Cell Biology Unit 2 ReviewChemical Foundations of Cells

Key Concepts

• Matter consists of elements and compounds made up of atoms, the fundamental units of matter
• Atoms contain protons, neutrons, and electrons arranged in a specific structure
• Chemical bonds, including ionic and covalent bonds, form between atoms to create molecules and compounds
• Water is a polar molecule with unique properties essential for life, such as cohesion, adhesion, and high specific heat capacity
  • Cohesion water molecules stick together due to hydrogen bonding
  • Adhesion water molecules are attracted to other substances
• Acids and bases are important in biological systems, influencing pH and chemical reactions
  • Acids donate hydrogen ions (H+) and have a pH below 7
  • Bases accept hydrogen ions and have a pH above 7
• Organic molecules, such as carbohydrates, lipids, proteins, and nucleic acids, are the building blocks of life
• Macromolecules are large, complex molecules formed by the polymerization of smaller subunits (monomers)
• Energy is required for life processes and is often stored in chemical bonds, such as those found in ATP (adenosine triphosphate)

Chemical Building Blocks

• Atoms are composed of protons, neutrons, and electrons
  • Protons positively charged particles located in the nucleus
  • Neutrons neutral particles located in the nucleus
  • Electrons negatively charged particles orbiting the nucleus in shells
• Elements are pure substances consisting of only one type of atom, identified by their atomic number (number of protons)
• Compounds are substances made up of two or more elements chemically combined in a specific ratio
• Chemical bonds form between atoms to create molecules and compounds
  • Ionic bonds form through the transfer of electrons between atoms, creating ions (cations and anions)
  • Covalent bonds form through the sharing of electrons between atoms
    • Single, double, or triple covalent bonds can form depending on the number of shared electron pairs
• Molecules are two or more atoms held together by chemical bonds
• Isotopes are atoms of the same element with different numbers of neutrons, resulting in different atomic masses

Water and Its Properties

• Water (H2O) is a polar molecule consisting of one oxygen atom covalently bonded to two hydrogen atoms
• Hydrogen bonds form between water molecules due to the attraction between the slightly positive hydrogen atoms and slightly negative oxygen atoms
• Water has a high specific heat capacity, requiring a large amount of energy to change its temperature, which helps regulate body temperature in living organisms
• Water has a high heat of vaporization, requiring a large amount of energy to convert from liquid to gas, which helps in evaporative cooling
• Water is an excellent solvent, capable of dissolving many polar and ionic substances due to its polarity
• Cohesion, the attraction between water molecules, allows for capillary action and the transport of water in plants
• Adhesion, the attraction between water molecules and other substances, allows water to "climb" up narrow tubes (capillary action)
• Surface tension, caused by cohesion, allows some organisms to walk on water (water striders) and helps in the formation of bubbles and droplets

Acids, Bases, and pH

• Acids are substances that donate hydrogen ions (H+) in aqueous solutions
  • Examples of acids include hydrochloric acid (HCl), sulfuric acid (H2SO4), and acetic acid (CH3COOH)
• Bases are substances that accept hydrogen ions (H+) in aqueous solutions
  • Examples of bases include sodium hydroxide (NaOH), potassium hydroxide (KOH), and ammonia (NH3)
• pH is a measure of the concentration of hydrogen ions (H+) in a solution, ranging from 0 to 14
  • A pH of 7 is neutral, below 7 is acidic, and above 7 is basic
  • The pH scale is logarithmic, meaning a change of one pH unit represents a tenfold change in H+ concentration
• Buffers are solutions that resist changes in pH when small amounts of acids or bases are added
  • Buffers contain a weak acid and its conjugate base or a weak base and its conjugate acid
  • Buffers are important in maintaining stable pH in biological systems (blood pH)
• Acids and bases play crucial roles in enzyme function, protein structure, and cellular processes

Organic Molecules in Cells

• Organic molecules are carbon-based compounds that are essential for life
• The four main classes of organic molecules in cells are carbohydrates, lipids, proteins, and nucleic acids
• Carbohydrates are composed of carbon, hydrogen, and oxygen atoms in a 1:2:1 ratio (CH2O)n
  • Monosaccharides are simple sugars and the monomers of carbohydrates (glucose, fructose)
  • Disaccharides are formed by the joining of two monosaccharides (sucrose, lactose)
  • Polysaccharides are long chains of monosaccharides (starch, cellulose, glycogen)
• Lipids are hydrophobic molecules that do not dissolve in water
  • Fatty acids are the building blocks of many lipids and consist of a hydrocarbon chain with a carboxyl group (COOH)
  • Triglycerides are formed by the joining of three fatty acids to a glycerol molecule and serve as energy storage
  • Phospholipids are the main components of cell membranes and have a hydrophilic head and hydrophobic tails
• Proteins are polymers of amino acids joined by peptide bonds
  • Amino acids are the monomers of proteins and have an amino group (NH2), a carboxyl group (COOH), and a variable side chain (R group)
  • Proteins have four levels of structure: primary (amino acid sequence), secondary (alpha helices and beta sheets), tertiary (3D folding), and quaternary (multiple polypeptide chains)
• Nucleic acids are polymers of nucleotides and store and transmit genetic information
  • DNA (deoxyribonucleic acid) is a double-stranded helix that stores genetic information
  • RNA (ribonucleic acid) is single-stranded and involved in protein synthesis (mRNA, tRNA, rRNA)

Macromolecules and Their Functions

• Macromolecules are large, complex molecules formed by the polymerization of smaller subunits (monomers)
• Carbohydrates serve various functions in cells, including energy storage (starch, glycogen), structural support (cellulose), and cell-cell recognition (glycoproteins)
• Lipids have diverse functions, such as energy storage (triglycerides), cell membrane structure (phospholipids), signaling (steroids), and insulation (waxes)
• Proteins perform a wide range of functions in cells, including catalysis (enzymes), structure (cytoskeleton), transport (hemoglobin), signaling (hormones), and defense (antibodies)
  • Enzymes are biological catalysts that lower the activation energy of chemical reactions, increasing reaction rates
  • Enzymes are specific to their substrates and have an active site where the reaction occurs
• Nucleic acids store and transmit genetic information
  • DNA stores genetic information in the form of genes, which code for proteins
  • RNA is involved in the process of protein synthesis, acting as a messenger (mRNA), a transfer molecule (tRNA), and a structural component of ribosomes (rRNA)
• The structure and function of macromolecules are intimately linked, and changes in structure can lead to changes in function

Energy and Chemical Reactions

• Energy is the capacity to do work or cause change and is required for all life processes
• Chemical reactions involve the breaking and forming of chemical bonds, which can either release or absorb energy
• Exergonic reactions release energy and are spontaneous (energy flows out)
  • Examples of exergonic reactions include combustion, cellular respiration, and the breakdown of ATP
• Endergonic reactions absorb energy and are non-spontaneous (energy flows in)
  • Examples of endergonic reactions include photosynthesis, the synthesis of ATP, and the synthesis of macromolecules
• Activation energy is the minimum energy required for a chemical reaction to occur
  • Enzymes lower the activation energy of chemical reactions, allowing them to proceed more quickly
• ATP (adenosine triphosphate) is the primary energy currency in cells
  • ATP consists of an adenosine molecule and three phosphate groups
  • Energy is stored in the high-energy bonds between the phosphate groups
  • The hydrolysis of ATP to ADP (adenosine diphosphate) and inorganic phosphate (Pi) releases energy for cellular work
• Coupled reactions link endergonic and exergonic reactions, allowing the energy released from an exergonic reaction to drive an endergonic reaction
  • The synthesis of ATP is often coupled to the breakdown of glucose during cellular respiration

Applying Chemical Principles to Cell Biology

• Understanding the chemical principles governing atoms, molecules, and chemical reactions is essential for understanding cell biology
• The structure and function of biological molecules, such as proteins and nucleic acids, are determined by their chemical properties
  • The amino acid sequence of a protein determines its folding and, consequently, its function
  • The base pairing rules (A-T, G-C) in DNA allow for the storage and replication of genetic information
• Chemical gradients, such as concentration and electrochemical gradients, drive many cellular processes
  • The sodium-potassium pump establishes concentration gradients that drive the transport of other molecules across cell membranes
  • The proton gradient generated during cellular respiration drives the synthesis of ATP through chemiosmosis
• Chemical signaling, such as hormone signaling and neurotransmission, relies on the specific binding of signaling molecules to receptors
  • The binding of a hormone to its receptor triggers a cascade of chemical reactions that lead to a cellular response
• The regulation of gene expression involves chemical modifications to DNA and proteins
  • DNA methylation can silence gene expression by preventing the binding of transcription factors
  • Histone acetylation can increase gene expression by making DNA more accessible to transcription machinery
• The study of cell biology is ultimately the study of the chemical processes that underlie life, and a strong foundation in chemistry is essential for understanding these processes