Transcript PPT
Chemical Foundations Cell Chemistry Molecules are compounds The interaction of these molecules with each other determines how the cell works The types of interactions that molecules have with each other depend on the chemical properties of each of the molecules Understanding the types of interactions allows one to understand and predict the functions of the molecules The Chemistry of Water • The intracellular environment is aqueous • 70-80% of cellular weight is water • Water is the most abundant molecule in biological systems • This is the medium in which the chemistry of life happens Water: How Does It Make You Feel? • Hydrophilic I WATER • Hydrophobic I WATER • Amphipathic I WATER Biomolecules are defined in part by how they relate to water. Time to “Bond” • Covalent Bonds Connect atoms into a molecule: within molecule bonds • Noncovalent Interactions Stabilize groups of atoms into functional structure: within and between molecule interactions – – – – Ionic bond Hydrogen bonds van der Waals interactions hydrophobic effect Covalent Bonds • Strong forces that hold atoms together into molecules • Form when atoms share (one pair or multiple pairs of ) electrons • Have fixed or specific geometric orientation Polar Covalent Bonds • What happens if one atom has a greater affinity for the electron? Water: polar molecule • Covalent Bonds Connect atoms into a molecule: within molecule bonds • Noncovalent Interactions Stabilize groups of atoms into functional structure: within and between molecule interactions – – – – Ionic bond Hydrogen bonds van der Waals interactions hydrophobic effect Ionic Interactions • Attractions between oppositely charged ions (cation+anion) • Do not have a specific geometry associated with them • Weaker than covalent bonds Hydration shell Hydrogen Bonds • Interactions of a positively charge H atom in a molecular dipole with unpaired electrons from another atom • This can occur within the same molecule or a different molecule • Properties of water: – High melting/boiling points – Ability to interact with other molecules Hydrogen Bond Potential Hydrogen Bond Interactions • Solubility of uncharged substances in an aqueous environment largely depends on the ability of that substance to form H bonds with water (Ionic Interactions) • Charged molecules and ions that interact with the dipole in water (Hydrogen Bond Interactions) can dissolved in water • Molecules with polar bonds that can easily form H bonds with water So, these molecules are hydrophilic (water liking) So how about nonpolar molecules? • Non-polar molecules – Do not contain charged groups – Do not possess a dipole moment – Do not become hydrated (do not interact well with water) − In biology, most common nonpolar molecules are the hydrocarbons (C – C; C – H) These molecules are hydrophobic (water fearing) Hydrophobic Interactions • Hydrophobic chemicals don’t form interactions with water – non-polar, uncharged • H-bonds form between water molecules, excluding hydrophobic substances – hydrophobic molecules end up clumped together Van der Waals Interactions • Weak, nonspecific attractive force created when two atoms approach each other closely • Occurs in all types of molecules, both polar and nonpolar • Particularly responsible for the cohesion between nonpolar molecules • ↑Distance ↓Strength • Strength in numbers Done ! • Covalent Bonds Connect atoms into a molecule: within molecule bonds • Noncovalent Interactions Stabilize groups of atoms into functional structure: within and between molecule interactions – – – – Ionic bond Hydrogen bonds van der Waals interactions hydrophobic effect Brief Summary Polar vs. Nonpolar Polar = parts are negatively charged and other parts are positively charged – This can be a formal charge (-) or (+) – This can be separation of charge but overall neutral molecule. Nonpolar = no separation of charge (neutral) - In biology, most common nonpolar molecules are the hydrocarbons - These molecules do not interact well with water Amphipathic - molecule having a polar and a nonpolar part Brief Summary Relative Bond Strengths Complementary shapes Macromolecules Major Biological Molecules: Proteins Nucleic Acids Carbohydrates Lipids How big is big? Molecular weight Oxygen = 16, Carbon = 12 Carbon dioxide = 44 Proteins - 5,000 to 150,000 Macro = large Chemical Building Blocks Biological macromolecules formed by covalent bonds between monomers in a dehydration reaction – Proteins – Nucleic Acids – Polysaccharides Phospholipids form the basic bilayer structure of biomembranes by non-covalent interactions Biological macromolecules formed by covalent bonds between monomers in a dehydration reaction – Proteins – Nucleic Acids – Polysaccharides MONOMERS POLYMER polymerization • Amino Acids • Nucleotides • Sugars Proteins Nucleic Acids Polysaccharides Proteins Proteins are made up of small subunits called amino acids There are 20 different types of amino acids Proteins do most of the jobs in cells Antibodies Enzymes Carry oxygen Transporters Structure (cell cytoskeleton) and many, many more… They can be hooked up in different orders to make a different protein Side Chain R H N C C H H O Amino Group (H2N) OH Carboxyl Group (COOH) Amino acid Each protein has an amino and a carboxyl group on it Proteins as Words ANALOGY: each amino acid is like a letter of the alphabet. Words are constructed by putting together letters in different orders (and different lengths) Sample words: and perform explanation supercalifragilisticexpialidocious Sample proteins Insulin - 51 a.a Rubisco - hundreds of a.a. Amino Acids The 20 AAs: Alanine (A) Arginine (R) Aspartate (D) Asparagine (N) Cysteine (C) Glycine (G) Glutamate (E) Glutamine(Q) Histidine (H) Isoleucine (I) Leucine (L) Lysine (K) Methionine (M) Phenylalanine (F) Proline (P) Serine (S) Threonine (T) Tryptophan (W) Tyrosine (Y) Valine (V) The amino acids can be grouped in terms of their chemical properties. −Ionized @ pH of 7 are the most hydrophilic −(+) Basic; (-) Acidic Amino Acids − Nonpolar side chain are hydrophobic and so poorly soluble in water − The larger the nonpolar side chain, the more hydrophobic the amino acid Protein Conformation • Primary structure: linear AA sequence • Secondary structure: folding of adjacent AAs into 3D shapes (α-helix, β sheets) – Hydrogen bonding β sheets α-helix Protein Conformation • Tertiary structure: overall conformation; domains – Non-covalent ionic interactions – Disulfide bridges Protein Conformation • Quaternary structure: multiple subunits (completely different polypeptide strings) Reminder: MONOMERS POLYMER polymerization • • • Amino Acids Nucleotides Sugars Proteins Nucleic Acids Polysaccharides Nucleic Acids Four building blocks in DNA Adenine Cytosine Guanine Thymine Four building blocks in RNA Adenine Cytosine Guanine Uracil DNA (deoxyribonucleic acid) RNA (ribonucleic acid) It’s amazing - isn’t it? Only 4 different building blocks make up all of the code for us. AND each of us is different even though there are only 4 types of building blocks. What makes us different???? Nucleotides Common structure: phosphate + five carbon sugar + base O Base 5-C sugar RNA How many types of base? DNA Nucleotides Common structure: phosphate + five carbon sugar + base O Base 5-C sugar AGC found in both DNA and RNA T is found only in DNA U only found in RNA Nucleotides Polymerization Nucleotides are hooked together through a phospodiester bond Its all of the phosphodiester bonds that make the phosphate backbone of nucleic acids Water is lost during this reaction too! Reminder: MONOMERS POLYMER polymerization • • • Amino Acids Nucleotides Sugars Proteins Nucleic Acids Polysaccharides Polysaccharides The building blocks of polysaccharides are simple sugars, or monosaccharides e.g. glucose, galactose, etc. Polysaccharides can be used: to store energy - glycogen, starch, as protection - chitin (bugs) as support - cellulose (plants), and to make glycoproteins Disaccharides, Polysaccharides Disaccharides- 2 monosaccharides Lactose= glucose + galactose Sucrose= glucose + fructose Cellulose Long chains arrayed in parallel sheets for strength • Glycosidic bonds ( C-O-C) link multiple sugars in a chain – water is lost in bond formation Summary Chemical Building Blocks Biological macromolecules formed by covalent bonds between monomers in a dehydration reaction – Proteins – Nucleic Acids – Polysaccharides Phospholipids form the basic bilayer structure of biomembranes by non-covalent interactions Phospholipids • Biomembranes- large flexible sheets – Boundries of cells and intracellular organelles – Assembled by non-covalent interactions • Phospholipids are the primary building blocks of biomembranes Amphipathic • Saturated vs. Unsaturated – absence or presence of double bonds in carbon chain – affects melting point – affects the shape of fatty acids Solid at room temp. Trans fats: solid margarine sticks Similarities and Differences of Biological Macromolecules Let’s name some things that each of the previous molecules have in common and are different in terms of polymerization. Lipids are not true macromolecules because they don’t undergo polymerization (but they are big!)