Transcript AP B 4,5 - apbiologyclass

AP Biology Chapters 4 and 5
• Chapter 4~
Carbon &
The Molecular
Diversity of Life
• Chapter 5~
The Structure &
Function of
Macromolecules
Concept 4.1: Organic chemistry is the study
of carbon compounds
•Organic chemistry is the study of
compounds that contain carbon
•Organic compounds range from simple
molecules to colossal ones
•Most organic compounds contain hydrogen
atoms in addition to carbon atoms
Concept 4.2: Carbon atoms can form diverse
molecules by bonding to four other atoms
•Electron configuration is the key to an atom’s
characteristics
•Electron configuration determines the kinds and
number of bonds an atom will form with other
atoms
Organic chemistry
• Carbon
•
•
•
•
tetravalence Makes large, complex
possible
tetrahedron In molecules with multiple
carbons, each carbon bonded to four
other atoms has a tetrahedral shape
However, when two carbon atoms are
joined by a double bond, the molecule
has a flat shape
shape determines function
•The electron configuration of carbon gives it
covalent compatibility with many different
elements
•The valences of carbon and its most frequent
partners (hydrogen, oxygen, and nitrogen) are
the “building code” that governs the
architecture of living molecules
Name
(a) Methane
(b) Ethane
c) Ethene
(ethylene)
Molecular
Formula
Structural
Formula
Ball-and-Stick
Model
Space-Filling
Model
Hydrocarbons
• Only carbon & hydrogen
(petroleum; lipid ‘tails’)
• Covalent bonding; nonpolar
• High energy storage
• Isomers (same molecular
•
formula, but different structure &
properties)
structural~differing covalent
bonding arrangement
• geometric~differing spatial
arrangement
• enantiomers~mirror images
pharmacological industry
(thalidomide)
Fig. 4-5
Ethane
(a) Length
Butane
(b) Branching
Propane
1-Butene
2-Butene
(c) Double bonds
2-Methylpropane
(commonly called isobutane)
Cyclohexane
d) Rings
Benzene
Fig. 4-6
Fat droplets (stained red)
(a) Mammalian adipose cells
(b) A fat molecule
Isomers
•Enantiomers are important in the pharmaceutical
industry
•Two enantiomers of a drug may have different effects
•Differing effects of enantiomers demonstrate that
organisms are sensitive to even subtle variations in
molecules
Drug
Condition
Effective
Enantiomer
Ineffective
Enantiomer
S-Ibuprofen
R-Ibuprofen
Ibuprofen Pain;
inflammation
Albuterol
Asthma
R-Albuterol
S-Albuterol
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

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

Concept 4.3: A small number of chemical
groups are key to the functioning of biological
molecules
•Distinctive properties of organic molecules depend not
only on the carbon skeleton but also on the molecular
components attached to it
•A number of characteristic groups are often attached to
skeletons of organic molecules
•Functional Groups
The seven functional groups that are most
important in the chemistry of life:
Hydroxyl group
Carbonyl group
Carboxyl group
Amino group
Sulfhydryl group
Phosphate group
Methyl group
Functional Groups, I
• Attachments that
replace one or more of
the hydrogen bonded to
the carbon skeleton of
the hydrocarbon
• Hydroxyl Group
• Each has a unique
property from one
organic compound to
another
• Carbonyl Group
H bonded to O;
alcohols;
polar (oxygen);
solubility in water
C double bond to O;
At end of H C :
aldehyde Otherwise:
ketone
Functional Groups, II
• Carboxyl Group
O double bonded to C to
hydroxyl; carboxylic acids;
covalent bond between
O and H;
polar; dissociation, H ion
• Sulfhydral Group
sulfur bonded to H;
thiols
• Phosphate Group
• Amino Group
N to 2 H atoms;
amines;
acts as a base (+1)
phosphate ion;
covalently attached
by 1 of its O to the C
skeleton;
CHEMICAL
GROUP
STRUCTURE
NAME OF
COMPOUND
Hydroxyl
In a hydroxyl group (—OH), a
hydrogen atom is bonded to an
oxygen atom, which in turn is
bonded to the carbon skeleton of
the organic molecule. (Do not
confuse this functional group
with the hydroxide ion, OH–.)
Alcohols (their specific names
usually end in -ol)
Carbonyl
The carbonyl group ( CO)
consists of a carbon atom
joined to an oxygen atom by a
double bond.
Ketones if the carbonyl group is
within a carbon skeleton
Aldehydes if the carbonyl group
is at the end of the carbon
skeleton
Carboxyl
When an oxygen atom is
double-bonded to a carbon
atom that is also bonded to
an —OH group, the entire
assembly of atoms is called
a carboxyl group (—COOH).
Carboxylic acids, or organic
acids
EXAMPLE
Acetone, the simplest ketone
Ethanol, the alcohol
present in alcoholic
beverages
Acetic acid, which gives vinegar
its sour taste
Propanal, an aldehyde
FUNCTIONAL
PROPERTIES
Is polar as a result of the
electrons spending
more time near the
electronegative
oxygen atom.
A ketone and an aldehyde may
be structural isomers with
different properties, as is the
case for acetone and propanal
These two groups are also
found in sugars, giving rise to
two major groups of sugars:
aldoses (containing an
aldehyde) and ketoses
(containing a ketone).
Has acidic properties
because the covalent bond
between oxygen and hydrogen
is so polar; for example,
Found in cells in the ionized
form with a charge of 1– and
called a carboxylate ion (here,
specifically, the acetate ion).
Fig. 4-10b
CHEMICAL
GROUP
Amino
Sulfhydryl
Phosphate
Methyl
STRUCTURE
The amino group
(—NH2) consists of a
nitrogen atom bonded
to two hydrogen atoms
and to the carbon skeleton.
NAME OF
COMPOUND
Amines
The sulfhydryl group
consists of a sulfur atom
bonded to an atom of
hydrogen; resembles a
hydroxyl group in shape.
Thiols
In a phosphate group, a
phosphorus atom is bonded to
four oxygen atoms; one oxygen
is bonded to the carbon skeleton;
two oxygens carry negative
charges. The phosphate group
(—OPO32–, abbreviated ) is an
ionized form of a phosphoric acid
group (—OPO3H2; note the two
hydrogens).
A methyl group consists of a
carbon bonded to three
hydrogen atoms. The methyl
group may be attached to a
carbon or to a different atom.
Methylated compounds
Organic phosphates
EXAMPLE
Glycine
Because it also has a
carboxyl group, glycine
is both an amine and
a carboxylic acid;
compounds with both
groups are called
amino acids.
FUNCTIONAL
PROPERTIES
Acts as a base; can
pick up an H+ from
the surrounding
solution (water, in
living organisms).
(nonionized)
(ionized)
Ionized, with a
charge of 1+, under
cellular conditions.
Glycerol phosphate
Cysteine
Cysteine is an important
sulfur-containing amino
acid.
Two sulfhydryl groups
can react, forming a
covalent bond. This
“cross-linking” helps
stabilize protein
structure.
Cross-linking of
cysteines in hair
proteins maintains the
curliness or straightness
of hair. Straight hair can
be “permanently” curled
by shaping it around
curlers, then breaking
and re-forming the
cross-linking bonds.
In addition to taking part in
many important chemical
reactions in cells, glycerol
phosphate provides the
backbone for phospholipids,
the most prevalent molecules in
cell membranes.
Contributes negative charge
to the molecule of which it is
a part (2– when at the end of
a molecule; 1– when located
internally in a chain of
phosphates).
Has the potential to react
with water, releasing energy
5-Methyl cytidine is a
component of DNA that has
been modified by addition of
the methyl group.
Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects
expression of genes.
Arrangement of methyl
groups in male and female
sex hormones affects
their shape and function.
Chapter 5
Macromolecules
Smaller organic molecules join together to form
larger molecules
macromolecules
4 major classes of
macromolecules:
carbohydrates
lipids
proteins
nucleic acids
Polymers
• Covalent monomers
• Condensation reaction
(dehydration reaction):One
monomer provides a
hydroxyl group while the
other provides a hydrogen
to form a water molecule
• Hydrolysis:bonds
between monomers are
broken by adding water
(digestion)
Carbohydrates, I
• Monosaccharides
•
•
•
•
√ CH 2 O formula;
√ multiple hydroxyl (-OH)
groups and 1 carbonyl
(C=O) group:
aldehyde (aldoses) sugar
ketone sugar
√ cellular respiration
√ raw material for amino
acids and fatty acids
Carbohydrates
Carbohydrates are composed of C, H, O
Function:
energy
raw materials

energy storage
 structural materials

Monomer: sugars
ex: sugars, starches, cellulose
Functional groups determine function
carbonyl
aldehyde
carbonyl
ketone
Sugar structure
5C & 6C sugars form rings in solution
Carbons are numbered
Numbered carbons
C 6'
5' C
4'
O
C
C 1'
energy stored in C-C bonds
C
3'
C 2'
Carbohydrates, II
• Disaccharides
√ glycosidic linkage
(covalent bond) between
2 monosaccharides
√ covalent bond by
dehydration reaction
• Sucrose (table
sugar)
• √ most common
disaccharide
Carbohydrates, III
•
•
•
Polysaccharides
Storage: Starch~ glucose
monomers
Plants: amyloplast
Animals: glycogen
• Polysaccharides
Structural:
Cellulose~ most abundant
organic
compound;
Chitin~exoskeletons; cell
walls of fungi; surgical thread
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

Cow
can digest cellulose well;
no need to eat other sugars
Gorilla
can’t digest cellulose well;
must add another sugar
source, like fruit to diet
Helpful bacteria
How can herbivores digest cellulose
so well?
BACTERIA live in their digestive
systems & help digest cellulose-rich
(grass) meals

Ruminants
Lipids
long term energy storage
concentrated energy
Lipids
•
•
•
•
•
•
•
•
No polymers; glycerol and fatty acid
Fats, phospholipids, steroids
Hydrophobic; H bonds in water exclude fats
Carboxyl group = fatty acid
Non-polar C-H bonds in fatty acid ‘tails’
Ester linkage: 3 fatty acids to 1 glycerol
(dehydration formation)
Triacyglycerol (triglyceride)
Saturated vs. unsaturated fats; single vs. double
bonds
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
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
Phospholipids
• 2 fatty acids instead of
3 (phosphate group)
• ‘Tails’ hydrophobic;
‘heads’ hydrophilic
• Micelle (phospholipid
droplet in water)
• Bilayer (double
layer);cell membranes
Why is this important?
Phospholipids create a barrier in water
define outside vs. inside
they make cell membranes!

Steroids
• Lipids with 4 fused carbon
rings
• Ex: cholesterol:
• cell membranes;
precursor for other
steroids (sex hormones);
atherosclerosis
Cholesterol
Important component of cell membrane
helps keep
cell membranes
fluid & flexible
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)
storage (bean seed proteins)

Proteins
• Importance:
instrumental in nearly everything organisms do; 50% dry weight of
cells; most structurally sophisticated molecules known
• Monomer: amino acids (there are 20) ~
carboxyl (-COOH) group, amino group (NH2), H atom, variable group
(R)….
• Variable group characteristics:
polar (hydrophilic), nonpolar (hydrophobic), acid or base
• Three-dimensional shape (conformation)
• Polymer: Polypeptides (dehydration reaction):
•
peptide bonds~ covalent bond; carboxyl group to amino
group (polar)
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

hemoglobin
growth
hormones
Amino acids
Structure
H O
| ||
H
—C—C—OH
—N—
|
H
R
central carbon
amino group
carboxyl group (acid)
Oh, I get it!
R group (side chain)
amino = NH2
variable group
acid = COOH
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)

Effect of different R groups: nonpolar &
hydrophobic
polar or charged & hydrophilic
Ionizing in cellular waters
H+ donors
H+ acceptors
Sulfur containing amino acids
Form disulfide bridges
covalent cross links betweens sulfhydryls
stabilizes 3-D structure

H-S – S-H
Building proteins
Peptide bonds
covalent bond between NH2(amine) of
one amino acid & COOH (carboxyl) of
another
C–N bond

peptide
bond
Primary 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!
Sickle cell anemia
Just 1
out of 146
amino acids!
I’m
hydrophilic!
But I’m
hydrophobic!
Secondary 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: keratin
-pleated sheet: silk
Secondary structure
•
Tertiary 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
Quaternary Structure
• Conformation:
2 or more polypeptide
chains aggregated into
1 macromolecule
• only then does polypeptide
become
functional protein
√collagen (connective
tissue)
√hemoglobin
Protein denaturation
In Biology,
size doesn’t matter,
SHAPE matters!
Unfolding a protein
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
Nucleic Acids
Function:
genetic material
stores information
genes
blueprint for building proteins
DNA  RNA  proteins
transfers information
blueprint for new cells
DNA
blueprint for next generation

proteins
G
C
T
A
A
C
G
T
A
C
G
T
A
Nucleic Acids
Examples:

RNA (ribonucleic acid)
single helix

DNA (deoxyribonucleic acid)
double helix
Structure:

monomers = nucleotides
RNA
DNA
Nucleotides
3 parts
nitrogen base (C-N ring)
pentose sugar (5C)

ribose in RNA
deoxyribose in DNA

phosphate (PO4) group
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)
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?
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?
DNA molecule
• Double helix
• H bonds between bases
join the 2 strands
• A :: T
• C :: G
H bonds?
Why is this important?
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?
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)
Another interesting note…
• ATP
Adenosine triphosphate
• modified nucleotide
• adenine (AMP) + Pi + Pi
+
+
ATP: An Important Source of Energy for Cellular
Processes
•One phosphate molecule, adenosine triphosphate (ATP),
is the primary energy-transferring molecule in the cell
•ATP consists of an organic molecule called adenosine
attached to a string of three phosphate groups
Fig. 4-UN4
Reacts
with H2O
P
P P
Adenosine
ATP
Pi
Inorganic
phosphate
P
P
Adenosine
ADP
Energy
Nucleic Acids, III
• Inheritance based on
DNA replication
• Double helix (Watson &
Crick - 1953)