🔬Biophysics Unit 3 – Biochemistry: Macromolecules & Cell Components

Key Macromolecules

• Macromolecules are large, complex molecules essential for life and include carbohydrates, lipids, proteins, and nucleic acids
• Formed by joining smaller subunits called monomers through dehydration synthesis reactions, which remove water molecules to create covalent bonds between monomers
• Polymers are long chains of monomers linked together through these reactions (polysaccharides, polypeptides)
• Macromolecules have diverse structures and functions determined by the specific arrangement and interactions of their monomers
  • Proteins form enzymes, structural components, and signaling molecules
  • Carbohydrates store energy and provide structural support (cellulose in plant cell walls)
• Macromolecules are assembled, modified, and degraded through tightly regulated cellular processes to maintain homeostasis
• Interactions between different types of macromolecules contribute to complex biological processes (DNA-protein interactions in gene regulation)
• Studying the structure and function of macromolecules is crucial for understanding cellular processes, disease mechanisms, and developing targeted therapies

Cell Structure Basics

• Cells are the fundamental units of life, capable of carrying out all essential functions such as metabolism, growth, and reproduction
• Two main types of cells: prokaryotic (bacteria and archaea) and eukaryotic (animals, plants, fungi, and protists)
  • Prokaryotic cells lack membrane-bound organelles and a true nucleus
  • Eukaryotic cells have a true nucleus and various membrane-bound organelles (mitochondria, endoplasmic reticulum)
• Cell membrane is a selectively permeable phospholipid bilayer that separates the cell interior from the external environment and regulates the passage of molecules
• Cytoplasm is the gel-like substance within the cell where organelles and other cellular components are suspended
• Nucleus contains the cell's genetic material (DNA) and is the site of DNA replication and transcription
  • Nuclear envelope is a double membrane that separates the nucleus from the cytoplasm
  • Nuclear pores allow selective transport of molecules between the nucleus and cytoplasm
• Ribosomes are the sites of protein synthesis and can be found freely in the cytoplasm or attached to the rough endoplasmic reticulum
• Endomembrane system includes the endoplasmic reticulum, Golgi apparatus, and lysosomes, which work together for protein and lipid synthesis, modification, and transport

Protein Structure and Function

• Proteins are linear polymers of amino acids joined by peptide bonds, which form through dehydration synthesis reactions between the carboxyl group of one amino acid and the amino group of another
• 20 different amino acids serve as the building blocks of proteins, each with a unique side chain (R group) that determines its chemical properties
• Protein structure is organized into four levels: primary, secondary, tertiary, and quaternary
  • Primary structure is the linear sequence of amino acids
  • Secondary structure refers to local folding patterns (α-helices and β-sheets) stabilized by hydrogen bonds
  • Tertiary structure is the overall three-dimensional shape of a polypeptide chain, stabilized by interactions between side chains (disulfide bridges, hydrophobic interactions)
  • Quaternary structure is the arrangement of multiple polypeptide subunits in a multi-subunit protein (hemoglobin)
• Protein folding is guided by the amino acid sequence and cellular chaperone proteins, which help proteins reach their native conformation
• Misfolded proteins can aggregate and cause cellular dysfunction, leading to diseases (Alzheimer's, Parkinson's)
• Proteins perform a wide range of functions, including catalysis (enzymes), transport (hemoglobin), structural support (collagen), and signal transduction (G protein-coupled receptors)
• Post-translational modifications (phosphorylation, glycosylation) can alter protein function and regulate cellular processes

Lipids and Membranes

• Lipids are a diverse group of hydrophobic molecules that include fats, oils, waxes, and steroids
• Three main types of lipids: triglycerides (energy storage), phospholipids (membrane components), and steroids (hormones and membrane components)
• Triglycerides consist of a glycerol molecule joined to three fatty acids by ester bonds
  • Fatty acids are long hydrocarbon chains with a carboxyl group at one end
  • Saturated fatty acids have single bonds between carbon atoms, while unsaturated fatty acids have one or more double bonds
• Phospholipids have a hydrophilic head (phosphate group) and two hydrophobic tails (fatty acids), making them amphipathic
  • Phospholipids spontaneously form bilayers in aqueous environments, with hydrophobic tails facing inward and hydrophilic heads facing outward
  • Phospholipid bilayers are the basic structure of cell membranes and organelle membranes
• Membrane proteins are embedded in or associated with the phospholipid bilayer and perform various functions (ion channels, receptors, enzymes)
• Cholesterol is a steroid that modulates membrane fluidity and permeability in animal cells
• Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids that organize signaling molecules and regulate cellular processes
• Lipid metabolism involves the synthesis, storage, and breakdown of lipids for energy production and membrane synthesis

Carbohydrates and Energy

• Carbohydrates are molecules composed of carbon, hydrogen, and oxygen atoms, typically in a 1:2:1 ratio (CH2O)n
• Three main types of carbohydrates: monosaccharides (simple sugars), disaccharides (two monosaccharides), and polysaccharides (long chains of monosaccharides)
  • Monosaccharides include glucose, fructose, and galactose
  • Disaccharides include sucrose (table sugar), lactose (milk sugar), and maltose (malt sugar)
  • Polysaccharides include starch (energy storage in plants), glycogen (energy storage in animals), and cellulose (structural support in plant cell walls)
• Carbohydrates are the primary energy source for cells and are broken down through glycolysis and cellular respiration to produce ATP
  • Glycolysis is a 10-step pathway that converts glucose into pyruvate, generating 2 ATP and 2 NADH molecules
  • Cellular respiration includes the Krebs cycle and electron transport chain, which further oxidize pyruvate to produce additional ATP, NADH, and FADH2
• Glucose is stored as glycogen in animal cells and as starch in plant cells for later use
• Pentose phosphate pathway is an alternative route for glucose metabolism that generates NADPH and ribose-5-phosphate (precursor for nucleotide synthesis)
• Carbohydrates also play important roles in cell signaling (glycoproteins, proteoglycans) and immune recognition (blood group antigens)

Nucleic Acids: DNA and RNA

• Nucleic acids are polymers of nucleotides that store and transmit genetic information
• Two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
• Nucleotides consist of a nitrogenous base, a pentose sugar (deoxyribose in DNA, ribose in RNA), and a phosphate group
  • Nitrogenous bases in DNA: adenine (A), thymine (T), guanine (G), and cytosine (C)
  • Nitrogenous bases in RNA: adenine (A), uracil (U), guanine (G), and cytosine (C)
• DNA is a double-stranded helix with complementary base pairing (A-T, G-C) between strands
  • DNA replication is the process of copying the genetic material before cell division, ensuring each daughter cell receives an identical set of chromosomes
  • DNA polymerase is the enzyme responsible for synthesizing new DNA strands using the original strands as templates
• RNA is typically single-stranded and has various functions in gene expression and regulation
  • Messenger RNA (mRNA) carries genetic information from DNA to ribosomes for protein synthesis
  • Transfer RNA (tRNA) delivers amino acids to ribosomes during translation
  • Ribosomal RNA (rRNA) is a structural and catalytic component of ribosomes
• Central dogma of molecular biology describes the flow of genetic information from DNA to RNA to proteins
  • Transcription is the synthesis of RNA from a DNA template, catalyzed by RNA polymerase
  • Translation is the synthesis of proteins from an mRNA template, carried out by ribosomes
• Mutations are changes in the DNA sequence that can alter gene function and lead to genetic disorders or evolutionary adaptations

Enzyme Kinetics

• Enzymes are biological catalysts that accelerate chemical reactions by lowering the activation energy
• Enzymes are highly specific to their substrates and reactions due to their unique three-dimensional structures
• Active site is the region of an enzyme where the substrate binds and the reaction occurs
  • Substrate specificity is determined by the shape and chemical properties of the active site
  • Induced fit model suggests that substrate binding causes conformational changes in the enzyme, optimizing the active site for catalysis
• Enzyme kinetics is the study of the rates of enzyme-catalyzed reactions and the factors that influence them
• Michaelis-Menten equation describes the relationship between substrate concentration and reaction rate:
  • $v = \frac{V_{max}[S]}{K_m + [S]}$
  • $v$ is the reaction rate, $V_{max}$ is the maximum reaction rate, $[S]$ is the substrate concentration, and $K_m$ is the Michaelis constant
• Lineweaver-Burk plot (double reciprocal plot) is used to determine $V_{max}$ and $K_m$ from experimental data
• Factors affecting enzyme activity include temperature, pH, substrate concentration, and the presence of inhibitors or activators
  • Optimal temperature and pH are specific to each enzyme and reflect the conditions in which they function best
  • Competitive inhibitors bind to the active site and compete with the substrate, increasing $K_m$ but not affecting $V_{max}$
  • Non-competitive inhibitors bind to a site other than the active site and decrease $V_{max}$ without changing $K_m$
• Allosteric regulation involves the binding of effector molecules to sites other than the active site, causing conformational changes that alter enzyme activity
  • Allosteric activators increase enzyme activity, while allosteric inhibitors decrease activity
  • Allosteric regulation allows for fine-tuning of metabolic pathways in response to cellular needs

Techniques for Studying Biomolecules

• Spectroscopy techniques use the interaction of electromagnetic radiation with matter to study the structure and properties of biomolecules
  • UV-visible spectroscopy measures the absorption of light in the UV and visible regions, often used to quantify proteins and nucleic acids
  • Fluorescence spectroscopy detects the emission of light from fluorescent molecules, used to study protein folding and interactions
  • Circular dichroism spectroscopy measures the differential absorption of left and right circularly polarized light, providing information on protein secondary structure
• Chromatography techniques separate mixtures of biomolecules based on their physical and chemical properties
  • Size-exclusion chromatography separates molecules based on their size and shape, often used to purify proteins and determine their molecular weight
  • Ion-exchange chromatography separates molecules based on their charge, using charged resins to selectively bind and elute proteins
  • Affinity chromatography uses specific interactions between molecules (antibody-antigen, enzyme-substrate) to purify proteins
• Electrophoresis techniques separate charged biomolecules in an electric field based on their size and charge
  • SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) is used to separate proteins based on their molecular weight
  • Agarose gel electrophoresis is used to separate DNA and RNA fragments based on their size
  • Isoelectric focusing separates proteins based on their isoelectric point (pI)
• Mass spectrometry measures the mass-to-charge ratio of ionized molecules, providing information on the molecular weight and structure of biomolecules
  • Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) are common ionization techniques for biomolecules
  • Tandem mass spectrometry (MS/MS) allows for the sequencing of peptides and identification of proteins
• X-ray crystallography determines the three-dimensional structure of biomolecules by analyzing the diffraction patterns of X-rays passed through a crystallized sample
  • Requires the formation of well-ordered protein or nucleic acid crystals
  • Provides high-resolution structural information, including the positions of individual atoms
• Nuclear magnetic resonance (NMR) spectroscopy uses the magnetic properties of atomic nuclei to study the structure and dynamics of biomolecules in solution
  • Provides information on the chemical environment and connectivity of atoms within a molecule
  • Can be used to study protein folding, ligand binding, and conformational changes