Biochemistry by Itzel Arriaga, Roberto Garcia, Ime Mbaba

B3

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 levelo Excited state: electrons at highest energy levelo 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 pH level of 1-6o [H+]>[OH-]

● Baseso Substance that reduces the

hydrogen ion concentration o ph level of 8-14o [H+]<[OH-]

● Pure water is neutral=pH level of 7, [H+]=[OH-] ● Buffers are substances that minimize changes in pH. They accept H+ when they are

depleted. ex. carbonic acid that moderates changes in pH 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 CH2O

● 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-

structuralo Chitin: makes up exoskeleton in arthropods

and some mushroom walls-structuralo Starch: used in plants-storageo Glycogen: used in the liver and the skeletal

muscle-storage

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 oilo 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 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 acidso 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 proteino Quaternary Structure: multiple polypeptide chains, ex. hemoglobin

Proteins Function ● Very important macromolecule that

has various functions:o Growth and repairo 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/Components

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 (CH2O)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 shape1 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 bases 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)

Carbohydrates: 1 point for each of the following (2 points maximum)

● Any monosaccharide (e.g. glucose, fructose, galactose, ribose, etc.): major energy source in living things

● Starch: plant storage form of energy

● Cellulose: fiber-like structural material used in plant cell walls

● Glycogen: animal short-term storage form of energy

● Chitin: structural material (arthropod exoskeleton and fungal cell walls)

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

Proteins: 1 point for each of the following (2 points maximum)

● Enzymes: speed up chemical reactions

● Antibodies: part of the immune system, which locate invading cells/substances in the body

● Any other example of a protein with function listed; such as Hemoglobin: an oxygen-transport protein in red blood cells

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.