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Subject and tasks of biological chemistry

• Biological chemistry, also known as biochemistry, studies chemical processes and substances within living organisms.
• It focuses on the structure, function, and interactions of biological molecules like proteins, nucleic acids, carbohydrates, and lipids.
• The subject includes enzyme kinetics, metabolism, cell signaling, and molecular genetics.
• Tasks:
  • Understanding chemical reactions in living organisms.
  • Investigating biomolecule structure and function.
  • Exploring the role of enzymes.
  • Studying metabolic pathways.
  • Investigating molecular mechanisms of genetic information transfer.
• Objects of biochemical research include molecules, cells, tissues, organs, and organisms.
• Branches of biochemistry:
  • Bioorganic chemistry: Study of organic compounds, e.g., amino acids, nucleotides.
  • Static biochemistry: Study of biomolecule structure and function in a static state.
  • Dynamic biochemistry: Study of biochemical processes and their changes over time.
  • Functional biochemistry: Study of the relationship between structure and function.
  • Molecular biology: Study of biological processes at the molecular level, e.g., DNA replication.
  • Medical biochemistry: Application of biochemical principles to understand and treat diseases.
• Biochemistry combines chemistry, biology, and physics to study living systems.

Primary structure of proteins

• Proteins are biomolecules essential for many critical roles in living organisms.
• The primary structure is the linear sequence of amino acids in the protein chain.
• The amino acid sequence determines the protein's unique identity and function.
• Properties of the peptide bond contribute to the stability and structure of proteins.
• Specificity of the primary structure:
  • The amino acid sequence is crucial for determining protein function.
  • Each amino acid has unique chemical properties influencing folding and interactions.
• Properties of the peptide bond:
  • The peptide bond is a covalent bond between the amino group of one amino acid and the carboxyl group of another.
  • It's rigid and planar due to resonance stabilization, limiting rotation.
  • The peptide bond contributes to the overall stability of the protein structure.

Secondary Structure of Proteins

• Secondary structure refers to local folding patterns from interactions between nearby amino acids.
• Two main types: alpha helices and beta sheets.
• Alpha helices:
  • The protein chain twists into a right-handed helix, stabilized by hydrogen bonds.
  • Hydrogen bonds form between the carbonyl oxygen of one amino acid and the amide hydrogen of another four residues away.
  • Common in proteins for structural stability.
• Beta sheets:
  • Neighboring segments align side by side, forming hydrogen bonds between backbone atoms.
  • Can be parallel or antiparallel.
  • Important for forming stable protein structures.

Tertiary Structure of Proteins

• Tertiary structure refers to the overall 3D arrangement of the protein chain.
• Includes how secondary structure elements fold and pack together.
• Stabilized by various bonds and interactions:
  • Hydrophobic interactions: Nonpolar amino acids cluster in the interior to avoid water.
  • Hydrogen bonds: Form between polar groups, contributing to stability.
  • Disulfide bonds: Covalent bonds between cysteine residues, creating stabilizing bridges.
  • Ionic interactions: Electrostatic interactions between charged amino acid side chains.
• Primary, secondary, and tertiary structures are linked and crucial for protein function.
• The amino acid sequence dictates folding into secondary and tertiary structures, determining overall shape and function.

Quaternary Structure of Proteins

• Quaternary structure: arrangement of multiple protein subunits (protomers).
• Proteins exhibit interactions between subunits, crucial for biological function.
• Examples: Hemoglobin, protein kinase.
• Protomer: Single protein subunit of a protein complex.
• Oligomer: Protein complex of multiple protomers. Can be homomeric (identical protomers) or heteromeric (different protomers).
• Conformational changes: assembly/dissociation of protomers is crucial to protein functions.
  • Hemoglobin: changes allow oxygen binding/release.
  • Protein kinase: regulates activity in phosphorylating target proteins.
• Biological functions of proteins: catalysis, support, transport, signaling, regulation.
• Protein-ligand interactions: Specific complementary interactions essential for biological functions.
  • Enzyme-substrate interactions: enzymes catalyze chemical reactions.
  • Hormone-receptor interactions: hormones initiate cellular responses.
• Quaternary structure, conformational changes, and protein-ligand interactions determine protein function.

Size and Shape of Protein Molecules

• Proteins are macromolecules made of amino acids essential for biological processes.
• Proteins vary in size from small peptides to large multi-subunit complexes.
• Shape is crucial for function, determining interactions with other molecules.
• Proteins can be globular or fibrous.
  • Globular proteins: Compactly folded, spherical shape (enzymes, transport proteins, antibodies).
  • Fibrous proteins: Elongated, thread-like structures (collagen, keratin).

Physical and Chemical Properties of Proteins

• Ionization: Amino acids with ionizable groups influence charge at different pH levels.
• Hydration: Proteins form hydrogen bonds with water, affecting solubility.
• Solubility: Varies with pH, temperature, ionic strength, and denaturing agents.
• Precipitation: Disrupting stabilizing interactions causes precipitation.

Separation of Proteins

• Salting out: Adding salts decreases solubility, causing precipitation.
• Electrophoresis: Separates proteins by size and charge using an electric field in a gel matrix.

Tests of Colloidal Stability

• Thymol Test: Assesses stability by adding thymol blue indicator, which changes color based on pH.
• Veltman's Test: Adds acids or bases to assess stability based on color or turbidity changes.

Paper Electrophoresis of Blood Proteins

• Proteinogram: Protein pattern after separation by paper electrophoresis.
• Separates proteins by charge and size, visualizing fractions in a sample.
• Understanding size, shape, properties, and separation methods is crucial for studying protein structure-function relationships.

Classification of Proteins

• Proteins can be classified based on composition, structure and function.
• Simple and Conjugated proteins are common for classification.
• Simple proteins examples include albumins and globulins, protamine’s, histones, prolamins and glutelins.
• Albumins and Globulins:
  • Albumins are water-soluble used for osmotic pressure maintenance, as well as transporting substances in the blood.
  • Globulins are a protein group contains enzymes, antibodies and transport proteins.
• Protamines are small arginine proteins found in sperm nuclei for DNA Compacting.
• Histones are basic nucleic proteins forming nucleosomes, the basic unit for chromatin structure.
• Prolamins are proteins that store seeds and help grains germinate, such as zein, hordein, gliadin.
• Glutelins are a seed rich protein in cereals serving various amino acids during seed development.
• Understanding protein classification facilitates for studying these proteins and their function, interactions, and how significant they are to biological systems.

Nucleic Acids

• Nucleic acids (DNA and RNA) store and transmit genetic information.
• Primary Structure:
  • Nucleic acids are polymers of nucleotides.
  • Each nucleotide contains a phosphate group, sugar (deoxyribose or ribose), and nitrogenous base (A, T, C, G in DNA; A, U, C, G in RNA).
  • Phosphodiester bonds link nucleotides between the 3' carbon of one sugar and the 5' carbon of the next.
• Secondary Structure of DNA:
  • DNA is double-stranded with antiparallel strands.
  • Bases pair via hydrogen bonds: A-T and G-C (Chargaff's rule).
  • The double helix provides stability and efficient replication.
• Parameters of DNA Double Helix:
  • Distance between base pairs is $3.4 \AA$