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CHAPTER 2CHAPTER 2
Basics of Life Chemistry
INTRODUCTIONINTRODUCTIONAll living things are composed of matter
– Any substance that has mass and occupies space
All matter made up of chemicals
– O, C, H, N, C, etcChemicals used for
– communication, defense, reproduction etc.
Features of matterFeatures of matterEnergy: all matter has energy: Life uses energy–Potential energy:
–Kinetic energy:
Composition of MatterComposition of MatterAtoms (e.g. H, O)
–Smallest unit of matter/building blocks
Form elements–Pure substances: one kind of atoms
Structure of an atom:Structure of an atom:Bohr ModelBohr Model
ProtonsNeutrons Electrons: form chemical bonds
– Orbits/energy levels
– insignificant weight
– form chemical bonds
Elements vary in Neutrons but not Elements vary in Neutrons but not protonsprotonsatomic number -> # of protons ( = # electrons)
– Constant (unique for an element)Atomic mass unit = mass of one protonNeutrons may vary for one element
– Isotope-Atoms of same element containing a different number of neutrons
Mass number = # protons + # neutronsAtomic weight: average weight of all isotopes
Compound Compound --
A substance formed by chemical union of atoms of 2 or more different elements in a specific ratio–E.g water: H2O
moleculemolecule --
smallest unit of a compound–water - H2O
–sucrose – C12H22O11
some are diatomic molecules–H2, O2, N2
Periodic Table of the ElementsPeriodic Table of the Elements - - Periodic Table of the ElementsPeriodic Table of the Elements - -
Provides information about elements– arrangement of elements by properties
– Name & chemical symbol for each element
– atomic number - # of protons (= # electrons)
– Atomic weight
What is a chemical bond?What is a chemical bond?
Attractive force that holds atoms of molecules together
ELECTRON DISTRIBUTION & chemical ELECTRON DISTRIBUTION & chemical bondsbonds
modern theory recognizes e- in “clouds” or energy levels– The further from the nucleus, the more energy
e-’s have Bohr model
– # varies with shell• 2 in the first• 8 in the second• 8 in the third (sometimes 18)
– generally 8 is the most stable configuration
ELECTRON DISTRIBUTION…ELECTRON DISTRIBUTION…cont’dcont’d
All atoms “want” 8 electrons in their outermost shells and will interact with other atoms to the end that all reach 8.
Basis for formation of molecules (compounds)
FORMATION OF MOLECULESFORMATION OF MOLECULES
atoms interact such that both (all) have 8 electrons in outermost orbit
thus, molecules are the most stable energy states for atoms and their electrons
attractions between atoms in a molecule are chemical bonds– attractions result from distributing electrons so that each
atom in the molecule has 8 in its outermost shell, at least part of the time
TYPES OF CHEMICAL BONDSTYPES OF CHEMICAL BONDS
IONIC-one atom loses electrons, other gains electrons– atom that loses electrons has a net positive charge
• cation
– atom that gains electrons has a net negative charge• anion
– unlike charges attract• molecules form
many elements in the body occur as ions (charged atom)– called electrolytes
Sodium ChlorideSodium Chloride
–chlorine - 7 electrons in the outer orbit
–sodium - 1 electron in the outer orbit
–Na+ + Cl- -> sodium chloride NaCl
TYPES OF CHEMICAL BONDS…TYPES OF CHEMICAL BONDS…cont’d)cont’d)
COVALENT-two atoms share one or more pairs of electrons
each has 8 electrons in its outermost orbit at least part of the time– non-polar covalent bond
• atoms share electrons equally– methane
– polar covalent bond• unequal sharing of electrons between atoms
– water
Covalent bonds (cont)-Covalent bonds (cont)-
form proteins, carbohydrate, lipids (fats) and nucleic acids
hydrogen -hydrogen -atomic number is 1
– has 1 proton & 1 electronenergy level 1 – needs 2 electrons
– forms 1 covalent bond
– only H2 exists naturally
• H-H -> structural formula
• H2 -> empirical
helium –helium –atomic number is 2
–2 electronsenergy level 1 – fillednoble gas
carbon –carbon –atomic number is 6
– 6 electronsenergy level 1 – filledenergy level 2 – has 4: Forms
• 4 covalent single bonds (formed by sharing a pair of electrons)
hydrogen bondshydrogen bonds (not really) (not really)
Form mostly between molecules, do not bond atoms
Always between H & O; or H & NEach weakMany hydrogen bonds form very strong
structureswater as an example
strength of bonds –strength of bonds –
covalent > ionic > hydrogen
IONIC COMPOUNDSIONIC COMPOUNDS
AcidsBases Salts
pH Scale -pH Scale -
Measures acidity /alkalinity or– H ion conc.
pH Scale - ranges from 0 to 14pH 7 = neutral
pH Scale -pH Scale -high [H+] = low pH / acid
–< 7low [H+] = high pH / base
–>7
Summary: Define these termsSummary: Define these terms– 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
Organic Chemistry, The Chemistry Organic Chemistry, The Chemistry of Lifeof Life
Organic Chemistry, The Chemistry Organic Chemistry, The Chemistry of Lifeof Life
Chapter 3
Inorganic molecules -Inorganic molecules - Inorganic molecules -Inorganic molecules -
do not contain carbon linked to H
ex: water, salt, sodium hydroxide
Organic molecules-Organic molecules-Organic molecules-Organic molecules-contain carbon linked to H and oxygen (N,
S, P also, but not always)– proteins
– lipids (fats)
– carbohydrates
– nucleic acids
Carbon / central atom Carbon / central atom can form 4 covalent bondsbonds spaced evenly | -- C -- | Can form long chainsCan combine with many other atoms
All organic Molecules have a All organic Molecules have a Carbon skeleton / backbone Carbon skeleton / backbone All organic Molecules have a All organic Molecules have a Carbon skeleton / backbone Carbon skeleton / backbone Linear or a ring (fig 3.3)
_________
Length & shape confers uniqueness
Functional groups attached– determines the chemical
property of the molecules
–
Functional groups -Functional groups -Amino group -
– -NH2
– found in amino acids and proteinsPhosphate group
– PO4
– found in phospholipidsSee figure 3.7
Formation of organic Formation of organic molecules-molecules-
Formation of organic Formation of organic molecules-molecules-
Monomer = single unit – amino acid
– GlucosePolymer / macromolecules
–Starch:• glu-glu-glu-glu…glu
Dehydration / SynthesisDehydration / Synthesis - -Dehydration / SynthesisDehydration / Synthesis - -
the linking together of monomers with covalent bonds
molecule of water removed energy requiringSee figure 3.8
Hydrolysis-Hydrolysis-Hydrolysis-Hydrolysis-unlinking of monomerswater molecule added
energy releasingSee figure 3.8
Carbohydrates - sugars and Carbohydrates - sugars and starchesstarches --
Carbohydrates - sugars and Carbohydrates - sugars and starchesstarches --
function -
– provides energy
– support – cellulose
– component of other organic molecule -• DNA-> deoxyribose sugar• RNA -> ribose sugar• ATP -> ribose sugar
Simple sugars: MonosaccharidesSimple sugars: Monosaccharides
Form complex CHO–glucose – (dextrose)
–fructose –
–galactose-
Simple sugars: Disaccharides -Simple sugars: Disaccharides -Simple sugars: Disaccharides -Simple sugars: Disaccharides -
lactose (milk sugar) ->– glucose + galactose
sucrose (table sugar) -> – glucose + fructose
Maltose (malt sugar)– Glucose + glucose
Polysaccharides - complex Polysaccharides - complex carbohydrates - carbohydrates - Polysaccharides - complex Polysaccharides - complex carbohydrates - carbohydrates -
Long chains of monosaccharides joined together
Examples are:
Starch -Starch - Starch -Starch -
Polymer of glucoseCHO/energy storage in plants
–amylopectin (trees shaped)
– amylose (straight)
–Figure 3.10
Glycogen -Glycogen - Glycogen -Glycogen -
“tree” shaped polymer of glucose
energy storage in animals–found in muscle and liver cells
–provides rapid bursts of energy
Cellulose -Cellulose -PolysaccharideCell walls of plant celluloseCannot be digested by humans : no
caloriesDigested by ruminants
Lipids–Lipids– Lipids–Lipids–
3 classes–true fats –
–phospholipids –
–steroids –fat -> solid at room temperatureoil -> liquid at room temperature
Consist of C, H, & small amounts ofConsist of C, H, & small amounts of OO - -
large, non-polar molecules – can not dissolve in water
formed by dehydration / synthesis
True (neutral) fats – True (neutral) fats –
function -function - True (neutral) fats – True (neutral) fats –
function -function - insulation -
– prevents loss of body heatcushion internal organsenergy storage -
– fat -> 9 calories per gram – sugar -> 4 calories per gram
Structure of true fats -Structure of true fats -Structure of true fats -Structure of true fats -
1, 2, or 3 fatty acids attached to glycerol
Fatty acid-Fatty acid-long carbon chaincarboxyl (-COOH)
group attached to the end
FATTY ACID: Fig. FATTY ACID: Fig.
Saturated Fatty AcidSaturated Fatty Acid
no double bonds / contains the maximum # of hydrogen atoms
from animal productsSolid at room temp
– examples: butter, lard
Unsaturated Fatty AcidUnsaturated Fatty Acidcontains C-C double bonds from plantsliquid at room temperature polyunsaturated fatty acids: many double bonds
– Ex: olive oil, soybean oilmonounsaturated fatty acids: one double bond
– Ex: sunflower oil, corn oil
Glycerol –Glycerol –3 C skeleton3 alcohol groups attached
–See page 56
Structure of lipidsStructure of lipids
Triglycerides–three fatty acids + one glycerol
–most abundant true fat in the body
Triglyceride: Triglyceride: Fig. 3.21Fig. 3.21
Omega –3 & 6 fatty acidsOmega –3 & 6 fatty acids
Essential fatty acidsUsed for growth & hormone prdndouble bond found after the 3rd
carbonAbundant in fish oil, soybeans
Hydrogenation -Hydrogenation - Hydrogenation -Hydrogenation -
Adding hydrogen to an unsaturated fat
solidifies the fatex: margarine
Phospholipids -Phospholipids - Phospholipids -Phospholipids -
1 Glycerol + 2 fatty acids + Phosphate cmpd
function - component of cell membranes
Steroids -Steroids - Steroids -Steroids - lipids without fatty acidsinterlocking rings
– cholesterol -• component of cell membranes• converted into bile salts (emulsify fat)• vitamin D
– hormones -• estrogen• testosterone
Proteins -Proteins - Proteins -Proteins -
function –structural -
•cell membranes
•muscle cells
•Hemoglobin
Protein function (cont) -Protein function (cont) -
regulation - –enzymes (organic catalysts)
–hormones- insulin, oxytocin
–antibodies - fight infection
Protein function (cont) -Protein function (cont) -Protein function (cont) -Protein function (cont) -
carriers - –lipoproteins - transport fats
• cholesterol
• triglycerides
• Phospholipids
Consist of –Consist of –Linked amino
acids (AA)Peptide bondsPolypeptide
chainOnly 20 AA
exist
Peptide bond: covalent bond Peptide bond: covalent bond between amino acidsbetween amino acids
Protein structure & Protein structure & OrganizationOrganization
Four levels of protein Four levels of protein organization -organization -
Four levels of protein Four levels of protein organization -organization -
primary - polypeptide chainsecondary - polypeptide chain
twists-– alpha helix (coil) - formed by
hydrogen bonds
– beta pleated sheet - formed by hydrogen bonds
Protein organization (cont) -Protein organization (cont) -
tertiary – 3 D– Folding of an
individual moleculequaternary – 4D
– interactions of individual 3D molecules
Changes in protein structure -Changes in protein structure -Changes in protein structure -Changes in protein structure -
sickle-cell anemia-–hemoglobin consist of 4
polypeptides–change in one amino acid causes
the hemoglobin to fold poorly –Forms a“sickle” shape under
increased oxygen demand
Denaturation-Denaturation-Denaturation-Denaturation-Change of a protein’s 3-D shapeBonds broken by
– heat, light, or pHnot reversible
–you can not unfry an egg!
Nucleic acids-Nucleic acids-Nucleic acids-Nucleic acids-function - component of DNA &
RNA–DNA - genetic code
–RNA - manufacturer of protein
Structure of nucleic acids -Structure of nucleic acids - Structure of nucleic acids -Structure of nucleic acids -
made up of nucleotides
Nucleotides -Nucleotides -
– 5- carbon simple suger• deoxyribose (DNA)• ribose (RNA)
– phosphate group– nitrogenous base
• Adenine• Guanine• Thymine • Cytosine• Uracil
NUCLEIC ACIDSNUCLEIC ACIDSDNA
–Genetic material–Nucleotides: building blocks
• 5-C sugar, deoxyribose• Phosphate• Nitrogenous Base• Adenine,Guanine,Thymine, Cytosine
NUCLEIC ACIDSNUCLEIC ACIDSDNA
– Double helix structure– Sugar-phosphate backbone– Bases complimentary paring
• A-T, C-G
– Coding strand• Protein synthesis
NUCLEIC ACIDSNUCLEIC ACIDSRNA
– Protein synthesis– Ribose sugar– Uracil base and no Thymine
3 forms of RNA– Messenger RNA : mRNA– Transfer RNA : tRNA– Ribosomal RNA : rRNA
SUMMARYSUMMARYChemistry of living things
– Based on Carbon
C atoms: all organic moleculesStructure of OM related to functionCommon OM
– CHO, Pns, Lipids, Nucleic acids
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