Download Ch. 4-5 - Carbon and Organic Chem

CH. 4 & 5
• Chapter 4~
Carbon &
The Molecular
Diversity of Life
• Chapter 5~
The Structure &
Function of Large
Molecules
Why study Carbon?
• All of life is built on carbon
• Cells
– ~72% H2O
– ~25% carbon compounds
•
•
•
•
carbohydrates
lipids
proteins
nucleic acids
– ~3% salts
• Na, Cl, K…
Chemistry of Life
• Organic chemistry is the study of carbon
compounds
• C atoms are versatile building blocks
– bonding properties
– 4 stable covalent bonds
H
H
C
H
H
Complex molecules assembled like TinkerToys
Hydrocarbons
• Combinations of C & H
– non-polar
• not soluble in H2O
• hydrophobic
– stable
– very little attraction
between molecules
• a gas at room temperature
methane
(simplest HC)
Hydrocarbons can grow
Isomers
• Molecules with same molecular formula but
different structures (shapes)
– different chemical properties
– different biological functions
6 carbons
6 carbons
6 carbons
Form affects function
• Structural differences create important
functional significance
– amino acid alanine
• L-alanine used in proteins
• but not D-alanine
– medicines
• L-version active
• but not D-version
– sometimes with
tragic results…
stereoisomers
Form affects function
• Thalidomide
– prescribed to pregnant women in 50s & 60s
– reduced morning sickness, but…
– stereoisomer caused severe birth defects
Diversity of molecules
• Substitute other atoms or groups around the
carbon
– ethane vs. ethanol
• H replaced by an hydroxyl group (–OH)
• nonpolar vs. polar
• gas vs. liquid
• biological effects!
ethane (C2H6)
ethanol (C2H5OH)
Functional groups
• Parts of organic molecules that are involved
in chemical reactions
– give organic molecules distinctive properties
hydroxyl
 carbonyl
 carboxyl

• Affect reactivity
amino
 sulfhydryl
 phosphate

– makes hydrocarbons hydrophilic
– increase solubility in water
Viva la difference!
• Basic structure of male & female hormones
is identical
– identical carbon skeleton
– attachment of different functional groups
– interact with different targets in the body
• different effects
Hydroxyl
• –OH
– organic compounds with OH = alcohols
– names typically end in -ol
• ethanol
Carbonyl
• C=O
– O double bonded to C
• if C=O at end molecule = aldehyde
• if C=O in middle of molecule = ketone
Carboxyl
• –COOH
– C double bonded to O & single bonded to OH
group
• compounds with COOH = acids
– fatty acids
– amino acids
Amino
• -NH2
– N attached to 2 H
• compounds with NH2 = amines
– amino acids
• NH2 acts as base
– ammonia picks up H+ from solution
Sulfhydryl
• –SH
– S bonded to H
• compounds with SH = thiols
• SH groups stabilize the structure of proteins
Phosphate
• –PO4
– P bound to 4 O
• connects to C through an O
• lots of O = lots of negative charge
– highly reactive
• transfers energy between organic molecules
– ATP, GTP, etc.
Polymers
– “mer” means unit
– “mono” means one
• Monomer-one unit
– “poly” means many
• Polymer-many units
• Polymers are made of many
monomers
19
Macromolecules
•Most macromolecules are
polymers, built from
monomers
• Four classes of life’s organic
molecules are polymers
–
–
–
–
Carbohydrates
Proteins
Nucleic acids
Lipids
20
The Synthesis and Breakdown of
Polymers
• Monomers form larger molecules by
condensation reactions called dehydration
synthesis
HO
1
2
3
H
Unlinked monomer
Short polymer
Dehydration removes a water
molecule, forming a new bond
HO
Figure 5.2A
1
H
HO
2
H2 O
3
4
H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
21
The Synthesis and Breakdown of
Polymers
• Polymers can disassemble by
– Hydrolysis (addition of water molecules)
HO
1
2
3
4
Hydrolysis adds a water
molecule, breaking a bond
HO
Figure 5.2B
1
2
3
H
H2 O
H
HO
H
(b) Hydrolysis of a polymer
22
Carbohydrates
• MONOSACCHARIDES are simple sugars in a 1:2:1
ratio
•
GLUCOSE
•
GALACTOSE = sugar found in milk
• FRUCTOSE = fruit sugar
• Chemical composition (C6 H12 O6)
Important Monosaccharides
Glucose
Carbohydrates
• DISACCHARIDES consist of two single
sugars(monosaccharides) linked together by glycosidic
linkage (Dehydration synthesis)
• Lactose = Milk sugar
• Sucrose = Table sugar
Carbohydrates
Carbohydrates
• POLYSACCHARIDE is a carbohydrate made of long chains of
sugars (3 or more monosaccharides)
• Starch - Plants convert excess sugars into starches for long-term
storage (Alpha linkage)
• Glycogen -Animals store glucose in the form of polysaccharide
glycogen in the liver and muscles to be used as quick energy
• Cellulose -a structural polysaccharide contained in the cell walls
of plants (ß linkage)
• Chitin – a polysaccharide found in the cell walls of fungi and the
exoskeletons of insects and arthropods
Starch
Glucose
Lipids
• Lipids are large, NONPOLAR organic molecules that
DO NOT dissolve in water
• Oils, fats, waxes, and steroids are lipid based
• Lipid molecules use less OXYGEN than carbohydrates
to store energy efficiently
• Used in biological membranes and as chemical
messengers
• Monomers – Fatty acids & Glycerol
Lipids
• UNSATURATED FATS are a liquid at room
temperature (OILS).
Double bonds can have
hydrogen added
• SATURATED FATS are solid at room temperature
NO double bonds
Saturated or Unsaturated Fatty Acids
Stearic acid
Oleic acid
Liquid at room temp
Solid at room temp
Triacylglycerol
Phospholipids – Make up the cell membrane
Hydrophilic vs Hydrophobic
Hydrophilic = Water loving
Hydrophobic = Water fearing
Steroids
• Steroids
– Are lipids characterized by a carbon skeleton consisting of
four fused rings
H3C
CH3
CH3
CH3
CH3
Figure 5.15
HO
36
Proteins
•
•
•
Chemical composition C-H-O-N-S
Proteins are made up of smaller monomers called AMINO ACIDS
Amino Acids differ ONLY in the type of R group they carry
Amino acids composed of 3 parts
1. Amino Group
2. Carboxylic group
3. R-group (Makes 20 different amino acids)
Peptide Bonds – link amino acids
20 Amino Acids
Protein Conformation
Primary Structure – sequence of amino acids
Secondary structure – Folding and coiling due
to H bond formation between carboxyl and
amino groups of non-adjacent amino acid. R
groups are NOT involved.
Tertiary structure – disulfide bridges, ionic
bonding, or h-bonding of R-groups
Quaternary structure – 2+ amino acid chains
R- group interactions, H bonds, ionic
interactions
Amino Acids
–
–
–
–
–
–
The polar uncharged amino acids are hydrophilic & can form hbonds
Serine
Threonine
Glutamine
Asparagine
Tyrosine
Cysteine
Amino Acids
The nonpolar amino acids are hydrophobic and are usually found in
the center of the protein. They also found in proteins which are
associated with cell membranes.
–
–
–
–
–
–
–
–
–
Glycine
Alanine
Valine
Leucine
Isoleucine
Methionine
Phenylalanine
Tryptophan
Proline)
Amino Acids
The electrically charged amino acids have electrical properties that
can change depending on the pH.
–
–
–
–
–
Aspartic Acid
Glutamic Acid
Lysine
Arginine
Histidine
Amino Acids
The electrically charged amino acids
(Aspartic Acid, Glutamic Acid, Lysine,
Arginine, and Histidine) have electrical
properties that can change depending on the
pH.
– Cysteine can form covalent disulfide bonds
– Proline had a unique structure and causes
kinks in the protein chain
Denaturing of Protein
Denaturing of Protein
• Transfer protein from aqueous solution to an
organic solvent (chloroform)
• Any chemical that disrupts h-bonds, ionic
bonds, & disulfide bridges
• Excessive heat
• Changes in pH
Enzymes
Act as CATALYSTS that can speed up some reactions by more
than a billion times!
Enzymes work by a physical fit (Lock and Key) between the enzyme
molecule and its SUBSTRATE, the reactant being catalyzed.
Enzymes reduces the activation energy for the chemical reaction to
occur.
After the reaction, the enzyme is released and is unchanged, so it
can be used many times
Enzyme names end in -ase
Enzyme & Substrate fit like
a lock & key (Shape specific)
pH or temperature can
change the active site
shape on any enzyme
Active site is where the
reactants bind to the enzyme
Activation Energy
The energy require to start a reaction is called Activation Energy
Nucleic Acids
Nucleic Acids
•RNA and DNA made of nucleic acids
•C-H-O-N-P atoms
•Polymers of nucleotides
•Nucleotides consist of a 5-carbon sugar, a
phosphate group, and a nitrogenous base.
•Store and transmit genetic information
Nucleic Acids