Transcript Chapter 2
The Molecules of Life Chapter 2 Preview • Review of chemical bonds (covalent, ionic, hydrogen bonds) • Small molecules important for life – Water (properties, pH, buffer) – Other small molecules • Macromolecules – – – – Protein Lipid Polysaccharide Nucleic acid Atoms and Elements • Atoms – Basic unit of all matter – three major components • Protons • Electrons • Neutrons Atoms and Elements • Elements – Substance that consists of a single type of atom • 92 naturally occurring elements – 99% of all living matter by weight made up of four » Carbon » Hydrogen » Oxygen » Nitrogen – Phosphorus and sulfur make up additional 0.5% Atoms and Elements • Each element is identified by two numbers – Atomic number • Number of protons occupying the nucleus – In an uncharged element this also equals the number of electrons – Atomic mass • Number of protons plus the number of neutrons Atoms and Elements • Electrons of each element are arranged in orbital • Each orbital contain a certain number of electrons • Each orbital must be filled before electrons occupy the next • Orbitals farthest from the nucleus have the highest energy • most stable when the outer orbital contains the maximum number of electrons – 2, 8, 8 etc. Chemical Bonds and the Formation of Molecules • To fill outer orbitals atoms form bonds with other atoms – Bonds :sharing or the gain or loss of electrons – Molecules are formed when atoms bond together • Valence: the number of electrons that an atom must gain or lose to fill its outer orbital. • types of chemical bonds (vary in strength) – Covalent bonds – Ionic bonds – Hydrogen bonds Covalent Bonds • Formed by sharing of electrons between atoms – Strong (difficult to break) • Requires significant energy – Enzyme – can be polar or non-polar Covalent Bonds – Non-polar covalent • Equal attraction – H-H or C-H – Organic compound » C-C bond Covalent Bonds – Polar covalent • Unequal attraction – Produces a slight charge within the molecule » O-H Ionic Bonds • gaining or losing electrons – Loss and gain of electrons leads to charged atoms (ions) • Cation • Anion • Charged atoms are attracted to each other and form a bond between ions – Ionic bond Ionic Bonds • Ionic bonds are weaker than covalent bonds – Bonds dissociate in water • Important among weak forces holding biological molecules together Hydrogen Bonds • Weak bonds formed between polar molecules – Most commonly between hydrogen and oxygen or nitrogen – Hydrogen bonds occur between molecules such as water and DNA • Covalent bonds are formed within the molecules – Covalent bonds hold atoms together – Hydrogen bonds hold molecules together Hydrogen Bonds • Weakest of the biological bonds – Constantly being formed and broken at room temperature – Large numbers of hydrogen bonds can hold molecules together firmly • Important for molecule-molecule such as enzymesubstrate interaction. questions • What is atomic number? • Cation is formed by: – Lose electron – Share electron – Gain electron • Which is the strongest chemical bond? – Ionic bond – Hydrogen bond – Covalent bond Small molecules of the Cell--water • Most important molecule is water – Makes up over 70% of all living organisms by weight – Importance of water depends on it unusual bonding properties Bonding Properties of Water • Bonding properties of water – Hydrogen bonds form between water molecules Bonding Properties of Water • Water is a great solvent. – Polar nature accounts for ability – Molecules dissolved must contain charged atoms – Ions become surrounded by water • Na+ and Cl- ions no longer able to bond to each other Important Property of solution--pH • Acidity is measured as pH – Defined as concentration of H+ ions • potential Hydrogen • Measured on logarithmic scale of 0 to 14 – Neutral is pH 7 (H+ and OH- ions are equal solution) – acid – base • [H+] x [OH-]=10-14 • Buffer system: help to maintain neutral pH. Other Small Molecules in the Cell • small organic and inorganic molecules – ~ 1% of dry weight of bacteria composed of inorganic ions • Na+, K+, Mg2+, Ca2+, Fe2+, Cl-, PO43- and SO42– Certain enzymes require positively charged ions for proper functioning – Negatively charged phosphate ions are essential in energy metabolism – Small organic molecules act as precursor metabolites • These are converted to the building blocks of macromolecules Macromolecules and Their Component Parts • Macromolecules are very large – Macro = large • Biological macromolecules are divided into four classes – Proteins – Polysaccharides (carbohydrates) – Lipids – Nucleic acids Macromolecules and Their Component Parts • All macromolecules are polymers – Poly = many – formed by joining smaller subunits together • dehydration reaction Macromolecules and Their Component Parts • Macromolecules are broken down into smaller subunits • hydrolysis questions • What is pH? • What is the function of buffer? • Macromolecules are formed by___ reaction of the subunits. hydrolysis dehydration Proteins and Their Functions • 50% of cell dry weight • Made up of amino acid subunits • Most versatile – Some responsibilities include • Catalyzing reactions • Composition and shape of certain bacterial structures • Gene regulation • Nutrient procurement Amino Acid Subunits • 20 different types of amino acids • common features for amino acids – The side chain differentiates the amino acids • Hydrophilic • Hydrophobic (contain methyl group) – Stereoisomers • L, D amino acid Peptide Bonds and Their Synthesis • peptide bonds – Formed between carboxyl group of one amino acid and the amino group of the following amino acid – Release water molecule Protein Structure • Protein function depends on the shape of the protein – Protein shape depends on the sequence of amino acids • Proteins have four structures – – – – Primary Secondary Tertiary Quaternary Protein Structure • Primary structure – Sequence of amino acids – In large part determines other protein features Protein Structure • Secondary structure – Primary structure folds into new configuration • Helical structure – Alpha (α) helix • Pleated structure – Beta (β) sheet – Results from weak bonds formed between amino acids • Certain sequences of the aa leads to distinct secondary structures Protein Structure • Tertiary structure – 3 dimensional structure – 2 major shapes • Globular • Fibrous – Becomes functional protein – Tertiary structure depends on primary structure and interaction with water. • Hydrophobic interaction • S-S bond (covalent) Protein Denaturation • Specific shape for proper function – breaking bonds within the protein disrupt structure • protein stop functioning • Denaturation can be reversible or irreversible – Environment determines reversibility • Heat • chemical Substituted Proteins • Proteins that has other kind of molecules covalently bond to side chain of amino acid. – Glycoprotein: sugar attached – Lipoprotein: lipid bond. questions • How many kinds of amino acid are there in a protein? • What is the primary structure of a protein? • What determine the shape of a protein? Carbohydrates • Carbohydrates are diverse group of molecules with various sizes • Play important roles in all organisms including – Common source of food and energy – Form part of nucleic acids – Form part of bacterial cell wall Carbohydrates • Carbohydrates contain carbon, hydrogen and oxygen in 1:2:1 ratio – CH2O • Monosaccharide – Classified by number of carbons in molecule – Most common monosaccharides • 5 and 6 carbon sugars Carbohydrates • Disaccharides – two monosaccharides joined through dehydration synthesis – Lactose and sucrose most common in nature • Glucose + galactose = lactose • Glucose + fructose = sucrose – Maltose less common • Glucose + glucose = maltose Carbohydrates • Polysaccharides – Serve different function – Cellulose most abundant organic molecule on earth • Polymer of glucose molecules • Principle constituent in plant cell wall – Glycogen is carbohydrate storage molecule of animals and some bacteria • Polymer of glucose subunits – Dextran storage molecule for carbon and energy for some bacteria • Polymer of glucose subunits Nucleic Acids • Two types of nucleic acid – DNA • Carry genetic code in all cells – RNA • Decodes sequence of DNA to produce proteins – Subunits of nucleic acids are nucleotides DNA • DNA are composed of 4 kinds of nucleotides. – Five carbon sugar • Deoxyribose – Phosphate molecule – Nitrogenous base • 4 kinds of base: A, T, G, C • DNA sequence are represented by base sequence DNA • Nucleotides joined through covalent bonding to form a DNA strand – phosphate of one nucleotide join the sugar of the adjacent nucleotide • Results in a sugar phosphate backbone • Direction 5’ to 3’ DNA • double stranded helical molecule – hydrogen bonding between bases from each strand • Specific pairing between bases A-T, G-C • Bases are complementary RNA • Involved in decoding DNA • Structure is similar to DNA – Uracil replace thymine – ribose in place of deoxyribose – RNA is generally shorter – Single stranded. questions • What is the subunit of DNA? • What is the difference between DNA and RNA? Lipids • Critical component of the cell membrane – Membranes act a gatekeepers to the cell • Heterogeneous group of molecules – Made up of different subunits • Defining feature – Insoluble in water • Can be divided into two general classes – Simple lipids – Compound lipids Simple Lipids • Contain only carbon, hydrogen and oxygen • Most common are called fats – Made of glycerol and fatty acid • Triglyceride • Fatty acids bond to glycerol covalently through dehydration synthesis Simple Lipids • Steroids are also considered simple lipids • insoluble in water • Sterol (with OH in one ring) – Example: cholesterol Compound Lipids • fatty acids, glycerol and other elements • Phospholipid most important compound lipid – a phosphate and two fatty acids attached to a glycerol molecule • Amphiphilic molecule Compound Lipids • Phospholipids – Major component in lipid cell membrane • bilayer of phospholipids • orientation • a barrier to the entry and exit of cellular substances questions • What is the major component of cell membrane? • What is the defining feature of lipid?