Basics of Life Chemistry

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CHAPTER 2

• Basics of Life Chemistry

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INTRODUCTION

• All living things are composed of and use
  chemicals
• Chemicals used for
• communication,
• defense,
• aggression,
• reproduction etc.

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Introduction

• Human composed of the chemicals
• O, C, H, N, C, etc
• All chemicals known as matter

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MATTER

• Any substance that has mass and occupies space

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Features of matter

• Energy all matter has energy
• Kinetic energy
• Potential energy

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Features of matter

• First law of thermodynamics
• Energy is never created or destroyed but can be
  converted from one form to the other.

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States of Matter

• Solid
• Molecules tightly packed strongly attracted to
  each other
• Kinetic energy lt liquids
• Fixed shape and volume under
• Liquid
• Molecules slightly further apart but strongly
  attracted
• Fixed volume under ordinary Ability to flow

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States of Matter

• Gas
• Molecules highly energetic
• Their collisions move them further apart
• Gas expands to fill container

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Composition of Matter

• Element
• Pure substances
• Atom (e.g. H, O)
• Smallest particle of an element

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Structure of an atom

• Bohr Model
• Nucleus
• Protons (ve charge)
• Neutrons (no charge)
• Electrons (-ve charge)
• Orbits/energy levels
• insignificant weight
• form chemical bonds

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compound -

• atoms combined in a fixed ratio
• E.g water H2O

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molecule -

• smallest part of a compound
• water - H2O
• sucrose C12H22O11

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Periodic Table of the Elements -

• arrangement of elements by properties
• chemical symbol for each element
• atomic number -gt of protons
• of protons of electrons
• atomic weight protons neutrons
• atomic weight - atomic number neutrons

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Isotope -

• element containing a different number of neutrons

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model of an atom Bohr Model

• electrons travel in energy levels
• level 1 lowest amount of energy
• filled by 2 electrons
• level 2 electrons with more energy
• levels 2 filled by 8 electrons
• Octet rule

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why do chemical bonds form?

• atoms with unfilled energy levels are unstable
• energy levels are filled by electrons thru
• sharing covalent bond
• donating ionic bond

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covalent bonds

• electron sharing
• two atoms share a pair of electrons
• H H
• one pair -gt single bond

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Covalent bonds (cont)-

• form proteins, carbohydrate, lipids (fats) and
  nucleic acids

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hydrogen -

• atomic number is 1
• has 1 proton 1 electron
• energy level 1 needs 2 electrons
• forms 1 covalent bond
• only H2 exists naturally
• H-H -gt structural formula
• H2 -gt empirical

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helium

• atomic number is 2
• 2 electrons
• energy level 1 filled
• noble gas

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carbon

• atomic number is 6
• 6 electrons
• energy level 1 filled
• energy level 2 has 4 Forms
• 4 covalent single bonds
• 2 covalent double bonds
• 1 covalent double bond, 2 covalent single bonds

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oxygen

• atomic number 8
• 8 electrons
• energy level 1 filled
• energy level 2 has 6
• forms 2 covalent single bonds
• 1 covalent double bond

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nitrogen

• atomic number 7
• 7 electrons -
• energy level 1 filled
• energy level 2 has 5
• forms 3 covalent single bonds
• 1 double, 2 singles

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ionic bonds -

• one atom donates an electron to another atom
• results in forming ions - atoms with an
  electrical charge
• cation -gt atom that has lost an electron ()
  charge
• anion -gt atom that has gained an electron (-)
  charge

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sodium chloride -

• chlorine - 7 electrons in the outer orbit
• sodium - 1 electron in the outer orbit
• Na Cl- -gt sodium chloride NaCl

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Calcium chloride -

• Calcium - 2 electrons in the outer orbit
• Chloride - 7 electrons in the outer orbit
• Cl- Ca2 Cl- -gt CaCl2

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hydrogen bonds (not really)

• Linkage that nearly always pairs hydrogen with
  either nitrogen or oxygen
• Connect molecules
• Represented as !
• weak force / strong in number

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strength of bonds

• covalent gt ionic gt hydrogen

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chemical reactions -

• change in energy
• energy is stored in the chemical bonds
• breaking a bond releases energy
• creating a bond requires energy
• rearrangement of molecular structure

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HCl NaOH -gt NaCl H20

• chemical equation
• reactants are listed on the left
• products are listed on the right
• -gt indicates a chemical reaction has occurred
• equation must be balanced

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IONIC COMPOUNDS

• ACIDS
• Releases hydrogen ions (H) in solution
• Strong acids HCL, H2SO4
• Weak acids Carbonic acid

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IONIC COMPOUNDS

• BASES
• Release hydroxide ion (OH-) negatively charged
• Alkaline substances
• Feels slippery on skin
• Sodium Hydroxide Na(OH-) strong base
• Sodium bicarbonate Weak base

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pH Scale -

• Measurement of acidity /alkalinity
• measures H ion conc.
• pH Scale - ranges from 0 to 14
• pH 7 neutral

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pH Scale -

• high H low pH / acid
• lt 7
• low H high pH / base
• gt7

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IONIC COMPUNDS

• SALTS
• Ionic compounds that do not release H or OH ions
• Neither acids or bases
• Result from reaction of an acid and a base
• Chemical reaction is called neutralization

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Summary

• Atom
• Element
• Molecule
• Compound
• Atomic mass unit
• Atomic number
• Chemical symbol
• Atomic nucleus
• Atomic weight
• Acids
• Bases
• Salt

• pH
• Proton
• Electron
• Neutron
• Ion
• Cation
• Anion
• Kinetic energy
• Chemical reaction
• Ionic Bond
• Covalent Bond
• Hydrogen Bond

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Organic Chemistry, The Chemistry of Life

• - Chapter 3

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Inorganic molecules -

• do not contain carbon
• ex water, salt, sodium hydroxide

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Organic molecules-

• organic organ (living)
• must contain carbon

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4 classes of organic molecules

• proteins
• lipids (fats)
• carbohydrates
• nucleic acids

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Carbon / central atom

• can form 4 covalent bonds
• bonds spaced evenly
• -- C --

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Carbon skeleton / backbone

• linear or a ring (fig 3.3)
• attached are functional groups
  ________________

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Functional groups -

• clusters of atoms attached to the carbon skeleton
• determines the chemical property of the molecules
• Figure 3.8

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Functional groups -

• Amine group -
• -NH2
• found in amino acids and proteins
• Phosphate group
• PO4
• found in phospholipids

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Formation of organic molecules-

• monomer single unit
• amino acid
• glucose

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Formation of organic molecules-

• polymer / macromolecules
• monomers joined together
• Sucrose
• glucose fructose
• Starch
• glu-glu-glu-gluglu

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Dehydration / Synthesis -

• the linking together of monomers
• molecule of water removed
• covalent bond links the monomers together
• energy requiring

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Hydrolysis-

• unlinking of monomers
• water molecule added at the junction
• energy releasing

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Carbohydrates - sugars and starches -

• function -
• provides energy - glucose, glycogen
• support cellulose

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Consist of C, H, O

• consist of carbon, hydrogen, and oxygen
• empirical formula -gt CxH2xOx
• equal of carbon and oxygen double hydrogen

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Name ends in ose

• name ends in ose
• triose, 3 carbons
• pentose, 5 carbons -gt fructose
• hexose, 6 carbons -gt glucose, galactose

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Monosaccharides

• Form complex CHO
• glucose (dextrose)
• fructose
• galactose-

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Disaccharides - two sugar monomers

• lactose (milk sugar) -gt
• glucose galactose
• sucrose (table sugar) -gt
• glucose fructose
• Maltose (malt sugar)
• Glucose glucose

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Polysaccharides - complex carbohydrates -

• many monomers arranged in branches or chains
• combined by dehydration / synthesis

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Starch -

• branched polymer of glucose
• energy storage in plants
• Amylopectin amylose

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Glycogen -

• tree shaped polymer of glucose
• energy storage in animals
• quickly hydrolyzed to glucose
• found in muscle and liver cells
• provides rapid bursts of energy

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Cellulose -

• Polysaccharide
• Cell walls of plant cellulose
• Cannot be digested by humans no calories
• Digested by ruminants

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Carbohydrates

• may be a component of another organic molecule -
• DNA (deoxyribonucleic acid) -gt deoxyribose sugar
• RNA (ribonucleic acid) -gt ribose sugar
• ATP (adenosine triphospate) -gt ribose sugar

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Lipids (fats)

• 3 sub-groups
• true fats
• phospholipids
• steroids

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Consist of C, H, small amounts of O -

• large, non-polar molecules
• can not dissolve in water
• oil water dont mix!
• formed by dehydration / synthesis

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Fat vs- oil -

• fat -gt lipid solid at room temperature
• oil -gt lipid liquid at room temperature

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True (neutral) fats function -

• insulation -
• prevents loss of body heat
• cushion internal organs
• energy storage -
• fat -gt 9 calories per gram
• sugar -gt 4 calories per gram

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Structure of true fats -

• 1, 2, or 3 fatty acids attached to glycerol

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Fatty acid-

• long carbon chain
• carboxyl (-COOH) group attached to the end

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FATTY ACID Fig. 3.21
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Glycerol

• 3 carbon skeleton
• 3 alcohol groups attached
• See page 56

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Triglycerides-

• three fatty acids one glycerol
• most abundant true fat in the body

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Triglyceride Fig. 3.22
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Saturated Fatty Acid

• no double bonds / contains the maximum of
  hydrogen atoms
• from animal products
• Solid at room temp
• examples butter, lard

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Unsaturated Fatty Acid

• contains double bonds / limits the of hydrogen
  atoms
• from plants
• usually liquid at room temperature

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polyunsaturated

• more than one double bond
• Ex olive oil, soybean oil

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Omega -3 fatty acids

• double bond found after the 3rd carbon
• many are essential
• hormones
• cell growth
• ex fish oil, soybeans

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Hydrogenation -

• add hydrogen to an unsaturated fat
• solidifies the fat
• ex margarine

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Phospholipids -

• structure - two fatty acids, one glycerol, one
  phosphate group
• function - component of cell membranes

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Steroids -

• lipids without fatty acids
• interlocking rings
• cholesterol -
• component of cell membranes
• converted into bile salts (emulsify fat)
• vitamin D
• hormones -
• estrogen
• testosterone

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Proteins -

• function
• structural -
• cell membranes
• muscle cells
• tendons
• Hemoglobin

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Protein function (cont) -

• regulation -
• enzymes (organic catalysts)
• hormones- insulin, oxytocin
• antibodies - fight infection

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Protein function (cont) -

• carriers -
• lipoproteins - transport non polar molecule
• cholesterol
• triglycerides
• Phospholipids

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Consist of

• made of monomers of amino acids (20 exist)
• amino group on one end
• carboxyl group on the other end
• R-group - functional group that determines
  properties

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Formed by dehydration / synthesis -

• peptide bonds between amino acids
• polypeptide - chain of linked amino acids

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Four levels of protein organization -

• primary - polypeptide chain
• secondary - polypeptide chain twists-
• alpha helix (coil) - formed by hydrogen bonds
• beta pleated sheet - formed by hydrogen bonds

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Protein organization (cont) -

• tertiary - 3 dimensional
• side chains (R-groups) bond together
• quaternary - interactions of individual
  polypeptides

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Changes in protein structure -

• sickle-cell anemia-
• hemoglobin consist of 4 polypeptides
• two alpha, two beta
• change in one amino acid causes the protein
  molecules to unwind sickle under increased
  oxygen demand

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Denaturation-

• breaking of hydrogen bonds due to heat, light, or
  pH
• change in structure
• not reversible
• you can not unfry an egg!

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Nucleic acids-

• function - component of DNA RNA
• DNA - genetic code
• RNA - manufacturer of protein

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Structure of nucleic acids -

• made up of nucleotides

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Nucleotides -

• 5- carbon simple suger
• deoxyribose (DNA)
• ribose (RNA0
• phosphate group
• nitrogenous base
• Adenine
• Guanine
• Thymine
• Cytosine
• Uracil

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NUCLEIC ACIDS

• DNA
• Genetic material
• Nucleotides building blocks
• 5-C sugar, deoxyribose
• Phosphate
• Nitrogenous Base
• Adenine,Guanine,Thymine, Cytosine

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NUCLEIC ACIDS

• DNA
• Double helix structure
• Sugar-phosphate backbone
• Bases complimentary paring
• A-T, C-G
• Coding strand
• Protein synthesis

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NUCLEIC ACIDS

• RNA
• Protein synthesis
• Ribose sugar
• Uracil base and no Thymine
• Pairing A-U, G-C
• 3 forms of RNA
• Messenger RNA mRNA
• Transfer RNA tRNA
• Ribosomal RNA rRNA

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SUMMARY

• Chemistry of living things
• Based on Carbon
• C atoms all organic molecules
• Structure of OM related to function
• Common OM
• CHO, Pns, Lipids, Nucleic acids