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Organic Molecules
Organic molecules are found in living things.
Contain Carbon, Hydrogen, and usually oxygen
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Organic Molecules are Macromolecules
Macromolecules (polymers) are formed from smaller building blocks called monomers.
Polymer Monomer
carbohydrate monosaccharides
protein amino acid
nucleic acid nucleotide
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Monomers combine to make polymers
Organic Molecules are Macromolecules
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Organic Molecules are Carbon Compounds
All of life is built on carbon Cells
~72% H2O ~25% carbon compounds
carbohydrates lipids proteins nucleic acids
~3% salts Na, Cl, K…
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Organic Molecules are Carbon Compounds Organic chemistry is the study of
carbon compounds C atoms are versatile building blocks
bonding properties 4 stable covalent bonds
HHC
H
H
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Hydrocarbons – a component of organic molecules
methane(CH4)
Made of carbons and hydrogens. Come in many shapes (Carbon’s versatility)
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Macromolecules
Building Blocksof Life
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Macromolecules Smaller organic molecules join together
to form larger molecules macromolecules
4 major classes of macromolecules: carbohydrates lipids proteins nucleic acids
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H2O
HO
HO H
H HHO
Polymers Long molecules built by linking repeating
building blocks in a chain monomers
building blocks repeated small units
covalent bonds
Dehydration synthesisDehydration synthesis
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H2O
HO
HO H
H HHO
How to build a polymer Synthesis
joins monomers by “taking” H2O out one monomer donates OH–
other monomer donates H+ together these form H2O
requires energy & enzymes
enzymeDehydration synthesisDehydration synthesis
Condensation reactionCondensation reaction
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H2O
HO H
HO H HO H
How to break down a polymer
Digestion use H2O to breakdown polymers
reverse of dehydration synthesis cleave off one monomer at a time
H2O is split into H+ and OH–
H+ & OH– attach to ends
requires enzymes releases energy
HydrolysisHydrolysis
DigestionDigestion
enzyme
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OH
OH
H
H
HO
CH2OH
HH
H
OH
O
Carbohydratesenergy
molecules
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Carbohydrates Carbohydrates are composed of C, H, O
carbo - hydr - ate
CH2O
(CH2O)x C6H12O6
Function: energy energy storage raw materials structural materials
Monomer: sugars
ex: sugars, starches, cellulosesugar sugar sugar sugar sugarsugar
C6H12O6(CH2O)x
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Sugars Most names for sugars end in -ose Classified by number of carbons
6C = hexose (glucose) 5C = pentose (ribose)
OH
OH
H
H
HO
CH2OH
HH
H
OH
O
Glucose
H
OH
HO
O H
HHO
H
Ribose
CH2OH
6 5
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Simple & complex sugars Monosaccharides
simple 1 monomer sugars glucose
Disaccharides 2 monomers sucrose
Polysaccharides large polymers starch
OH
OH
H
H
HO
CH2OH
H
H
H
OH
O
Glucose
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Building sugars Dehydration synthesis
|glucose
|glucose
monosaccharides disaccharide
|maltose
H2O
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Building sugars Dehydration synthesis
|fructose
|glucose
monosaccharides
|sucrose
(table sugar)
disaccharide
H2O
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Polysaccharides Polymers of sugars
costs little energy to build easily reversible = release energy
Function: energy storage
starch (plants) glycogen (animals)
in liver & muscles
structure cellulose (plants) chitin (arthropods & fungi)
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Linear vs. branched polysaccharides
starch(plant)
glycogen(animal)
energystorage
slow release
fast release
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Polysaccharide diversity Molecular structure determines function
isomers of glucose structure determines function…
in starch in cellulose
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Digesting starch vs. cellulose
starcheasy todigest
starcheasy todigest enzyme
cellulosehard todigest
cellulosehard todigest
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Cellulose Most abundant organic
compound on Earth herbivores have evolved a mechanism to
digest cellulose most carnivores have not
that’s why they eat meat to get their energy & nutrients
cellulose = undigestible roughage
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Any Questions?
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Lipids: Fats & Oils
long term energy storageconcentrated energy
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Lipids Lipids are composed of C, H, O
long hydrocarbon chains (H-C)
“Family groups” fats phospholipids steroids
Do not form polymers big molecules made of only 3 subunits not a continuing chain
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Fats Structure:
glycerol (3C alcohol) + fatty acid fatty acid =
long HC “tail” with carboxyl (COOH) group “head”
dehydration synthesis
H2O
enzyme
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Building Fats Triglycerides
3 fatty acids linked to glycerol
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Dehydration synthesis
dehydration synthesis
H2O
H2O
H2O
H2O
enzyme
enzyme
enzyme
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Fats store energy Long HC chain
polar or non-polar? hydrophilic or hydrophobic?
Function: energy storage
concentrated 2x carbohydrates
cushion organs insulates body
think whale blubber!
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Saturated fats All C bonded to H No C=C double bonds
long, straight chain most animal fats solid at room temp.
contributes to cardiovascular disease (atherosclerosis) = plaque deposits
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Unsaturated fats C=C double bonds in
the fatty acids plant & fish fats vegetable oils liquid at room temperature
the kinks made by doublebonded C prevent the molecules from packing tightly together
mono-unsaturated?poly-unsaturated?
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“Trans” fats are a type of isomer Fatty acid tails are hydrocarbons.
Unsaturated fats have double bonds between carbons.
Form follows function!
Trans fats are straight and solidify at room temperature.
Cis (olive oil)
Trans (partially hydrogenated vegetable oil)
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Saturated vs. unsaturatedsaturated unsaturated
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Phospholipids Structure:
glycerol + 2 fatty acids + PO4
PO4 = negatively charged
Polar Head
Hydrophilic
Non-polar tail
Hydrophobic
Attracted to Water
Repelled by Water
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Why is this important? Phospholipids create a barrier in water
define outside vs. inside they make cell membranes!
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Cholesterol Important cell component
animal cell membranes precursor of all other steroids
including vertebrate sex hormones high levels in blood may contribute to
cardiovascular disease
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Cholesterol
helps keep cell membranes
fluid & flexible
Important component of cell membrane
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Any Questions?
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Proteins
Multipurposemolecules
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Proteins Most structurally & functionally diverse group Function: involved in almost everything
enzymes (pepsin, DNA polymerase) structure (keratin, collagen) carriers & transport (hemoglobin, aquaporin) cell communication
signals (insulin & other hormones) receptors
defense (antibodies) movement (actin & myosin)
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Proteins Structure
monomer = amino acids 20 different amino acids
polymer = polypeptide protein can be one or more polypeptide
chains folded & bonded together large & complex molecules complex 3-D shape
Rubisco
hemoglobin
growthhormones
H2O
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Amino acids Structure
central carbon amino group carboxyl group (acid) R group (side chain)
variable group different for each amino acid confers unique chemical
properties to each amino acid like 20 different letters of an
alphabet can make many words (proteins)
—N—H
HC—OH
||O
R
|—C—
|
H
Oh, I get it!amino = NH2 acid = COOH
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Building proteins Peptide bonds
covalent bond between NH2 (amine) of one amino acid & COOH (carboxyl) of another
C–N bond
peptidebond
dehydration synthesisH2O
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Effect of different R groups:Nonpolar amino acids
Why are these nonpolar & hydrophobic?Why are these nonpolar & hydrophobic?
nonpolar & hydrophobic
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Effect of different R groups:Polar amino acids
polar or charged & hydrophilic
Why are these polar & hydrophillic?Why are these polar & hydrophillic?
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Protein structure & function
hemoglobin
Function depends on structure 3-D structure
twisted, folded, coiled into unique shape
collagen
pepsin
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Primary (1°) structure Order of amino acids in chain
amino acid sequence determined by gene (DNA)
slight change in amino acid sequence can affect protein’s structure & its function just one amino acid change can
make all the difference!
lysozyme: enzyme in tears & mucus that kills bacteria
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Secondary (2°) structure “Local folding”
folding along short sections of polypeptide interactions between
adjacent amino acids H bonds
weak bonds between R groups
forms sections of 3-D structure -helix -pleated sheet
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Tertiary (3°) structure “Whole molecule folding”
interactions between distant amino acids hydrophobic interactions
cytoplasm is water-based
nonpolar amino acids cluster away from water
H bonds & ionic bonds disulfide bridges
covalent bonds between sulfurs in sulfhydryls (S–H)
anchors 3-D shape
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Quaternary (4°) structure More than one polypeptide chain bonded
together only then does polypeptide become
functional protein hydrophobic interactions
collagen = skin & tendons hemoglobin
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Protein structure (review)
amino acid sequence
peptide bonds
1°
determinedby DNA R groups
H bonds
R groupshydrophobic interactions
(H & ionic bonds)
3°multiple
polypeptideshydrophobic interactions
4°
2°
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Sickle cell anemia
I’mhydrophilic!
But I’mhydrophobic!
Just 1out of 146
amino acids!
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Protein denaturation Unfolding a protein
conditions that disrupt H bonds, ionic bonds temperature pH salinity
alter 2° & 3° structure alter 3-D shape
destroys functionality
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Nucleic AcidsInformation
storage
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proteinsproteins
DNADNA
Nucleic Acids Function:
genetic material stores information
genesblueprint for building proteins
DNA RNA proteins
transfers informationblueprint for new cellsblueprint for next generation
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AA
A
A
TC
G
CG
TG
C
T
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Nucleic Acids Examples:
RNA (ribonucleic acid) single helix
DNA (deoxyribonucleic acid) double helix
Structure: monomers = nucleotides
RNADNA
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Nucleotides 3 parts
nitrogen base (C-N ring) pentose sugar (5C)
ribose in RNA deoxyribose in DNA
phosphate (PO4) group
Nitrogen baseI’m the
A,T,C,G or Upart!
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Types of nucleotides 2 types of nucleotides
different nitrogen bases purines
double ring N base adenine (A) guanine (G)
pyrimidines single ring N base cytosine (C) thymine (T) uracil (U)
Purine = AGPure silver!
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Nucleic polymer Backbone
Sugar-phosphate N bases hang off the
sugar-phosphate backbone
Dangling bases?Why is this important?
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Pairing of nucleotides Nucleotides bond between
DNA strands H bonds purine :: pyrimidine A :: T
2 H bonds G :: C
3 H bonds
Matching bases?Why is this important?
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DNA molecule Double helix
H bonds between bases join the 2 strands A :: T C :: G
H bonds?Why is this important?
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Copying DNA Replication
2 strands of DNA helix are complementary have one, can build other
Matching halves?Why is this
a good system?
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When does a cell copy DNA? When in the life of a cell does DNA have
to be copied? cell reproduction
mitosis gamete production
meiosis
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DNA replication“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”
James WatsonFrancis Crick
1953
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Watson and Crick … and others…
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Maurice Wilkins… and…
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Rosalind Franklin (1920-1958)
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MacromoleculesReview Carbohydrates
Empirical formula CH2O Functions: Quick energy (sugar), energy
storage in plants (starch), structure (cellulose in plants, chitin in fungi + arthropods)
Monomer = monosaccharide Polymer = polysaccharide
OH
OH
H
H
HO
CH2OH
HH
H
OH
O
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MacromoleculesReview Lipids
Made of C, H, and a few O Functions: Energy storage in
animals (triglycerides), Cell membrane structure (phospholipids), hormones (steroids)
Fats made of 1 Glycerol, 3 Fatty acids
Fatty acids can be saturated (no C-C double bonds) or unsaturated (C-C double bonds)
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MacromoleculesReview Proteins
Made of C, H, O, N, S, P Many diverse functions
Enzymes Membrane channels Hormones Structure
Monomer = amino acids Polymer = polypeptide 3-D shape determined by amino acid
sequence. Crucial to protein function 1°, 2°, 3°, 4° levels of organization
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Macromolecules Review Nucleic Acids
Information storage Examples: DNA and RNA Complementary base pairing
genetic code can be copied A – T C – G Purine – Pyrimidine Hydrogen bonds hold nitrogenous
bases together Monomer = nucleotides
Sugar, phosphate, nitrogenous base