Download AP Biology 2007-2008 Chemistry of Carbon Building

Chemistry of Carbon
Building Blocks of Life
AP Biology
2007-2008
Why study Carbon?
 All of life is built on carbon
 Cells
~72% H2O
 ~25% carbon compounds

 carbohydrates
 lipids
 proteins
 nucleic acids

AP Biology
~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
AP Biology
H
Complex molecules assembled like TinkerToys
AP Biology
Hydrocarbons
 Combinations of C & H

non-polar
 not soluble in H2O
 hydrophobic
stable
 very little attraction
between molecules

 a gas at room temperature
AP Biology
methane
(simplest HC)
Hydrocarbons can grow
AP Biology
Isomers
 Molecules with same molecular formula
but different structures (shapes)
different chemical properties
 different biological functions

6 carbons
6 carbons
AP Biology
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

AP Biology
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

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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!
AP Biology
ethane (C2H6)
ethanol (C2H5OH)
Functional groups
 Parts of organic molecules that are
involved in chemical reactions

give organic molecules distinctive
properties
hydroxyl
 carbonyl
 carboxyl

amino
 sulfhydryl
 phosphate

 Affect reactivity
makes hydrocarbons hydrophilic
 increase solubility in water

AP Biology
Viva la difference!
 Basic structure of male & female
hormones is identical



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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
AP Biology
Carbonyl
 C=O

O double bonded to C
 if C=O at end molecule = aldehyde
 if C=O in middle of molecule = ketone
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Carboxyl
 –COOH

C double bonded to O & single bonded
to OH group
 compounds with COOH = acids
 fatty acids
 amino acids
AP Biology
Amino
 -NH2

N attached to 2 H
 compounds with NH2 = amines
 amino acids
 NH2 acts as base
 ammonia picks up H+ from solution
AP Biology
Sulfhydryl
 –SH

S bonded to H
 compounds with SH = thiols
 SH groups stabilize the structure of proteins
AP Biology
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.
AP Biology
Macromolecules
Building Blocks
of Life
AP Biology
2007-2008
Macromolecules
 Smaller organic molecules join together
to form larger molecules

macromolecules
 4 major classes of
macromolecules:
carbohydrates
 lipids
 proteins
 nucleic acids

AP Biology
Polymers
 Long molecules built by linking repeating
building blocks in a chain

monomers
 building blocks
 repeated small units

H 2O
covalent bonds
HO
H
HO
H
Dehydration synthesis
HO
AP Biology
H
How to build a polymer
 Synthesis

You gotta
be open to
“bonding!
joins monomers by “taking” H2O out
 one monomer donates OH–
 other monomer donates H+
 together these form H2O

H 2O
requires energy & enzymes
HO
H
Dehydration synthesis
HO
H
enzyme
Condensation reaction
AP Biology
HO
H
How to break down a polymer
Breaking up
is hard to do!
 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
HO
 releases energy
H2O

enzyme
H
Hydrolysis
AP Biology
Digestion
HO
H
HO
H
Carbohydrates
AP Biology
CH2OH
H
O
H
OH
H
H
OH
HO
H
OH
Carbohydrates
energy
molecules
AP Biology
2006-2007
Carbohydrates
 Carbohydrates are composed of C, H, O

carbo - hydr - ate
CH2O
(CH22O)
O)xx
C66H12
O
(CH
12 66
Function:
energy
 raw materials
materials

energy storage
 structural

 Monomer: sugars
 ex: sugars, starches, cellulose
AP Biology sugar sugar sugar sugar sugar sugar sugar
sugar
Sugars
 Most names for sugars end in -ose
 Classified by number of carbons
6C = hexose (glucose)
 5C = pentose (ribose)
 3C = triose (glyceraldehyde)

CH2OH
H
O
H
OH
6H
HO
H
AP Biology
OH
Glucose
H
CH2OH
OH
C
O
H
HO
H
5
OH
O
H
HO
H
Ribose
H
H
H
C
OH
C
3OH
H
Glyceraldehyde
Functional groups determine function
carbonyl
aldehyde
carbonyl
ketone
AP Biology
Numbered carbons
C 6'
5' C
O
4' C
C1'
energy stored in C-C bonds
C3'
AP Biology
C2'
Simple & complex sugars
 Monosaccharides
simple 1 monomer sugars
 glucose

 Disaccharides
2 monomers
 sucrose

 Polysaccharides
large polymers
 starch

AP Biology
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
CH2OH
H
O
H
OH
H
H
OH
HO
Glucose
H
OH
Building sugars
 Dehydration synthesis
monosaccharides
|
glucose
AP Biology
H2O
|
glucose
disaccharide
|
maltose
glycosidic linkage
Building sugars
 Dehydration synthesis
monosaccharides
|
glucose
AP Biology
H2O
|
fructose
Let’s go to the
videotape!
disaccharide
|
sucrose
(table sugar)
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Polysaccharides
 Polymers of sugars
costs little energy to build
 easily reversible = release energy

 Function:

energy storage
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
 starch (plants)
 glycogen (animals)
 in liver & muscles

structure
 cellulose (plants)
 chitin (arthropods & fungi)
AP Biology
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Linear vs. branched polysaccharides
slow release
starch
(plant)
energy
storage
What does
branching do?
glycogen
(animal)
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fast
release
Let’s go to the
videotape!
Polysaccharide diversity
 Molecular structure determines function
in starch
in cellulose
isomers of glucose
 structure determines function…

AP Biology
Digesting starch vs. cellulose
starch
easy to
digest
enzyme
cellulose
hard to
digest
enzyme
AP Biology
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
AP Biology
But it tastes
like hay!
Who can live
on this stuff?!
Helpful bacteria
 How can herbivores digest cellulose so well?

BACTERIA live in their digestive systems & help digest
cellulose-rich (grass) meals
a dna ™emiTkciuQ
rosserpmoced )desserpmocnU( F FIT
.erutcip siht ees ot dedeen era
Caprophage
Ruminants
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Tell Ime
about
eat
the rabbits,
WHAT!
again,
George!
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Lipids: Fats & Oils
AP Biology
Lipids
long term energy storage
concentrated energy
AP Biology
2006-2007
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 smaller subunits
 not a continuing chain

AP Biology
Fats
 Structure:

glycerol (3C alcohol) + fatty acid
 fatty acid =
long HC “tail” with carboxyl (COOH) group “head”
enzyme
H2O
dehydration synthesis
AP Biology
Building Fats
 Triacylglycerol
3 fatty acids linked to glycerol
 ester linkage = between OH & COOH

hydroxyl
AP Biology
carboxyl
Dehydration synthesis
H2O
dehydration synthesis
enzyme
H2O
enzyme
H2O
AP Biology
enzyme
HO
Fats store energy
 Long HC chain
Why do humans
like fatty foods?
polar or non-polar?
 hydrophilic or hydrophobic?

 Function:

energy storage
 concentrated
 all H-C!
 2x carbohydrates
cushion organs
 insulates body

AP Biology
 think whale blubber!
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
AP Biology
Unsaturated fats
 C=C double bonds in
the fatty acids
plant & fish fats
 vegetable oils
 liquid at room temperature

 the kinks made by double
bonded C prevent the
molecules from packing
tightly together
mono-unsaturated?
poly-unsaturated?
AP Biology
Saturated vs. unsaturated
saturated
unsaturated
AP Biology
Phospholipids
 Structure:

glycerol + 2 fatty acids + PO4
 PO4 = negatively charged
It’s just like a
penguin…
A head at one end
& a tail
at the other!
AP Biology
Phospholipids
 Hydrophobic or hydrophilic?
fatty acid tails = hydrophobic
 PO4 head = hydrophillic
“attracted to water”
 split “personality”

Come here,
No, go away!
Come here,
No, go away!
interaction with H2O
is complex & very
important!
AP Biology
“repelled by water”
Phospholipids in water
 Hydrophilic heads “attracted” to H2O
 Hydrophobic tails “hide” from H2O

can self-assemble into “bubbles”
 bubble = “micelle”
 can also form a phospholipid bilayer
 early evolutionary stage of cell?
water
bilayer
AP Biology
water
Why is this important?
 Phospholipids create a barrier in water
define outside vs. inside
 they make cell membranes!

Tell them
about soap!
AP Biology
Steroids
 Structure:

4 fused C rings + ??
 different steroids created by attaching different
functional groups to rings
 different structure creates different function

examples: cholesterol, sex hormones
cholesterol
AP Biology
Cholesterol
 Important cell component
animal cell membranes
 precursor of all other steroids

 including vertebrate sex hormones

AP Biology
high levels in blood may contribute to
cardiovascular disease
Proteins
AP Biology
Proteins
Multipurpose
molecules
AP Biology
2008-2009
Proteins
 Most structurally & functionally diverse group
 Function: involved in almost everything







AP Biology
enzymes (pepsin, DNA polymerase)
structure (keratin, collagen)
carriers & transport (hemoglobin, aquaporin)
cell communication
 signals (insulin & other hormones)
 receptors
defense (antibodies)
movement (actin & myosin)
storage (bean seed proteins)
Proteins
 Structure

H2O
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
hemoglobin
AP Biology
Rubisco
growth
hormones
Amino acids
 Structure
central carbon
 amino group
 carboxyl group (acid)
 R group (side chain)

H O
H
| ||
—C— C—OH
—N—
|
H
R
 variable group
 different for each amino acid
 confers unique chemical
properties to each amino acid
 like 20 different letters of an
AP Biology
alphabet
 can make many words (proteins)
Oh, I get it!
amino = NH2
acid = COOH
Effect of different R groups:
Nonpolar amino acids
 nonpolar & hydrophobic
Why are these nonpolar & hydrophobic?
AP Biology
Effect of different R groups:
Polar amino acids
 polar or charged & hydrophilic
AP Biology
Why are these polar & hydrophillic?
Ionizing in cellular waters
AP Biology
H+ donors
Ionizing in cellular waters
AP Biology
H+ acceptors
Sulfur containing amino acids
 Form disulfide bridges


covalent cross links betweens sulfhydryls
stabilizes 3-D structure
H-S – S-H
You wondered
why perms
smell like
rotten eggs?
AP Biology
Building proteins
 Peptide bonds
covalent bond between NH2 (amine) of
one amino acid & COOH (carboxyl) of
another
 C–N bond

H2O
dehydration synthesis
AP Biology
peptide
bond
Building proteins
 Polypeptide chains have direction
N-terminus = NH2 end
 C-terminus = COOH end
 repeated sequence (N-C-C) is the
polypeptide backbone

 can only grow in one direction
AP Biology
Protein structure & function
 Function depends on structure

3-D structure
 twisted, folded, coiled into unique shape
pepsin
hemoglobin
AP Biology
collagen
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

 even just one amino acid change
can make all the difference!
AP Biology
lysozyme: enzyme
in tears & mucus
that kills bacteria
Sickle cell anemia
I’m
hydrophilic!
AP Biology
Just 1
out of 146
amino acids!
But I’m
hydrophobic!
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
AP Biology
Secondary (2°) structure
AP Biology
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
AP Biology
sulfurs in sulfhydryls (S–H)
 anchors 3-D shape
Quaternary (4°) structure
 More than one polypeptide chain bonded
together

only then does polypeptide become
functional protein
 hydrophobic interactions
AP Biology = skin & tendons
collagen
hemoglobin
Protein structure (review)
R groups
hydrophobic interactions
disulfide bridges
(H & ionic bonds)
3°
multiple
polypeptides
hydrophobic
interactions
1°
amino acid
sequence
peptide bonds
determined
by DNA
AP Biology
4°
2°
R groups
H bonds
Protein denaturation
 Unfolding a protein

In Biology,
size doesn’t matter,
SHAPE matters!
conditions that disrupt H bonds, ionic
bonds, disulfide bridges
 temperature
 pH
 salinity

alter 2° & 3° structure
 alter 3-D shape

destroys functionality
 some proteins can return to their functional shape
after denaturation, many cannot
AP Biology
Chaperonin proteins
 Guide protein folding


AP Biology
provide shelter for folding polypeptides
keep the new protein segregated from
cytoplasmic influences
Nucleic acids
AP Biology
2006-2007
Nucleic Acids
Information
storage
AP Biology
2006-2007
Nucleic Acids
 Function:

genetic material
 stores information
 genes
 blueprint for building proteins

DNA
DNA  RNA  proteins
 transfers information
 blueprint for new cells
 blueprint for next generation
AP Biology
proteins
G
C
T
A
AP Biology
A
C
G
T
A
C
G
T
A
Nucleic Acids
 Examples:

RNA (ribonucleic acid)
 single helix

DNA (deoxyribonucleic acid)
 double helix
 Structure:

AP Biology
monomers = nucleotides
DNA
RNA
Nucleotides
 3 parts
nitrogen base (C-N ring)
 pentose sugar (5C)

 ribose in RNA
 deoxyribose in DNA

phosphate (PO4) group
Are nucleic acids
charged molecules?
AP Biology
Nitrogen base
I’m the
A,T,C,G or U
part!
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)
AP Biology
Purine = AG
Pure silver!
Nucleic polymer
 Backbone
sugar to PO4 bond
 phosphodiester bond

 new base added to sugar of
previous base
 polymer grows in one direction

N bases hang off the
sugar-phosphate backbone
Dangling bases?
Why is this important?
AP Biology
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?
AP Biology
DNA molecule
 Double helix

H bonds between bases
join the 2 strands
 A :: T
 C :: G
H bonds?
Why is this important?
AP Biology
Copying DNA
 Replication

2 strands of DNA helix are
complementary
 have one, can build other
 have one, can rebuild the
whole
Matching halves?
Why is this
a good system?
AP Biology
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
AP Biology
Interesting note…
 Ratio of A-T::G-C
affects stability
of DNA molecule


2 H bonds vs. 3 H bonds
biotech procedures
 more G-C =
need higher T° to
separate strands

high T° organisms
 many G-C

parasites
 many A-T (don’t know why)
AP Biology
Another interesting note…
 ATP
Adenosine triphosphate

modified nucleotide
 adenine (AMP) + Pi + Pi
+
AP Biology
+
Macromolecule
Review
AP Biology
2006-2007
Carbohydrates
 Structure / monomer

monosaccharide
 Function
energy
 raw materials
 energy storage
 structural compounds

glycosidic bond
 Examples

AP Biology
glucose, starch, cellulose, glycogen
Lipids
 Structure / building block

glycerol, fatty acid, cholesterol, H-C chains
 Function
energy storage
 membranes
 hormones

 Examples

AP Biology
ester bond (in a fat)
fat, phospholipids, steroids
Proteins
 Structure / monomer
amino acids
 levels of structure

 Function
enzymes
 transport
 signals

defense
 structure
 receptors

peptide bond
 Examples

AP Biology
digestive enzymes, membrane
channels, insulin hormone, actin
Nucleic acids
 Structure / monomer

nucleotide
 Function

information storage
& transfer
 Examples

AP Biology
DNA, RNA
phosphodiester bond