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UNIT II - BIOCHEMISTRY

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Title: UNIT II - BIOCHEMISTRY


1
UNIT II - BIOCHEMISTRY
  • Hillis Ch 2-3
  • Big Campbell Ch 2-5
  • Baby Campbell Ch 2-3

2
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

3
II. WATER
  • Properties of Water Due to its Polarity (Polar
    covalent bonds)
  • Hydrogen bonds

4
II. WATER
  • Stickiness
  • Cohesion
  • Surface Tension how difficult it is to
    stretch/break the surface
  • Adhesion
  • Capillary Action

5
Cohesion/Adhesion contribute to transport of
water and nutrients against gravity in plants.
6
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

7
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

8
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-

9
  • 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-

10
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11
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.

12
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

13
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
14
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
15
Phosphate -OPO3 known as organic phosphates Gives molecule negative charge react with water to release energy
Methyl -CH3 Affects the expression of DNA
16
Functional Group ID
17
IV. THE BIOMOLECULES
  • Most are _polymers__ made up of single units
    called _monomers__
  • Four Main Groups
  • CARBOHYDRATES
  • LIPIDS
  • PROTEINS
  • NUCLEIC ACIDS

18
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

19
IV. BIOMOLECULES, cont
  • Hydrolysis
  • __WATER BREAKING/SPLITTING_
  • Covalent bonds between monomers broken Releases
    energy reaction accelerated with enzymes

20
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.

21
V. PROTEINS, cont
22
V. PROTEINS, cont
23
V. PROTEINS, cont
24
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
25
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

26
V. PROTEINS, cont
  • Primary Sequence of amino acids

27
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

28
V. PROTEINS, cont
  • Tertiary - Involves interactions between R groups
    of amino acids. Helps to give each protein its
    unique shape.

29
V. PROTEINS, cont
  • Quaternary Proteins that are formed from
    interactions between 2 or more polypeptide chains
    folded together. Examples include hemoglobin,
    collagen, chlorophyll

30
V. PROTEINS, cont
31
V. PROTEINS, cont
32
V. PROTEINSProtein Function
33
V. PROTEINSProtein Function, cont
34
V. PROTEINSProtein Function, cont
  • Cell Communication

35
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

36
V. PROTEINS, contEnzymes
37
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

38
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.

39
  • Inhibition of Enzyme Function
  • Competitive inhibitor mimics normal substrate
  • Non-competitive inhibitor attaches to another
    part of enzyme changes shape of active site

40
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

41
V. PROTEINS, cont
  • Regulation, cont
  • Feedback Inhibition
  • As end product is synthesized and accumulates,
    enzyme is inactivated ? switches off metabolic
    pathway

42
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

43
VI. CARBOHYDRATES, cont
  • Hexoses
  • Glucose
  • Fructose
  • Galactose

44
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45
VI. CARBOHYDRATES, cont
  • Disaccharides
  • 2 monosaccharides covalently bonded together
    through dehydration synthesis
  • Example
  • Sucrose
  • Lactose
  • Maltose

46
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

47
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

48
VII. LIPIDS
  • Very diverse group
  • Non-polar, hydrophobic molecules
  • Hydro_phobic__
  • Not true polymers
  • Four groups
  • Fats oils
  • phospholipids
  • steroids
  • waxes

49
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

50
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.

51
Fats, cont.
  • Saturated fat
  • Unsaturated fat

52
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.

53
VII. LIPIDS, cont
  • Steroids Consist of 4-rings with different
    functional groups attached.
  • Cholesterol steroid found in animal cell
    membranes
  • Precursor for sex hormones

54
VII. LIPIDS, cont
  • Waxes
  • One fatty acid attached to an alcohol
  • Very hydrophobic
  • Used as coating, lubricant

55
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

56
VIII. NUCLEIC ACIDS, cont
  • Nitrogen Bases
  • Pyrimidines Single-ringed structure
  • Thymine
  • Cytosine
  • Uracil
  • Purines Double-ringed structure
  • Adenine
  • Guanine

57
VIII. NUCLEIC ACIDS, cont
  • DNA
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