UNIT II - BIOCHEMISTRY

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UNIT II - BIOCHEMISTRY

• Hillis Ch 2-3
• Big Campbell Ch 2-5
• Baby Campbell Ch 2-3

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I. THE MOLECULES OF LIFE

• Molecules are formed when two or more _atoms__
  come together to form covalent bonds.
• Created when electrons are __shared__
• Single Covalent Bond
• Double Covalent Bond
• Triple Covalent Bond
• Very _strong/stable__
• Non-polar Covalent Bond
• formed when electronegativity
  
• of atoms is the same. EX H2, O2
• Polar Covalent Bond
• formed when one atom is more
• electronegative unequal sharing of
• electrons results in slight charges at
• either end of molecule
• EX H2O Oxygen most electro

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II. WATER

• Properties of Water Due to its Polarity (Polar
  covalent bonds)
• Hydrogen bonds

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II. WATER

• Stickiness
• Cohesion
• Surface Tension how difficult it is to
  stretch/break the surface
• Adhesion
• Capillary Action

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Cohesion/Adhesion contribute to transport of
water and nutrients against gravity in plants.
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II. WATER, cont

• Regulation of Temperature
• High specific heat
• High heat of vaporization
• Density of solid water _lt_ density of
• liquid water
• Impt if ice sank, all ponds,
• lakes would freeze at
• bottom

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II. WATER, cont

• 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

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II. WATER, cont

• Dissociation of Water
• Rare, but measurable phenomenon
• Occasionally a H atom participating in a H bond
  between 2 water molecules shifts from one
  molecule to the other. This leaves behind an
  electon, transferring a H. The one that lost a
  proton is now an OH- ion with a charge of -1.
  The proton bonds to the other water molecule
  making that one a hydronium ion.
• (2)H2O ? H3O OH-

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• In aqueous solution at 25C, total conc of
  HOH- 1x10-14
• Neutral solution ? H OH- therefore H
  1 x 10-7
• pH Provides a means for a compressed
  measurement of H
• -log10H (negative logarithm base 10)
• Acid Substance that dissolves in water to
  __increase_ H
• H _gt___ 1 x 10-7 pH __lt__ 7 EX HCl
• Base - Substance that dissolves in water to
  _decrease_ H
• H _lt___ 1 x 10-7 pH _gt_ 7 EX NaOH
• pH of Water 7 H OH-

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II. WATER, cont

• Buffers
• Maintain a constant pH by donating, accepting H
• Bicarbonate Buffer System
• Very important buffer system in blood
• pH of blood _7.4_
• Carbonic acid H2CO3 is formed when CO2 reacts
  with water in blood plasma
• H2CO3
  HCO3 - H
• - If pH rises, reaction proceeds to the right and
  more carbonic acid dissociates, replenishing H
  ions.
• - If pH drops (H concentration rises), reaction
  proceeds to the left removing H ions by forming
  H2CO3.

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III. ORGANIC CHEMISTRY THE STUDY OF CARBON

• Atomic Structure of C
• Atomic Number of C 6
• 6 protons
• 6 electrons
• __4___ valence electrons
• Hydrocarbon composed on only C-H impt in
  fossil fuels. Hydrophobic
• Isomer compounds with the same of
  elements/atoms, but a different structural
  arrangement. See Ex

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III. ORGANIC CHEMISTRY, cont
Functional Group Structure Characteristics
Hydroxyl -OH may be written as HO- Very polar forms ols (alcohols)
Carbonyl CO, also written -CO Ketone if carbonyl group is within the carbon skeleton
Carbonyl CO, also written -CO 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
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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
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Phosphate -OPO3 known as organic phosphates Gives molecule negative charge react with water to release energy
Methyl -CH3 Affects the expression of DNA
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Functional Group ID
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IV. THE BIOMOLECULES

• Most are _polymers__ made up of single units
  called _monomers__
• Four Main Groups
• CARBOHYDRATES
• LIPIDS
• PROTEINS
• NUCLEIC ACIDS

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IV. BIOMOLECULES, cont

• Dehydration Synthesis
• Also called _CONDENSATION REACTION__
• Reaction that occurs to build polymers
• Forms __COVALENT_ bond between 2 monomers
• _WATER_lost as waste product
• Requires energy input, enzymes

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IV. BIOMOLECULES, cont

• Hydrolysis
• __WATER BREAKING/SPLITTING_
• Covalent bonds between monomers broken Releases
  energy reaction accelerated with enzymes

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V. 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
• Amino group
• Carboxyl group
• Carbon, known as alpha carbon
• R group ? variable component gives each amino
  acid its unique properties. Determines whether
  amino acid is classified as polar, non-polar,
  acidic, or basic.

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V. PROTEINS, cont
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V. PROTEINS, cont
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V. PROTEINS, cont
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V. PROTEINS, cont

• Amino Acid ? Protein
• Dehydration synthesis results in formation of a
  peptide bond
• Polypeptide many amino acids covalently bonded
  together

N-terminus
C-terminus
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V. PROTEINS, cont

• Protein Conformation
• Proteins shape is related to its function.
  Generally, a protein must recognize/bind to
  another molecule to carry out its function.
• Denaturation - A change in a proteins shape.
  Results in a loss of proteins ability to carry
  out function.
• Four levels of protein structure
• Primary
• Secondary
• Tertiary
• Quaternary

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V. PROTEINS, cont

• Primary Sequence of amino acids

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V. 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

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V. PROTEINS, cont

• Tertiary - Involves interactions between R groups
  of amino acids. Helps to give each protein its
  unique shape.

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V. PROTEINS, cont

• Quaternary Proteins that are formed from
  interactions between 2 or more polypeptide chains
  folded together. Examples include hemoglobin,
  collagen, chlorophyll

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V. PROTEINS, cont
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V. PROTEINS, cont
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V. PROTEINSProtein Function
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V. PROTEINSProtein Function, cont
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V. PROTEINSProtein Function, cont

• Cell Communication

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V. PROTEINS, cont

• Enzymes
• Biological catalysts that act by lowering
  activation energy that is, the amount of energy
  needed to get the reaction going
• Only catalyze reactions that would normally occur

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V. PROTEINS, contEnzymes
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V. PROTEINS, cont

• Enzymes, cont
• Recycled not used up or changed by the reaction
• Temperature and pH sensitive
• Substrate specific
• May require a co-factor or co-enzyme to be
  functional

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V. PROTEINS, cont

• Induced fit As enzyme envelops substrate, a
  slight change takes place in bond angles in the
  active site of the enzyme, orientation of atoms.
  Chemical groups on the side chains of the AAs of
  the enzyme interact with the chemical groups of
  the substrate. Allows chemical rxns to occur
  more readily.

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• Inhibition of Enzyme Function
• Competitive inhibitor mimics normal substrate
• Non-competitive inhibitor attaches to another
  part of enzyme changes shape of active site

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V. PROTEINS, cont

• Regulation of Enzyme Function
• Allosteric Regulation
• Binding of a molecule to enzyme that affects
  function of protein at another site
• May act as activators or inhibitors

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V. PROTEINS, cont

• Regulation, cont
• Feedback Inhibition
• As end product is synthesized and accumulates,
  enzyme is inactivated ? switches off metabolic
  pathway

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VI. 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
• Pentoses
• Ribose
• Deoxyribose

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VI. CARBOHYDRATES, cont

• Hexoses
• Glucose
• Fructose
• Galactose

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VI. CARBOHYDRATES, cont

• Disaccharides
• 2 monosaccharides covalently bonded together
  through dehydration synthesis
• Example
• Sucrose
• Lactose
• Maltose

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VI. CARBOHYDRATES, cont

• Polysaccharides
• Many monosaccharides covalently bonded together
  through dehydration synthesis
• 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

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VI. 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
• Chitin found in arthropod exoskeleton, cell
  walls of fungi

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VII. LIPIDS

• Very diverse group
• Non-polar, hydrophobic molecules
• Hydro_phobic__
• Not true polymers
• Four groups
• Fats oils
• phospholipids
• steroids
• waxes

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VII. LIPIDS, cont

• Fats Oils
• Composed of glycerol 3 fatty acids
• Glycerol 3-C alcohol
• Fatty acids long hydrocarbon chains ending with
  carboxyl group
• AKA triglycerides
• Used for energy storage

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VII. 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.

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Fats, cont.

• Saturated fat

• Unsaturated fat

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VII. 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.

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VII. LIPIDS, cont

• Steroids Consist of 4-rings with different
  functional groups attached.
• Cholesterol steroid found in animal cell
  membranes
• Precursor for sex hormones

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VII. LIPIDS, cont

• Waxes
• One fatty acid attached to an alcohol
• Very hydrophobic
• Used as coating, lubricant

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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

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VIII. NUCLEIC ACIDS, cont

• Nitrogen Bases
• Pyrimidines Single-ringed structure
• Thymine
• Cytosine
• Uracil
• Purines Double-ringed structure
• Adenine
• Guanine

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VIII. NUCLEIC ACIDS, cont

• DNA