UNIT I - BIOCHEMISTRY

UNIT I - BIOCHEMISTRY Big Campbell ~ Ch 1-5 Baby Campbell ~ Ch 1-3

I. INTRODUCTION TO BIOLOGY • Characteristics of Life • Living things …… • are made of __________ • grow & ______________ • _____________ to their environment • obtain and use ________ • maintain ____________ • are based on a universal _____________ ______ • ________________ • ________________

I. INTRODUCTION TO BIOLOGY, CONTINUED • Unity & Diversity of Life • Evolution explains both unity & diversity • Continuity of life based on DNA • Two types of cells • All organisms can be placed in one of 3 domains • Form vs Function → Structures are adapted for specific functions; conversely, function of a structure determines how it is constructed

I. INTRODUCTION TO BIOLOGY, CONTINUED • Unity & Diversity of Life, continued • Levels of Organization (Big – Small) • Biosphere • Ecosystem • Community • Population • Organism • Organelle • Molecule • Atom

II. CHEMICAL BASIS OF LIFE • __________________ • Cannot be broken down without losing characteristic properties • Six elements in greatest concentration in living things are

II. CHEMICAL BASIS OF LIFE, CONTINUED • Atoms • Smallest unit of matter that retains properties of that element • Atomic Mass

II. CHEMICAL BASIS OF LIFE, CONTINUED • Chemical Bonds • Chemical behavior of atom determined by ______________ electrons • Atoms interact with other atoms to complete their valence shells, either by ________________ or ________________ electrons

II. CHEMICAL BASIS OF LIFE, CONTINUED • Types of Chemical Bonds • ____________ – Results when one atom has a much stronger attraction for electrons than another • One atom has a greater __________________________. Electron(s) are transferred resulting in formation of ions. Bond forms due to charge attraction – easily broken • Cation - • Anion -

II. CHEMICAL BASIS OF LIFE, CONTINUED • _________________ – Much stronger that results from ___________ a pair of valence electrons. • Forms a molecule. • One pair of electrons shared = single covalent bond • Two pair of electrons shared = double covalent bond. • ______________ covalent bond – formed when electronegativity of atoms is the same; H2 • ___________ covalent bond – formed when one atom is more electronegative; unequal sharing of electrons results in slight charges at either end of molecule http://users.skynet.be/eddy/ion_vs_covalent.swf

III. WATER • Polarity of Water

III. WATER, continued • Properties of Water • ______________ “bonds” • “Stickiness” • _______________ • _______________ • Helps maintain a stable temperature • Has a high specific heat and a high heat of vaporization • Density of “solid” water ____ density of liquid water • Important to environment; insulates lakes, oceans

III. WATER, continued • Solvent of Life (not universal…..but versatile) • _________________ – “Water-loving”; polar molecules “pull apart” ionic compounds & other polar molecules • ________________ – “Water-hating”; non-ionic and non-polar substances are repelled by water

III. WATER, continued • Dissociation of Water • Rare, but measurable phenomenon • (2)H2O → H3O+ + OH- → H+ + OH- • pH = measurement of H+ conc • -log10[H+] • [H+] [OH-] = 1 x 10-14 • Acid – Substance that dissolves in water to increase H+; [H+] > 1 x 10-7; pH < 7 • Base - Substance that dissolves in water to decrease H+; [H+] < 1 x 10-7; pH > 7 • Water is a neutral substance; [H+] = [OH-] • Buffers – Maintain a constant pH by donating, accepting H+ • Very important buffer system in blood to keep pH at 7.4

IV. ORGANIC CHEMISTRY – THE STUDY OF CARBON • Atomic Structure of C • 6 total electrons; therefore has 4 valence electrons • Shares e- to fill valence shell; can form up to 4 covalent bonds • Hydrocarbon • Isomer – Molecules with same atomic make-up; different arrangement of atoms

IV. ORGANIC CHEMISTRY, continued • Functional Groups • Hydroxyl – Polar due to greater electronegativity of oxygen. Found in alcohols. “-ol” • Carbonyl • Aldehyde – carbonyl group at end of C-skeleton • Ketone – carbonyl group within C-skeleton

IV. ORGANIC CHEMISTRY, continued • Carboxyl – Acts an acid by donating H+ • Amino – Acts as a base by picking up H+

IV. ORGANIC CHEMISTRY, continued • Sulfhydryl – Important in stabilizing protein structure • Phosphate – Typically an anion; gives its molecule a negative charge

V. ORGANIC CHEMISTRY, continued

V. THE BIOMOLECULES • Most are ____________ made up of single units called ____________ • The different classes of macromolecules differ in the nature of their monomers, but the chemical mechanisms that cells use to make and break polymers are basically the same.

V. BIOMOLECULES, continued • _____________________________ (condensation) • One monomer provides –H, the other provides –OH • As a result…… • A water molecule forms • 2 original monomers covalently bond together to form polymer • Requires input of energy, use of enzymes

V. BIOMOLECULES, continued • ____________________ - “Break apart with water” • Covalent bonds between monomers are broken when hydrogen from a water molecule attaches to one monomer and the hydroxyl group attaches to adjacent monomer. • Releases energy; reaction accelerated with enzymes • Example - digestion

VI. CARBOHYDRATES • Provide fuel, act as building material • Generally, formula is a multiple of ___________ • Contain carbonyl group & multiple hydroxyl groups • Monomer = __________________________

VI. CARBOHYDRATES, continued • Hexoses • Glucose • Fructose • Galactose • Monosaccharides – usually found as ringed structures • Pentoses • Ribose • Deoxyribose

VI. CARBOHYDRATES, continued • _____________________ • 2 monosaccharides joined by a ________________ ______________________, a covalent bond formed during dehydration synthesis • Example • Sucrose – (glucose + fructose) • Lactose – (glucose + galactose) • Maltose – (glucose + glucose)

VI. CARBOHYDRATES, continued • ________________________ • Many monosaccharides covalently bonded via glycosidic linkages formed during dehydration synthesis • Storage Polysaccharides • Structural Polysaccharides

VI. CARBOHYDRATES, continued • Storage polysaccharides • ▪ __________________ – ___________ store glucose as starch in cell structures called ______________. Starch has helix shape due to bond angles. Humans have enzymes to hydrolyze starch to glucose monomers. • ▪ __________________ – Storage form of glucose in _________. More highly-branched than starch. In humans, found mainly in liver, muscle cells

VI. CARBOHYDRATES, continued • Structural polysaccharides (structure is different than storage polysaccharides) • __________________ – polymer of glucose. Every other glucose is upside down which forms parallel strands of glucose molecules held together with H-bonds • Cows/Termites • _______________ – found in arthropod exoskeleton, cell walls of fungi

Non-polar, ____________________ molecules Hydrocarbons Fats& Oils Not true polymers but they are very large molecules Macromolecules assembled through dehydration synthesis Glycerol = 3-C alcohol Fatty acids – long hydrocarbon chains ending with carboxyl group Triglyceride = glycerol + 3 fatty acids Used for energy storage – contain > 2X energy as carbs VII. LIPIDS Fatty Acid Glycerol

____________________ “Saturated with hydrogens” All _____________ bonds. Typically from animal source, _________ at room temp. Associated with greater health risk. ______________________ Contain ____________ bonds, fewer H-atoms. Results in “kinked” hydrocarbon chain. Typically from _________ source, liquid at room temp. VII. LIPIDS, continued

___________________________ Contain _______ fatty acids attached first 2-carboxyl groups of glycerol. Phosphate group is attached to 3rd carboxyl which has a negative charge. Therefore molecule is partially hydrophilic (_________) and partially hydrophobic (_________) . Found in all cell membranes. Phospholipid bilayer VII. LIPIDS, continued

VII. LIPIDS, continued Waxes One fatty acid attached to an alcohol. Very hydrophobic. Used as coating, lubricant Steroids Consist of 4-rings with different functional groups attached. _____________________ Found in animal cell membranes Precursor for sex hormones

VIII. PROTEINS • Important for functions such as…… (Table 5.1, Pg. 72) • Structural ______________ (very complex!) • Storage • _________________ of substances • Signaling • Movement • ______________ disease • ________________________ – Proteins are large polymers made up of amino acid monomers. • All amino acids have the same basic structure: • Amino group • Carboxyl group • Carbon, known as ___________ carbon • _________________ → variable component; gives each amino acid its unique properties. Determines whether amino acid is classified as polar, non-polar, acidic, or basic.

VIII. PROTEINS, continued These R-groups are non-polar……..therefore these amino acids are non-polar

VIIII. PROTEINS, continued These R-groups are polar……..therefore these amino acids are polar These R-groups either proton donors or proton acceptors……..therefore these amino acids have acidic or basic properties

VIII. PROTEINS, continued • Amino Acid → protein • Dehydration synthesis results in formation of a ____________ bond • _____________________ – many amino acids covalently bonded together • At one end there is a free ___________ group (N terminus) and at the other end is a free ______________ group (C terminus)

VIII. PROTEINS, continued • Amino acid sequence determines the protein’s ______ conformation • Protein Conformation • Protein’s __________ is related to its _________________. • Generally, a protein must recognize/bind to another molecule to carry out its function. • _______________________ - A change in a protein’s shape. Which results in a loss of protein’s ability to carry out function. • Four levels of protein structure • Primary • Secondary • Tertiary • Quaternary

__________ – Sequence of amino acids VIII. PROTEINS, continued

________________ – 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 _________________ – created from H-bonds forming within one pp chain __________________ – H-bonds form between aa in parallel pp chains VIII. PROTEINS, continued

__________________ - Involves interactions between R groups of amino acids. Helps to give each protein its unique shape. __________________ interactions – amino acids with non-polar R groups cluster together at core of protein. _________________ bridges – important in reinforcing shape of protein; covalent bonds that form between sulfhydryl R groups of amino acids, cysteine VIII. PROTEINS, continued

_______________ – Proteins that are formed from interactions between 2 or more polypeptide chains folded together. Examples: Hemoglobin, collagen, chlorophyll VIII. PROTEINS, continued

__________________ Biological catalysts that act by lowering _________________________; that is, the amount of energy needed to get the reaction going Only catalyze reactions that would normally occur Recycled – not used up or changed by the reaction Temperature, pH, and salt sensitive Substrate specific VIII. PROTEINS, continued

____________________ – As enzyme envelops substrate, a slight change takes place in bond angles, orientation of atoms. Allows chemical rxns to occur more readily Inhibition of Enzyme Function __________________ inhibitor – mimics normal substrate ____________________ inhibitor – attaches to another part of enzyme; changes shape of active site VIII. PROTEINS, continued

Regulation of enzyme function ____________ regulation – binding of a molecule to enzyme that affects function of protein at another site __________________ ______________ – as end product is synthesized and accumulates, enzyme is inactivated → switches off metabolic pathway VIII. PROTEINS, continued

VIII. NUCLEIC ACIDS • Nucleic acid group includes DNA, RNA, ATP • Structure of Nucleic Acids • Monomers = nucleotides • Nucleotides composed of • Pentose – deoxyribose or ribose • Phosphate group • Nitrogen base • Pyrimidine – Contains 6-membered ring of C, N atoms • Cytosine – found in DNA, RNA • Thymine – found in DNA • Uracil – found in RNA • Purine – Larger; consists of 6-membered ring + 5-membered ring • Adenine – found in DNA, RNA, ATP • Guanine – found in DNA, RNA

Nucleotide polymers – Formed through dehydration synthesis. Phosphate group of one nucleotide covalently binds to sugar of next. Forms backbone of alternating P-group and sugar. DNA – Forms double helix. Two polynucleotide strands run in opposite directions – referred to as antiparallel. H-bonds form between N-bases in the center VIII. NUCLEIC ACIDS, continued

UNIT I - BIOCHEMISTRY