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Semester 1: Biological Chemistry
Structure of atoms, molecules and chemical bonds
Structure of atoms, molecules and chemical bonds
Atoms
Atoms are the basic building blocks of matter. Each atom consists of a nucleus, made up of protons and neutrons, surrounded by electrons that orbit the nucleus. The number of protons determines the atomic number and the identity of the element. Atoms can exist independently or bond with other atoms to form molecules.
Molecules
Molecules are formed when two or more atoms bond together. They can be simple, like O2 (oxygen gas), or complex, like proteins and nucleic acids. The structure and function of a molecule are determined by the types and arrangements of the atoms it contains. Molecules can be polar or nonpolar, affecting their interactions with other molecules.
Chemical Bonds
Chemical bonds are the forces that hold atoms together in a molecule. There are three main types of chemical bonds: ionic bonds, covalent bonds, and metallic bonds. Ionic bonds occur when electrons are transferred from one atom to another, creating charged ions. Covalent bonds involve the sharing of electrons between atoms. Metallic bonds involve a sea of electrons flowing around positively charged metal ions.
Importance in Biological Chemistry
Understanding the structure of atoms, molecules, and chemical bonds is crucial in biological chemistry. Biological processes such as metabolism, enzymatic reactions, and cellular structure are fundamentally based on the interactions between atoms and molecules. The properties of molecules influence their biological functions, making molecular structure a vital focus of study in zoology.
Principles of biophysical chemistry pH, buffer, reaction kinetics, Thermodynamics
Principles of Biophysical Chemistry
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pH is a measure of the acidity or basicity of a solution. It is defined as the negative logarithm of the hydrogen ion concentration.
pH scale ranges from 0 to 14. A pH of 7 is considered neutral, below 7 is acidic, and above 7 is basic.
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Buffers are solutions that resist changes in pH upon the addition of small amounts of acid or base.
Typically consist of a weak acid and its conjugate base or a weak base and its conjugate acid.
Buffers are crucial for maintaining stable pH environments in biological systems, thus affecting enzymatic activity.
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Reaction kinetics is the study of the rates of chemical reactions and the factors affecting them.
Expresses how the rate depends on the concentration of reactants.
Understanding kinetics helps in the design of drugs and understanding metabolic pathways.
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Thermodynamics is the study of energy transformations, particularly the relationships between heat, work, temperature, and energy in biological systems.
Involves the laws of thermodynamics like energy conservation, entropy, and free energy.
Thermodynamics helps predict reaction spontaneity and equilibrium in biological processes.
Stabilizing interactions Vander Waals, electrostatic, hydrogen bonding, hydrophobic interaction
Stabilizing Interactions in Biological Chemistry
Vander Waals Forces
Vander Waals forces are weak attractive forces that occur between molecules due to transient dipoles formed when electron clouds fluctuate. These interactions are significant in biological systems as they contribute to the overall stability and structure of macromolecules such as proteins and nucleic acids. Their cumulative effect can stabilize molecular structures despite their individual weakness.
Electrostatic Interactions
Electrostatic interactions arise from the attraction between charged groups. In biological contexts, these forces play a crucial role in protein folding, enzyme activity, and substrate binding. Charged amino acids on protein surfaces can interact with other charged groups, influencing protein conformation and stability, which is fundamental for biological function.
Hydrogen Bonding
Hydrogen bonds form between an electronegative atom and a hydrogen atom bonded to another electronegative atom. In biological molecules, such as water, DNA, and proteins, these bonds are essential for maintaining structure and stability. In DNA, hydrogen bonds between base pairs provide the stability necessary for double helix formation.
Hydrophobic Interaction
Hydrophobic interactions occur when nonpolar molecules aggregate in aqueous environments to minimize their exposure to water. This effect is crucial in protein folding, where hydrophobic amino acid side chains tend to cluster away from water, contributing to the three-dimensional structure of proteins. Hydrophobic interactions also play a significant role in membrane formation and stability.
Composition structure of biomolecules carbohydrates, lipids, proteins, nucleic acids and vitamins
Composition structure of biomolecules
Carbohydrates
Carbohydrates are organic compounds composed of carbon, hydrogen, and oxygen. They serve as a primary energy source for living organisms. The basic building blocks are monosaccharides, which can combine to form disaccharides and polysaccharides. Key examples include glucose, fructose, sucrose, and starch.
Lipids
Lipids are a diverse group of hydrophobic molecules, including fats, oils, and phospholipids. They are composed mainly of carbon and hydrogen, with some oxygen. Lipids are essential for energy storage, cellular structure, and signaling. Notable types include triglycerides, phospholipids, and steroids.
Proteins
Proteins are polymers of amino acids linked by peptide bonds. They contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. Proteins play critical roles in enzymatic activity, structural support, transport, and immune responses. Proteins exhibit four levels of structure: primary, secondary, tertiary, and quaternary.
Nucleic Acids
Nucleic acids, including DNA and RNA, are long polymers made up of nucleotide monomers. Each nucleotide consists of a sugar, a phosphate group, and a nitrogenous base. DNA encodes the genetic information, while RNA plays a crucial role in protein synthesis and gene regulation.
Vitamins
Vitamins are organic molecules required in small amounts for various biochemical functions. They are divided into two categories: water-soluble (e.g., B-complex, vitamin C) and fat-soluble (e.g., vitamins A, D, E, K). Each vitamin serves specific roles in metabolism, immune function, and overall health.
Bioenergetics, glycolysis, oxidative phosphorylation
Bioenergetics, Glycolysis, and Oxidative Phosphorylation
Bioenergetics
Bioenergetics is the study of energy flow through living systems. It involves understanding how organisms convert food into usable energy to maintain cellular functions. This concept is crucial in cellular respiration, where energy derived from nutrients is transformed into ATP.
Glycolysis
Glycolysis is the metabolic pathway that converts glucose into pyruvate, generating a small amount of ATP and NADH. It occurs in the cytoplasm and is anaerobic, meaning it does not require oxygen. Glycolysis consists of ten enzymatic reactions and serves as the foundational pathway for both aerobic and anaerobic respiration.
Oxidative Phosphorylation
Oxidative phosphorylation is the final stage of cellular respiration, taking place in the mitochondria. It involves the electron transport chain and chemiosmosis to produce large amounts of ATP. During this process, electrons derived from NADH and FADH2 are transferred through protein complexes, leading to the pumping of protons across the inner mitochondrial membrane, creating an electrochemical gradient that drives ATP synthesis.
Principles of catalysis, enzymes and enzyme kinetics, enzyme regulation, mechanism of enzyme action, isoenzymes
Principles of catalysis, enzymes and enzyme kinetics, enzyme regulation, mechanism of enzyme action, isoenzymes
Catalysis is the process of accelerating a chemical reaction by the presence of a catalyst, which is not consumed during the reaction.
Catalysis where the catalyst is in the same phase as the reactants.
Catalysis where the catalyst and reactants are in different phases.
Temperature
Concentration of reactants
Presence of inhibitors or activators
Enzymes are biological catalysts that speed up biochemical reactions without being consumed.
Specificity: Enzymes are specific to substrates.
Efficiency: Enzymes can increase reaction rates significantly.
Regulation: Enzyme activity can be modulated.
Enzyme kinetics studies the rates of enzyme-catalyzed reactions.
A model describing the rate of enzymatic reactions with a single substrate.
A double reciprocal plot of the Michaelis-Menten equation to determine kinetic parameters.
Vmax: Maximum reaction velocity.
Km: Substrate concentration at half Vmax.
Allosteric regulation: Binding of regulators at sites other than the active site.
Covalent modification: Chemical modification of enzymes (e.g., phosphorylation).
Feedback inhibition: End products inhibit their own synthesis.
Substrate binding: Substrate binds to the enzyme's active site.
Transition state: Enzyme stabilizes the transition state.
Catalysis: Chemical reaction occurs, converting substrate to product.
Product release: Product is released, and the enzyme returns to its original state.
Isoenzymes are different forms of an enzyme that catalyze the same reaction but differ in structure and regulatory properties.
Tissue specificity: Different tissues may express different isoenzymes.
Regulatory roles: Isoenzymes may be regulated differently.
Conformation of proteins Ramachandran plot, secondary, tertiary and quaternary structure domains motifs and folds
Conformation of Proteins
Ramachandran Plot
The Ramachandran plot is a graphical representation used to visualize the dihedral angles phi and psi of amino acid residues in protein structure. It helps in assessing the conformational space allowed by the amino acids in a polypeptide chain. Certain regions of the plot correspond to favorable conformations, leading to secondary structures such as alpha helices and beta sheets.
Secondary Structure
Secondary structure refers to local conformations of a protein, stabilized by hydrogen bonds. Common types include alpha helices, which are right-handed coils, and beta sheets, which can be parallel or antiparallel. The nature of these structures is influenced by the sequence of amino acids.
Tertiary Structure
The tertiary structure represents the overall 3D shape of a polypeptide, formed by interactions between the side chains of the amino acids. These interactions include hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bridges. The folding of the protein into its tertiary form is essential for its functional activity.
Quaternary Structure
Quaternary structure refers to the assembly of multiple polypeptide chains into a single functional unit. This organization is crucial for the function of many proteins, as it can affect their biochemical properties and interactions. Common examples include hemoglobin and antibodies.
Domains
Domains are distinct functional and structural units within a protein. Each domain can have its own specific function, and proteins may contain multiple domains, contributing to the overall function of the protein. Domains are often evolutionarily conserved.
Motifs
Motifs are short, recurring patterns in protein structure that are associated with particular functions. Unlike domains, motifs do not fold independently. Common examples include the helix-turn-helix motif found in DNA-binding proteins.
Folds
Protein folds refer to the unique 3D structures formed by the entire polypeptide chain, resulting from the arrangement of various secondary structures and domains. The concept of protein folds encompasses the classification of proteins based on their overall shape, which is crucial for understanding protein function and evolution.
Conformation of nucleic acids A-, B-, Z-DNA, t-RNA, micro-RNA
Conformation of Nucleic Acids
A-DNA
A-DNA is a right-handed double helix that is more compact than B-DNA. It is typically formed in dehydrated conditions and features 11 base pairs per turn. The major groove is narrow and deep, while the minor groove is wide and shallow. A-DNA is thought to play a role in the storage of genetic information under specific cellular conditions.
B-DNA
B-DNA is the most common form of DNA found in living cells, characterized by a right-handed helical structure with 10.5 base pairs per turn. It features wide major and minor grooves which facilitate the binding of proteins. B-DNA is typically associated with the replication and transcription of genetic information.
Z-DNA
Z-DNA is a left-handed helical form of DNA, which has a zigzag backbone structure. It is less common than A and B forms and consists of 12 base pairs per turn. Z-DNA is thought to be involved in transcriptional regulation and may play a role in gene expression. Its formation is influenced by the presence of high salt conditions and certain DNA sequences.
t-RNA
Transfer RNA (t-RNA) is a key molecule in protein synthesis, carrying amino acids to the ribosome for incorporation into polypeptides. t-RNA has a cloverleaf structure that facilitates its function, featuring distinct arms for amino acid attachment and anticodon regions for mRNA recognition. The proper conformation of t-RNA is crucial for accurate translation.
micro-RNA
Micro-RNAs (miRNAs) are short, non-coding RNA molecules involved in post-transcriptional regulation of gene expression. They function by binding to complementary sequences on target mRNA, leading to mRNA degradation or inhibition of translation. The conformation of miRNAs is essential for their binding specificity and regulatory functions in various biological processes.
Stabilizing interactions in biomolecules Stability of protein and nucleic acid structures hydrogen bonding, covalent bonding, hydrophobic interactions and disulfide linkage
Stabilizing interactions in biomolecules
Hydrogen Bonding
Hydrogen bonds are weak attractions between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom. In biomolecules, they play a crucial role in maintaining the secondary and tertiary structures of proteins as well as the base pairing in nucleic acids. Hydrogen bonds contribute to stabilizing the three-dimensional configurations that are essential for biological function.
Covalent Bonding
Covalent bonds involve the sharing of electron pairs between atoms. In proteins, peptide bonds are formed between amino acids, creating polypeptide chains essential for protein structure. Nucleic acids are stabilized by phosphodiester bonds between nucleotides. Covalent bonds provide significant stability to biomolecules, forming the backbone of protein and nucleic acid structures.
Hydrophobic Interactions
Hydrophobic interactions occur when nonpolar molecules or regions of molecules aggregate to avoid contact with water. In proteins, hydrophobic amino acids tend to be buried in the interior of the protein structure, while polar amino acids are exposed to the aqueous environment. This interaction is vital for protein folding and maintaining structure. Similarly, in nucleic acids, base stacking interactions contribute to stability.
Disulfide Linkage
Disulfide linkages are covalent bonds formed between sulfur atoms of cysteine residues within a protein. These bonds contribute to the stability of the protein's tertiary structure by creating bridges that can link different parts of a polypeptide chain or different polypeptide chains. Disulfide bonds are particularly important in extracellular proteins that must retain stability in various conditions.
