Transcript Biological Molecules , Great and Small

Biological Molecules , To
Branch or Not to Branch?
Chapter 3/AP Bio.
Biochemistry
Cells have molecules with low
molecular weight, less than 300 and
over 10,000 (high) molecular weight ,
but few intermediate. Large
molecules are called macro, made
of small molecules linked together.
All are made of chains of C atoms.
C and H containing compounds are
organic; organic chemistry is the
study of them and biochemistry is
the study of chemical reactions in
living organisms. There are 4
classes of molecules that form living
structures.
Sugars, amino acids, nucleotides
and lipids are the main
biochemicals. Sugars form longchained polysaccharides (starch).
Amino Acids form proteins, or
nucleic acids like DNA (genes).
Lipids (fats) don’t form long chains.
Lipids form sheets like cell
membranes. Evidence that all life
on earth has a common ancestor is
supported by most organisms using
sugar as an energy source and a
million+ species use the same 20
amino acids.
Structures can be made of long
chains of C atoms. C bonds to the
next C by a single or double
covalent bond; H atoms link to the
sides. These are called hydrocarbon
chains . Ex. Octane. 8 C’s and 18
H’s.
Hydrocarbon chains form rings. C
can form covalent bonds at certain
angles. C rings usually have 5 or 6
C atoms. If atoms of the rings are
formed by alternating single and
double bonds the ring is flat. If they
use single bonds they bend into a
chair or boat shape.
The structure of a molecule
determines its function. “Functional
groups” predict properties of
molecules. (Functional groups are
life attachments on a swiss army
knife.) Combinations of functional
groups determine the way a
molecule acts.
Ethane has 2 C’s , 3 H’s attach to
each. It is 9% of natural gas.
Ethanol is like ethane with a hydroxyl
group (-OH). The extra O makes
ethanol different from ethane. It is a
solvent.
Ethanol is hydrophilic, dissolves
readily with water because of the
slight + charge of the H in the –OH
group. In acetic acid the C is
attached to the carboxyl group, COOH, resulting in acetic acid like
vinegar, with a sour smell and bite.
The structure of a molecule determines its function. “Functional groups”
predict properties of molecules. (Functional groups are life attachments on
If we substitute an amino
group, NH2, the molecule tends to be
basic , it attracts H ions forming NH3+.
a swiss army knife.)
H
C-C-N
H
2 other functional
groups are –SH
(sulfhydryl) and
phosphate (PO4).
Again the properties are different. It
has an ammonia smell. Most amines
are bad-smelling. Cadavarine gives
a rotting smell to corpses.
Functional groups are shown
attached to an R in the amino acids
that make up proteins. (Table 3-1)
Building organic molecules requires
starting with a C skeleton. Whether
the molecule is hydrophobic,
hydrophilic, or both, (amphipathic)
depends on polarity of molecular
bonds, determining how it reacts
with water.
The 4 kinds of building blocks are:
1.Lipids – fatty, non-polar, do not dissolve
in water.
2.Sugars-2 H’s and 1 O for every C atom.
3.Amino acids- contain both amino and
carboxyl groups.
4.Nucleotides- consist of a nitrogen ring,
a sugar, and a phosphoric acid.
3 of these form long chains.
1. Sugars can form polysaccharides.
2. Nucleotides can form nucleic acids.
3.Amino acids can form proteins.
Lipids do not form long chains.
Proteins and nucleic acids form
unbranched chains but can be
complex as they coil and fold into 3D shapes. These shapes determine
their function.
Polysaccharide chains can have many
branches. Bonds that hold
macromolecules together have to be
strong enough to not fall apart but
can break easily when catalyzed.
Enzymes make or break chemical
bonds. Removing 2 H’s and 1 O
from between 2 molecules joins
them in a reaction called a
dehydration condensation
reaction (1 molecule of H2O is
removed). They can be broken by
adding one molecule of H2O,
hydrolysis.
Glycosidic bonds join sugars. Peptide
bonds join amino acids. Triglycerides
are formed by hydrolysis. See p.50
for a description of hydrophilic and
hydrophobic ends of the phospholipid
cell membrane. Hydrophobic tails of
phospholipids form an oily interior
and hydrophilic ends turn outward.
Outer and inner membranes have this
structure.
Steroids- hydrocarbon chains with 4
rings form hormones. The starting
one is cholesterol. With 4 rings,
different functional groups can attach
causing variations in their effects.
Cells can make testosterone from
progesterone. Estrogen is made from
testosterone.
Some sugars form short chains
(oligosaccharides). The longest are
polysaccharides – including
thousands of simple sugars, starch in
bread, cellulose in wood.
Ribose and deoxyribose are 5 C
sugars in DNA and RNA. All sugars
and polysaccharides are
carbohydrates, 1 molecule of water
for every C. H atoms are on one side
and hydroxyl (-OH-) groups on the
other side. Most dissolve well in
water.
Cholesterol
is not bad for you! You can’t live
without it. It is on the outer
membranes of cells. It comes from
the liver and diet. 180mg./deciliter is
average for young people but you get
more as you age. It travels in
lipoprotein complexes.
Low density lipoproteins (LDL’s)
deliver cholesterol to cells. HDL’s
remove cholesterol to the liver where
it forms bile. HDL’s are good
because they get rid of LDL’s.
Excess LDL’s can build up in arteries
forming deposits called plaques.
Plaques cause hardening of the
arteries by atherosclerosis which
increases blood pressure and risk of
heart attack. Smoking reduces HDL’s.
Many other variables are related to
heart attack risk.
Sugar is a basic energy source for all
organisms. Simple ones are
monosaccharides, (3 to 9 C’s).
Glucose and fructose have 6 C’s.
Cells link these by dehydration
condensation formed by glycosidic
bonds. 2 sugars form a disaccharide
(sucrose is table sugar).
Monosaccharides and disaccharides
store energy for a few hours.
Polysaccharides (starches) can store
energy for weeks or years. Glucose
is blood sugar. Most biochemical
reactions are related to glucose.
Making glucose stores energy.
Linking chains of glucose stores
energy as glycogen.
Glycogen has short branches so
enzymes can easily release glucose as
needed. Plants store starch as
amylopectin or as amylase. Other
polysaccharides are chitin (makes up
the exoskeleton of arthropods).
Wood, paper, and cotton are
cellulose.
Properties of polysaccharides depend
on the kind of sugar and how they
are joined. The most important to us
are: starch, cellulose, and glycogen.
Glycogen is released as glucose as
we need it, starch is broken into
glucose by digestion, but cellulose is
indigestible to us and forms fiber.
Cellulose has straight chains of
glucose which supports plants.
Animals that digest cellulose use
microorganisms that secrete enzymes
that break it down. So grazing
animals get lots of nutrients from
grass but we do not.
Cellulose that is good for our
digestion are oligosaccharides, short
chains. They can attach to proteins
forming glycoproteins found on cell
membranes and help cells to
remember one another. Inside cells
glycoproteins help tell a cell where to
send new proteins.
Nucleotides are building blocks of DNA
and RNA. They have 3 parts: sugar
(ribose or deoxyribose), one or more
phosphate groups and a nitrogen
base. Most cells use 5 bases; 2 – ring
purines (adenine and guanine), and 1ring pyrimidines (thymine, cytosine,
and uracil).
Thymine has a methyl group,CH3, not
found in uracil. Nucleotides with 1, 2,
or 3 phosphates as in ATP (adenosine
triphosphate) play a central role in
production of energy.
ATP is the immediate source of
energy for all biological processes.
Energy from breakdown of glucose
is stored in ATP and can be released
by hydrolysis of a phosphate bond.
Nucleotides of nucleic acids are linked
together by phosphodiester bonds into
long unbranched chains such as in DNA
or RNA. DNA contains genes. RNA is
an interpreter.
Polypeptides are made of amino acids
joined by peptide bonds that form
proteins. Proteins perform thousands of
functions: support bones, transport
molecules, regulate passage of ions.
Humans have about 80,000 kinds.
Collagen is the most common. It
strengthens connective tissue in
tendons, bones, muscle, and skin.
Elastin makes the skin stretchy.
Keratin toughens hair and nails.
Hemoglobin binds to oxygen. Proteins
act as hormones, antibodies, and
poisons. Glycoproteins on cell
surfaces help other molecules to
recognize them, important in the
immune response.
Proteins like neurotransmitters make
nerve cells communicate. Enzymes
speed up chemical reactions. Each
protein is made of chains of amino
acids. The chain is a polypeptide. A
protein can be a simple chain or can
be 3,500 or more amino acids long.
Each amino acid has a carboxyl
group, -COOH and an amino group,
NH2. They are attached to the same
C called the alpha-carbon which also
attaches to the R group. In most
amino acids the alpha - carbon,
carboxyl group, and amino groups
are the same. (not proline).
The R groups are different,
varying in functional groups and
length. R groups’ side chains
determine the properties of the
amino acid and then the
polypeptide.
Each amino acid in a chain is oriented
the same way as the others , amino,
carboxl, amino, carboxyl… forming a
backbone. The R groups hang off
the side not involved in peptide
bonds but may interact with each
other.
All proteins have different shapes
related to function. They are
classified as globular like hemoglobin.
Fibrous proteins form keratin (hair),
and collagen (skin).
Proteins may have up to 4 levels of
structure.
1.The primary structure is the amino
acid sequence of the peptide chain.
2.The secondary structure is its
shape.
Ex. of secondary. The alpha - Helix is
twisted like a phone cord. Another is
beta - pleated sheets with the pleats
held together by sticky H bonds. A
collagen helix consists of 3
polypeptide chains wound around
each other.
3.The tertiary structure (conformation)
is the 3 dimensional folding of the
entire polypeptide chain into another
shape.
4.The quaternary structure is the
fitting together of 2 or more folded
chains.
Even changing one amino acid can
destroy a protein’s biological activity.
In hemoglobin substituting valine for
glutamic acid produces defective
hemoglobin that causes sickle cell
anemia.
Polypeptides are linear, not branched
like polysaccharides. But they can
coil into helices, sheets, or balls and
act like a single huge molecule. The
alpha helix, beta sheet and alpha
collagen allow them to function in
an organism as building materials.
The alpha-helix and beta-structure
are made of repeating sequences so
globular proteins are more flexible as
they fold. They have more diverse
roles than fibrous proteins. Globular
proteins can be hormones,
antibodies, or enzymes.
Tertiary folding is caused by
interaction of side chains. Side
chains may be polar, non polar,
proton donors or acceptors. They
cause the 3 –D structure that is
stable in certain chemical
environments. Changes in a chemical
environment can change the shape
and activity of a protein.
Seconds after it forms a polypeptide takes
shape determined by the sequence of the
amino acids.
A biochemist, Anfinsen, studied the
enzyme ribonuclease that breaks
bonds in RNA. First he chemically
interferred with hydrogen bonds and
hydrophobic interactions changing the
enzyme’s shape and ability to
function. (denatured)
After removing ribonuclease from the
altered environment it again became
active. So the right amino acid
sequence and right chemical
environment are all that is needed to
determine the enzyme’s 3-D shape.
Anfinsen showed that there are
obstacles to protein- folding. In a
cell, concentration of protein and
other molecules is high. Peptide
chains form bonds with other
peptides (promiscuous interactions).
To prevent this some enzymes and
special proteins called chaperones
bind to new polypeptides and help
them fold to the correct shape.