on ribosomes
• Transfer RNA (tRNA) molecules bring amino acids to the ribosome, matching their anticodon to the mRNA codon
• The ribosome catalyzes the formation of peptide bonds between the amino acids, resulting in the synthesis of a polypeptide chain

Slide 21: Protein Synthesis

• Protein synthesis is the process by which cells build proteins based on the instructions encoded in DNA
• It involves two main steps: transcription and translation
• Transcription takes place in the nucleus, where DNA is transcribed into mRNA
• Translation occurs in the cytoplasm, where mRNA is translated into a sequence of amino acids to form a protein

Slide 22: Protein Structure Determination

• Determining the structure of proteins is crucial for understanding their functions and roles in biological processes
• X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are commonly used methods for protein structure determination
• X-ray crystallography involves the analysis of diffraction patterns produced by X-rays passing through a crystalline protein sample
• NMR spectroscopy uses the interaction of a protein with magnetic fields to study its structure

Slide 23: Enzymes

• Enzymes are biological catalysts that accelerate the rate of chemical reactions in living organisms
• They are typically proteins, but certain RNA molecules called ribozymes can also act as enzymes
• Enzymes lower the activation energy of reactions, allowing them to occur more rapidly
• Enzyme activity is influenced by factors such as temperature, pH, and substrate concentration

Slide 24: Enzyme Kinetics

• Enzyme kinetics is the study of how enzymes function and their reaction rates
• The Michaelis-Menten equation describes the relationship between enzyme activity and substrate concentration
• Enzymes exhibit saturation kinetics, meaning that as substrate concentration increases, the reaction rate levels off at the enzyme’s maximum velocity (Vmax)
• The substrate concentration at which the reaction rate is half of Vmax is called the Michaelis constant (Km)

Slide 25: Reaction Mechanisms

• Enzymes catalyze reactions by following specific reaction mechanisms
• The lock-and-key model suggests that enzymes have an active site with a specific shape that matches the substrate’s shape
• The induced-fit model proposes that the enzyme’s active site undergoes conformational changes upon substrate binding
• Enzymes can perform various types of reactions, including oxidation-reduction, hydrolysis, and isomerization

Slide 26: Metabolism

• Metabolism refers to the sum of all chemical reactions that occur in an organism
• Anabolism involves the synthesis of complex molecules from simpler ones, typically requiring energy
• Catabolism involves the breakdown of complex molecules into simpler ones, releasing energy
• Metabolic pathways are interconnected series of reactions that regulate metabolic processes and energy flow in cells

Slide 27: Carbohydrate Metabolism

• Carbohydrate metabolism is the process by which carbohydrates are synthesized, broken down, and converted into energy
• Glycolysis is the initial step in carbohydrate metabolism, converting glucose into pyruvate
• Aerobic respiration occurs in the presence of oxygen, where pyruvate is further metabolized in the citric acid cycle and electron transport chain
• Anaerobic respiration occurs in the absence of oxygen, resulting in the conversion of pyruvate into lactate or ethanol

Slide 28: Lipid Metabolism

• Lipid metabolism involves the synthesis, breakdown, and utilization of lipids in the body
• Fatty acids undergo beta-oxidation, which breaks them down into acetyl-CoA to generate energy
• Lipogenesis is the process of synthesizing fatty acids and triglycerides from acetyl-CoA in the liver
• Lipids are stored in adipose tissue and can be hydrolyzed to release fatty acids for energy production

Slide 29: Nucleic Acid Metabolism

• Nucleic acid metabolism involves the biosynthesis and degradation of nucleotides, the building blocks of nucleic acids
• Purines (adenine and guanine) and pyrimidines (cytosine, thymine/uracil) are synthesized through complex biochemical pathways
• Nucleotides are essential for DNA and RNA synthesis, energy transfer (ATP), and signaling molecules (cyclic AMP)
• Nucleotide catabolism involves the breakdown of nucleotides into nucleosides and then individual nitrogenous bases

Slide 30: Biochemical Pathways

• Biochemical pathways refer to the interconnected series of chemical reactions that occur within an organism
• They are essential for the efficient utilization of nutrients, energy production, and maintenance of cellular homeostasis
• Examples of biochemical pathways include glycolysis, the citric acid cycle, electron transport chain, and oxidative phosphorylation
• Understanding these pathways is crucial for comprehending the overall functioning of biochemical systems in living organisms

======