Biochemistry
by Itzel Arriaga, Roberto Garcia, Ime Mbaba
B3
Matter
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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
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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
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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
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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 1-6
o [H+]>[OH-]
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Bases
o Substance that reduces the hydrogen
ion concentration
o ph level of 8-14
o [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
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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
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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-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
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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
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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 and a hydrophobic tail
(bilayer in the cell membrane)
Lipids cont
Proteins Structure
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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
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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
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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 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 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)
Lipids: 1 point for each of the following (2 points
maximum)
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Triglycerides: energy storage, insulation,
shock absorption
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Phospholipids: Main structural component
of membranes, where they arrange in
bilayers.
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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)
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Proteins: 1 point for each of the
following (2 points maximum)
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Enzymes: speed up chemical
Any monosaccharide (e.g. glucose,
reactions
fructose, galactose, ribose, etc.): major
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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
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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
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DNA: contains the genetic code for proteins passed from one generation to another
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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.