Download biochemistry - Bioscience High School

BIOCHEMISTRY
AP BIOLOGY
I. Atoms in Organic Molecule
A.
B.
C.
Organic = molecules with carbon and
found in living things
Common Atoms = C, O, H, N
Other Atoms = S, P
II. Importance of Carbon
A.
B.
C.
Valence number of 4 – forms four bonds
Backbone of all organic molecules
Functional groups attach to form specific
properties
Four Valence electrons means
four bonds…
Hydrocarbons

Contain only carbon & hydrogen
atoms
Carbon can
form an
endless
diversity of
carbon
skeletons
Large Hydrocarbons:


Are the main molecules in the gasoline we
burn in our cars
The hydrocarbons of fat molecules provide
energy for our bodies
Shape of Organic Molecules
Each
type of
organic molecule
has a unique threedimensional shape
The shape
determines its
function in an
organism
Functional Groups

Groups of atoms that give properties to the
compounds to which they attach
Phosphate group

Used to transfer energy
III. Bonding Organic Molecules



Covalent bonds are used to form the
backbone of organic molecules
Formed by dehydration synthesis (removal
of water to make room for new bonds)
Broken by hydrolysis (replacing the water
as bonds are broken apart)
Giant Molecules - Polymers



Large molecules are called
polymers
Polymers are built
from smaller molecules
called monomers
Biologists call them
macromolecules
Examples of Polymers
Proteins
Lipids
Starch
Nucleic Acids
Most Macromolecules are Polymers

Polymers are made by stringing together many
smaller molecules called monomers
Nucleic Acid
Monomer
Linking Monomers
Cells link monomers in the process of dehydration
synthesis (removing a molecule of water)
Remove
OH
Remove
H
H2O Forms
Breaking Down Polymers
Cells break down macromolecules by a process
called hydrolysis (adding a molecule of water)
Water added to split a double sugar
IV. Types of Organic Molecules
A.
B.
C.
D.
Carbohydrates – energy formation –
sugars and starches
Lipids – storage and insulation – fats and
oils
Proteins – enzymes run all body reactions
Nucleic acids – store genetic information
– DNA and RNA
V. Carbohydrates
A. General Information
1.
2.
3.
4.
Made of C, H, O
Basic shape is a ring of carbons with –OH
and –H groups attached to the carbons
Isomers = same number of C, O, and H
but arranged differently
Grouped based on number of rings in
molecule
B. Monosaccharides
1.
Mono = one - one ring
2.
Many isomers (glucose, alpha and beta;
fructose; galactose) which react differently
in the body
Function – used in energy releasing
reactions
3.
Glucose –
the most common monosaccharide
Isomers
Glucose &
fructose are
isomers because
they’re structures
are different, but
their chemical
formulas are the
same
Rings
In aqueous (watery) solutions,
monosaccharides form ring structures

C. Dissacharides
1.
Formed from two monosaccharides
OH HO
+
2.
3.
+ H 2O
Glycosidic bonds = covalent bonds in carbs
formed by dehydration synthesis
Found mostly in plants – common example is
sucrose – used as a transport sugar
D. Polysaccharides
1.
2.
Many rings (100’s)
Purposes depend on way the rings are
constructed
a.
b.
Storage = starch in plants and glycogen in
animals
Structure = cellulose in plant cell walls and
chitin in fungus cell walls or insect
exoskeletons
Examples of Polysaccharides
Glucose Monomer
Starch
Glycogen
Cellulose
Starch
Starch is an example of a polysaccharide in
plants
Plant cells store starch
for energy
Potatoes and grains are
major sources of starch
in the human diet
Glycogen
Glycogen is an example of
a polysaccharide in animals
Animals store excess
sugar in the form of
glycogen
Glycogen is similar in
structure to starch
Cellulose
Cellulose is the most abundant organic
compound on Earth
It forms cable-like fibrils in the
tough walls that enclose plants
It is a major component of
wood
It is also known as dietary fiber
Cellulose
SUGARS
Dietary Cellulose

Most animals cannot derive nutrition from
fiber
They have
bacteria in
their digestive
tracts that can
break down
cellulose
Sugars in Water

Simple sugars and double sugars dissolve
WATER
readily in water
MOLECULE
They are
hydrophilic,
or “waterloving”
SUGAR
MOLECULE
Lipids
VI. Lipids
A.
General Information
1.
2.
Fats and oils are triglycerides.
Constructed of a 3 carbon alcohol called
glycerol and three long chains of
hydrocarbons called fatty acids.
Lipid structure
H
Dehydration synthesis removed –OH
and –H as bond forms
H - C – O - fatty acid
H - C – O - fatty acid
H - C – O - fatty acid
H
Fats

Dietary fat consists largely of the molecule
triglyceride composed of glycerol and three
fatty acid chains
Fatty Acid Chain
Glycerol
Dehydration links the fatty acids to Glycerol
B. Functions of Triglycerides
1.
2.
3.
Storage of chemical energy
Insulation
Padding
C. Types of Fatty Acids
Unsaturated fatty acids have less than the
maximum number of hydrogens bonded to the
carbons (a double bond between carbons)
Saturated fatty acids have the
maximum number of hydrogens bonded
to the carbons (all single bonds
between carbons)
Single
Bonds in
Carbon
chain
Double bond in carbon
chain
Triglyceride
Glycerol
Fatty Acid Chains
Fats in Organisms
Most animal fats have a high proportion of
saturated fatty acids & exist as solids at room
temperature (butter, margarine, shortening)
Saturated fats stack and block arteries.
Fats in Organisms

Most plant oils tend to be low in saturated
fatty acids & exist as liquids at room
temperature (oils)
D. Other types of Lipids
Found in this group because they
are insoluble in water.
1.
2.
3.
4.
Phospholipids – a phosphate group
replaces one fatty acid. Found in cell
membranes.
Terpenes = pigments such as chlorophyll
Prostaglandins = chemical messengers
Steroids = parts of hormones
Steroids
The
carbon skeleton of
steroids is bent to form 4
fused rings
Cholesterol
Cholesterol is
the “base
steroid” from
which your body
produces other
steroids
Estrogen
Testosterone
Estrogen & testosterone are also steroids
Synthetic Anabolic Steroids
They
are variants of
testosterone
Some athletes use
them to build up
their muscles quickly
They can pose
serious health risks
Lipids
Lipids are hydrophobic –”water fearing”
Nonpolar bonds on hydrophobic fatty acids.
Polar bonds on hydrophilic glycerol.
This means that lipids do not dissolve in water.
Includes
fats,
waxes,
steroids,
& oils
FAT MOLECULE
VII. Protein
A.
Building Blocks
1.
Composed of chains of amino acids
H
H2N – C – COOH
R
2. Amino acids come in 20 types and only the
R groups vary. R groups fall into three
categories – nonpolar, polar, and ionized.
3. R groups interact and form bonds with one
another.
Structure of Amino Acids
Amino
acids have a
central carbon with 4
things boded to it:
Amino
group
Amino group -NH3
Carboxyl group –COOH
Hydrogen -H
Side group -R
Carboxyl
group
R group
Side
groups
Serine-polar
Leucine -nonpolar
Linking Amino Acids
Cells link amino acids
together to make
proteins
The process is
called dehydration
synthesis
Peptide bonds
form to hold the
amino acids
together
Carboxyl Amino
Side
Group
Dehydration
Synthesis
Peptide Bond
Nonpolar
(hydrophobic)
Polar
(hydrophilic)
Charged
(Negative/Positive)
B. How to build a protein
1. PRIMARY STRUCTURE
Straight chain of amino acids
or a polypeptide
(A peptide bond is a
dehydration synthesis bond
between two amino acids)
B. How to build a protein
2. SECONDARY STRUCTURE - Chain forms
helix or pleated sheet. (Motif = some parts are
helix and some parts are sheet)
motif
B. How to build a protein
3. TERTIARY STRUCTURE – Helix forms three
dimensional shape as R groups interact.
Hydrophobic
interactions
What holds the tertiary structure?
Disulfide bridges
2. Ionic bonds
3. Hydrogen bonds
between polar R groups
4. Hydrophobic
interactions
1.
4. QUATERNARY STRUCTURE – not
always present – two or more tertiary
structures bond together, usually with a
metal atom as the center
Types of Proteins
Storage
Structural
Contractile
Transport
62
Functions of Proteins
1.
2.
3.
4.
5.
6.
7.
8.
Structural – support, tendons & ligaments
Storage – egg whites store amino acids
Transport – carry substances, hemoglobin
Hormones – coordinate body, insulin
Receptors – built into membranes
Contractile – movement, muscle fibers
Defensive – antibodies fight disease
Enzymes – accelerate reactions, digest molecules
Denaturating Proteins
Changes in temperature & pH can
denature (unfold) a protein so it no
longer works
Cooking denatures
protein in eggs
Milk protein separates into
curds & whey when it
denatures
Denaturalization


Proteins are denatured when their 3-D
shape changes. An incorrect shape can not
bond with other molecules correctly and
the enzyme does not function.
Denaturalization occurs by



Temperature / heat
pH changes
Excessive salts
VIII. Nucleic Acids
A.
General notes
1.
2.
Two basic types – DNA (long molecules
which store all of our genetic information
and never leave the nucleus) and RNA
(short molecules that are copies of one gene
of the DNA and used to direct protein
synthesis)
The organelle chromatin is composed of
DNA wrapped around proteins to form a
double helix.
B. Structure
1.
2.
A nucleotide has three parts – a sugar
(monosaccharide), a phosphate functional
group, and a nitrogen base.
Nitrogen bases are rings of carbon, nitrogen,
and hydrogen. They come in five major types
(A, T, C, G, and U).
Nucleic
acids are
polymers of
nucleotides
Nitrogenous base
(A,G,C, or T)
Phosphate
group
Thymine (T)
Sugar
(deoxyribose)
Phosphate
Base
Sugar
Nucleotide
Bases
Each
DNA nucleotide
has one of the
following bases:
–Adenine (A)
Thymine (T)
Cytosine (C)
–Guanine (G)
–Thymine (T)
–Cytosine (C)
Adenine (A)
Guanine (G)
RNA – Ribonucleic Acid
Ribose sugar
has an extra –
OH or
hydroxyl group
It has the
base uracil (U)
instead of
thymine (T)
Nitrogenous base
(A,G,C, or U)
Uraci
l
Phosphate
group
Sugar (ribose)
C. Functions
1.
2.
Storage of genetic instruction
Using genetic instructions to
create proteins.