UNIT II - BIOCHEMISTRY Big Campbell ~ Ch 2-5 Baby Campbell ~ Ch 2-3
UNIT II - BIOCHEMISTRYBig Campbell ~ Ch 2-5
Baby Campbell ~ Ch 2-3
I. CHEMICAL BASIS OF LIFE
• Elementso Cannot be broken down without losing characteristic
propertieso Six elements in greatest concentration in living things are
Sulfur Phosphorus Oxygen Nitrogen Carbon Hydrogen
o Defined by Atomic # which is = #of protons and the #of electrons in most cases
I. CHEMICAL BASIS OF LIFE, cont
• Atomso Smallest unit of matter
that retains properties of that element Protons (+); found in
nucleus Neutrons (neutral);
found in nucleus Electrons (-); found in
electron clouds.
o Atomic Mass = p + no Isotopes – when an
atom has a different atomic mass, Ex: C12, C13, C14
I. CHEMICAL BASIS OF LIFE, cont• Chemical Bonds
o Chemical behavior of atom determined by valence electronso Atoms interact with other atoms to complete their valence shells,
either by transferring or sharing electrons
I. CHEMICAL BASIS OF LIFE, cont
• Types of Chemical Bondso Ionic – Results when one atom has a much stronger
attraction for electrons than another; one atom has a greater electronegativity. Electron(s) are transferred resulting in formation of ions. Bond forms due to charge attraction. Strength is dependent on environment
I. CHEMICAL BASIS OF LIFE, conto Covalent Bonds – More stable;
results from sharing a pair of valence electrons. Forms a molecule. One pair of electrons shared = single covalent bond; two pair of electrons shared = double covalent bond.Non-polar covalent bond –
formed when electronegativity of atoms is the same
Polar covalent bond – formed when one atom is more electronegative; unequal sharing of electrons results in slight charges at either end of molecule
II. WATER• Properties of Water Due to its
Polarityo Hydrogen “bonds”
II. WATERo “Stickiness”
Cohesion Surface Tension
AdhesionCapillary Action
II. WATER, conto Regulation of Temperature
High specific heat High heat of vaporization
o Density of “solid” water _<_ density of liquid water
II. WATER, conto Solvent of Life
Hydrophilic “Water-loving” Polar molecules
“pull apart” ionic compounds & other polar molecules
Hydrophobic “Water-hating” Non-ionic and non-
polar substances are repelled by water
II. WATER, cont
• Dissociation of Watero Rare, but measurable phenomenono (2)H2O → H3O+ + OH- → H+ + OH-
o In aqueous solution at 25˚C, total conc of [H+] [OH-] = 1x10-14
Neutral solution → [H+] = [OH-]; therefore [H+] = 1 x 10-7
o pH = Provides a means for a compressed measurement of [H+] -log10[H+]
o Acid – Substance that dissolves in water to __increase_ [H+] [H+] _>___ 1 x 10-7; pH __<__ 7
o Base - Substance that dissolves in water to _decrease_ [H+] [H+] _<___ 1 x 10-7; pH _>_ 7
o pH of Water = 7
II. WATER, cont
o Buffers Maintain a constant pH by donating, accepting H+
Bicarbonate Buffer System Very important buffer system in blood pH of blood = _7.4_
III. ORGANIC CHEMISTRY – THE STUDY OF CARBON
• Atomic Structure of Co Atomic Number of C = 6
6 protons 6 electrons __4___ valence electrons
o Hydrocarbon – composed on only C-H; impt in fossil fuels. Hydrophobic
o Isomer – compounds with the same #of elements/atoms, but a different structural arrangement. See Ex…
Four Ways Carbon skeletons can vary
III. ORGANIC CHEMISTRY, contFunctional Group Structure Characteristics
Hydroxyl-OH may be written as HO-
Very polar; forms “ –ols” (alcohols)
Carbonyl
C=O, also written -CO Ketone – if carbonyl group is within the carbon skeleton
Aldehydes – if carbonyl group is at the end of the carbon skeleton.
Carboxyl-COOH; c alled carboxylic acids
Acts as an acid; donates H+ to solution
III. ORGANIC CHEMISTRY, cont
Functional Group Structure Characteristics
Amino-NH2; called amines Acts as a base; removes H+
from solution
Sulfhydryl-SH; called thiols Important in stabilizing protein
structure; forms disulfide bridges
Phosphate-OPO3; known as organic phosphates
Gives molecule negative charge; react with water to release energy
Methyl-CH3 Affects the expression of
DNA
IV. THE BIOMOLECULES
• Most are polymers made up of single units called monomers
• Four Main Groups CARBOHYDRATES
LIPIDS
PROTEINS
NUCLEIC ACIDS
IV. BIOMOLECULES, cont• Dehydration Synthesis
o Also called _CONDENSATION REACTION__o Reaction that occurs to build polymerso Forms __COVALENT_ bond between 2 monomerso _WATER_lost as waste producto Requires energy input, enzymes
IV. BIOMOLECULES, cont• Hydrolysis
o “__WATER BREAKING/SPLITTING_”o Covalent bonds between monomers broken Releases energy;
reaction accelerated with enzymes
V. CARBOHYDRATES
• Provide fuel, act as building material• Generally, formula is a multiple of CH2O
• Contain carbonyl group & multiple hydroxyl groups• Monomer = monosaccharides• Monosaccharides – usually found as ringed structures
o PentosesRibose
Deoxyribose
V. CARBOHYDRATES, conto Hexoses
GlucoseFructoseGalactose
V. CARBOHYDRATES, cont• Disaccharides
o 2 monosaccharides covalently bonded together through dehydration synthesis
o ExampleSucroseLactoseMaltose
V. CARBOHYDRATES, cont• Polysaccharides
o Many monosaccharides covalently bonded together through dehydration synthesis
o Two main groups Energy Storage Polysaccharides
Starch – Plants store glucose as starch in cell structures called plastids. Humans have enzymes to hydrolyze starch to glucose monomers.
Glycogen – Storage form of glucose in animals. More highly-branched than starch. In humans, found mainly in liver, muscle cells
V. CARBOHYDRATES, cont Structural polysaccharides
Cellulose – polymer of glucose. Every other glucose is upside down – forms parallel strands of glucose molecules held together with H-bonds
V. CARBOHYDRATES, contStructural polysaccharides• Chitin – found in arthropod
exoskeleton, cell walls of fungi
VI. LIPIDS• Very diverse group• Non-polar, hydrophobic molecules• Hydro_phobic__• Not true polymers• Four groups
Fats & oils phospholipids steroids waxes
VI. LIPIDS, cont
• Fats& Oilso Composed of
glycerol + 3 fatty acids
o Glycerol = 3-C alcohol
o Fatty acids – long hydrocarbon chains ending with carboxyl group
o AKA triglycerideso Used for energy
storage
VI. LIPIDS, cont
Saturated fats – “Saturated with hydrogens”; contain all single bonds. Typically from animal source, solid at room temp. Associated with greater health risk.
Unsaturated fats – Contain double bonds, fewer H-atoms. Results in “kinked” hydrocarbon chain. Typically from plant source, liquid at room temp.
Fats, cont.
• Saturated fat • Unsaturated fat
VI. LIPIDS, cont
• Phospholipids 2 fatty acids
attached first 2-carboxyl groups of glycerol.
Negatively-charged phosphate group is attached to 3rd carboxyl
Partially polar and partially non-polar
Found in all cell membranes.
Phospholipid, cont.
VI. LIPIDS, cont• Waxes – One fatty acid attached to an alcohol. Very
hydrophobic. Used as coating, lubricant• Steroids – Consist of 4-rings with different functional
groups attached. o Cholesterol – steroid found in animal cell membranes;
precursor for sex hormones
Steroids, cont.
VII. PROTEINS
• Important part of virtually all cell structures, processes, reactions
• Amino Acids – Proteins are large polymers made up of amino acid monomers. All amino acids have the same basic structure:
o Amino groupo Carboxyl groupo Carbon, known as alpha carbono R group → variable component; gives each amino acid its unique
properties. Determines whether amino acid is classified as polar, non-polar, acidic, or basic.
VII. PROTEINS, cont
VII. PROTEINS, cont
VII. PROTEINS, cont
VII. PROTEINS, cont
• Amino Acid → Proteino Dehydration synthesis results in formation of a peptide bondo Polypeptide – many amino acids covalently bonded together
VII. PROTEINS, cont
• Protein Conformation o Protein’s shape is related to its function. Generally, a
protein must recognize/bind to another molecule to carry out its function.
o Denaturation - A change in a protein’s shape. Results in a loss of protein’s ability to carry out function.
o Four levels of protein structurePrimarySecondaryTertiaryQuaternary
VII. PROTEINS, cont
Primary – Sequence of amino acids
VII. PROTEINS, cont Secondary – Coiling of polypeptide chain due to formation of H-bonds
between H of amino end of one aa and OH of carboxyl end of another aa Alpha helix – created from H-bonds forming within one pp chain Beta pleated sheet – H-bonds form between aa in parallel pp chains
VII. PROTEINS, cont Tertiary - Involves
interactions between R groups of amino acids. Helps to give each protein its unique shape.
VII. PROTEINS, cont
Quaternary – Proteins that are formed from interactions between 2 or more polypeptide chains folded together. Examples include hemoglobin, collagen, chlorophyll
VII. PROTEINS, cont• Enzymes
o Biological catalysts that act by lowering activation energy; that is, the amount of energy needed to get the reaction going
o Only catalyze reactions that would normally occuro Recycled – not used up or changed by the reactiono Temperature and pH sensitiveo Substrate specific
VII. PROTEINS, cont
o Induced fit – As enzyme envelops substrate, a slight change takes place in bond angles, orientation of atoms. Allows chemical rxns to occur more readily
o Inhibition of Enzyme Function Competitive inhibitor – mimics
normal substrate Non-competitive inhibitor –
attaches to another part of enzyme; changes shape of active site
VII. PROTEINS, conto Regulation of enzyme
function Allosteric Regulation –
binding of a molecule to enzyme that affects function of protein at another site
Feedback Inhibition – as end product is synthesized and accumulates, enzyme is inactivated → switches off metabolic pathway
VIII. NUCLEIC ACIDS
• Nucleic acid group includes DNA, RNA, ATP
• Monomers = _NUCLEOTIDES_ Composed of
Pentose deoxyribose (DNA) ribose (RNA)
Phosphate group Nitrogen base
• Polymers formed through _dehydration synthesis__ Phosphate group of one
nucleotide covalently binds to sugar of next
VIII. NUCLEIC ACIDS, cont Nitrogen Bases
Pyrimidines – Single-ringed structure
Thymine Cytosine Uracil
Purines – Double-ringed structure
Adenine Guanine
VIII. NUCLEIC ACIDS, cont• DNA