Biochemistry by Itzel Arriaga Roberto Garcia Ime Mbaba

Biochemistry by Itzel Arriaga, Roberto Garcia, Ime Mbaba B 3

Matter ● Made from the building blocks known as atoms o Atoms: contain subatomic particles § protons, neutrons, electrons o Ground state: electrons at the lowest energy level o Excited state: electrons at highest energy level o Isotopes: atoms with one element that varies in the # of neutrons in the nucleus

Chemical Bonding ● Bonds are the attraction of the same electrons o The main types are: § Ionic Bonds: ● Transfer of electrons, either can gain (anion) or lose (cation) an electron § Covalent Bonds: ● Share electrons which will create a molecule ● Can be a single, double, or triple bond ● May not be equal sharing=polar, if equal=nonpolar § Hydrogen Bond: (more of an intermolecular force, not a bond) ● Polar molecules that are bonded to a hydrogen atom o Ex. oxygen, nitrogen, or fluorine

Water Structure ● ● Water is a very important substance in our daily life It is a highly polar molecule made up of an oxygen (-) atom and two hydrogen (+) atoms Its hydrogen bonds make them unique Can hold no more than four hydrogen atoms

Properties of Water ● Water has many different properties: o High Specific Heat: resist changes as the temperature fluctuates and provides a stable environment for organisms o High Heat of Vaporization: water can change phases into water vapor, to help cool off the body through evaporation of sweat o Universal Solvent: Its high polarity allows other polar and ionic substances to be dissolved o Strong Cohesion Tension: water molecules attract to each other and stick to themselves which allows insects to walk on water o Ice floats: less dense than liquid water, based on its crystalline structure

Acids and Bases ● Acids o Substance that increase the hydrogen ion concentration o p. H level of 1 -6 o [H+]>[OH-] ● ● ● Bases o Substance that reduces the hydrogen ion concentration o ph level of 8 -14 o [H+]<[OH-] Pure water is neutral=p. H level of 7, [H+]=[OH-] Buffers are substances that minimize changes in p. H. They accept H+ when they are depleted. ex. carbonic acid that moderates changes in p. H of blood plasma and in the ocean.

Carbon ● ● A covalent bond that can hold 4 valence electrons Shape and multiple bonds is important for enzymes and protein channels Bonds with nitrogen, oxygen and hydrogen most commonly Isomers: compounds that have the same molecular formula but have different properties. o Three types are: § Structural isomers-order of atoms is different § Enantiomers-molecules mirror each other § Cis-trans isomers-have a different spatial arrangement in double bonds

Functional Groups

Carbohydrates Structure & Function ● ● ● Serves as fuel and a building material for the body, exists in a ratio of 1 carbon: 2 hydrogen: 1 oxygen or CH 2 O Monosaccharides are simple sugars, ex: glucose, fructose Simple sugar (dehydration synthesis=release of one water molecule) simple sugar=disaccharide Polysaccharides are many monosaccharides join together Most common polysaccharides: o Cellulose: makes up plant cell walls-structural o Chitin: makes up exoskeleton in arthropods and some mushroom walls-structural o Starch: used in plants-storage o Glycogen: used in the liver and the skeletal musclestorage

Carbohydrates cont

Nucleic Acid Structure & Function ● ● ● Encodes all genetic/hereditary information Only two types RNA and DNA Made up of: o nucleotide (adenine, guanine, thymine, cytosine, uracil-only in RNA) § nucleotides are held by hydrogen bonds § Purine + Pyrimidines o sugar (deoxyribose or ribose) o phosphate

Nucleic Acid Structure cont

Lipids Structure & Function ● ● ● Nonpolar structural properties that are hydrophobic (not soluble in water) Most are made up 1 glycerol and 3 fatty acids (triglyceride) Functions: o Fats: hydrocarbon chain that comes in two types § Saturated: contain single bonds, liquid at room temp. , ‘bad’ fat, ex. butter § Unsaturated: contain double bonds, liquid at room temp. , healthy fat, ex. palm oil o Steroids: contain four fused rings that is a hormone in the endocrine system § ex. cholesterol, testosterone, estradiol o Phospholipids: modified lipids that has a hydrophilic head and a hydrophobic tail (bilayer in the cell membrane)

Lipids cont

Proteins Structure ● ● Basic structure is an amino acid that are joined together by peptide bonds o made of an anime group, carboxyl group and a variable R They have different levels of structure o Primary Structure: order of amino acids o Secondary Structure: , interaction of primary structure to form an amino acids chain that is held by peptide bonds that contains alpha helix and beta pleated sheet o Tertiary Structure: joining of amino acid chains to create a 3 -D shape of a protein o Quaternary Structure: multiple polypeptide chains, ex. hemoglobin

Proteins Function ● Very important macromolecule that has various functions: o Growth and repair o Cell signaling (peptides) o Cell transport (receptors, channels) o Regulation/Endocrine system (hormones such as insulin lowers body sugar) o Enzymatic activity (catalyzes chemical reactions) o Movement (muscle contraction such as actin and myosin) o Defense/Immune system (antibodies)

Proteins Function cont

Macromolecules Summary Macromolecules Monomers/Component s Examples Functions Carbohydrates Monosaccharides cellulose, sugar, glycogen, starch Energy, storage and structural Nucleic Acids Nucleotides (nitrogenous base, phosphate group, and sugar) RNA and DNA Heredity (genes), code for amino acids sequence Lipids Fatty Acids and Glycerol Fats and Oil Insulation, major energy source Proteins Amino Acids Hemoglobin, pepsin, collagen Enzymes, movement

AP Bio Essay Question 1. All life on Earth is carbon based. Our carbon basis allows for the formation of complex molecules. Pick three of the four groups of complex carbon based molecules (macromolecules) and for each: a) For each group, discuss the structural components of the molecule group. b) For each group, discuss two examples of molecules that belong to each of the groups that you chose. Briefly describe their function. c) All of these groups of molecules are created from monomers joining to form polymers. Explain the process that joins these molecules.

AP Bio Essay Answers (A) A. Discuss the structural components of the molecule group. (8 points possible) Carbohydrates: 1 point for each of the following (2 points maximum) ● Polymers are built of chains of monosaccharides joined by glycosidic linkages ● Have the molecular formula (CH 2 O)n ● Hydroxyl group is attached to each carbon ● One carbon contains a carbonyl group ● In aqueous solutions many monosaccharides form rings Lipids: 1 point for the following (1 point maximum) ● Consist mostly of hydrocarbons ● Triglycerides consist of a single glycerol and three fatty acids 1 point for the following (1 point maximum) ● Glycerol is an alcohol with three carbons ● Fatty Acids are long hydrocarbon chains with a carboxyl group at one end ● Unsaturated fatty acid chains contain one or more double bonds between carbons causing ● "kinks" in the chain, while saturated fatty acid chains do not contain double bonds. ● Phospholipids consist of glycerol, 2 fatty acids, and a phosphate group. ● Steroids consist of four carbon rings with no fatty acid tails

AP Bio Essay Answers cont (A) Proteins: 1 point for the following (1 point maximum) ● Chains of amino acid monomers connected by peptide bonds ● Have a 3 -dimensional globular shape 1 point for the following (1 point maximum) ● Amino acids are molecules that consist of a carboxyl group, an amino group and an R-group ● Interactions created by R-groups on different amino acids results in the unique folding of an ● individual polypeptide Nucleic Acids: 1 point for the following (1 point maximum) ● Consist of Nucleotide Monomers ● Nucleotides are made up of a 5 -carbon sugar, a phosphate group, and a nitrogenous base 1 point for the following (1 point maximum) ● Backbone created by phosphate groups of one nucleotide forming strong covalent bonds with ● the sugar of the next nucleotide ● In RNA, a single helix structure is formed ● In DNA, nitrogenous base pair to form a double helix structure

AP Bio Essay Answers (B) B: For each group, discuss two examples of molecules that belong to each of the groups that you chose. Briefly describe their function. (7 points possible) Lipids: 1 point for each of the following (2 points maximum) ● Triglycerides: energy storage, insulation, shock absorption ● Phospholipids: Main structural component of membranes, where they arrange in bilayers. ● ● Waxes: Lipids that serve as coatings for plant parts and as animal coverings. Steroids: Component of animal cell membranes and/or modified to form sex hormones Carbohydrates: 1 point for each of the following (2 points maximum) ● ● ● Proteins: 1 point for each of the following (2 points maximum) ● Enzymes: speed up chemical Any monosaccharide (e. g. glucose, reactions fructose, galactose, ribose, etc. ): major ● Antibodies: part of the energy source in living things immune system, which locate Starch: plant storage form of energy invading cells/substances in the body Cellulose: fiber-like structural material used ● Any other example of a in plant cell walls protein with function listed; Glycogen: animal short-term storage form such as Hemoglobin: an of energy oxygen-transport protein in Chitin: structural material (arthropod red blood cells exoskeleton and fungal cell walls) Nucleic Acids: 1 point for each of the following ● DNA: contains the genetic code for proteins passed from one generation to another ● RNA: functions in actual synthesis of proteins coded for by DNA

AP Bio Essay Answer (C) C: All of these groups of molecules are created from monomers joining to form polymers. Explain the process that joins these molecules. (2 points possible) 1 point for each of the following: ● Condensation reaction called dehydration synthesis ● Monomers are linked together by covalent bonds and water is lost from the two joining molecules.