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BIOCHEMISTRY NOTES
Chapter 3 and Chapter 6, Sections 6.3 and 6.4
I. ORGANIC MOLECULES
A. organic molecules vs inorganic molecules
1. organic molecules
a. contain carbons covalently bonded to each other & at least one hydrogen atom
b. are the molecules that make up living things
2. inorganic molecules - molecules that make up nonliving things
B. Four different kinds of organic molecules
p. 36, Figure 3.4
1. carbohydrates
3. proteins
2. lipids
4. nucleic acids
C. All four kinds of organic molecules contain functional groups
Figure 3.5, page 36
1. are particular atoms or clusters of atoms that are covalently bonded to carbon
2. Functional groups have consistent characteristics whenever they appear in organic
compounds, no matter what the rest of the molecule is like
D. The structure of organic molecules have a certain direction; if their atoms aren’t bonded together
correctly, then they can’t perform their function
II. HOW ORGANIC MOLECULES INTERACT WITH EACH OTHER
A. The reactions that occur in the cell to build, rearrange, and split up organic compounds
require two things: energy input and enzymes
B. Five categories of reactions:
1. Functional group transfer
2. Electron transfer
3. Rearrangement
4. Condensation (Dehydration Synthesis) – two molecules join together
5. Hydrolysis (Cleavage) – a molecule splits into two smaller ones
C. Definitions
1. monomer = small molecule that is linked with other monomers to form large molecules,
called polymers
2. Organic molecules are made by putting small molecules together to make a large molecule
3. Monomers are bonded together to form polymers by a reaction called condensation, or
dehydration synthesis
4. Polymers are broken down into monomers by a cleavage reaction called hydrolysis
5.
MONOMERS
POLYMERS
Monosaccharides ------------ carbohydrates (polysaccharides)
fatty acids
-----------lipids (fats)
amino acids -----------proteins
nucleotides ----------nucleic acids
d. Dehydration Synthesis Reaction (Condensation Reaction)
P. 37, Figure 3.6
1. Definition: combines two monomers together with a covalent bond to form a polymer
2. during the reaction, a water molecule is lost because one monomer loses a H atom, and the
other loses a OH
3. once they are combined, the monomers are now called RESIDUES because they each have
lost an atom or two
4. this reaction requires energy (endothermic)
5. Polymerization = chemical reaction where 2 or more small molecules combine to form
larger molecules that contain repeating structural units of the original molecules
E. Hydrolysis Reaction
1. Breaks the bond between two monomers within a polymer to reform the monomers; it
breaks up the polymer
2. Requires the addition of a water molecule (to replace the atoms lost by the monomers
during the condensation reaction)
3. this reaction releases energy (exothermic)
BIOCHEMISTRY, P. 2
III. The Central Role of the Carbon Atom
A. Important facts concerning the carbon atom in terms of its biological role:
1. carbon is used in storage compounds in organisms and in cell formation in organisms
2. carbon is able to form nonpolar covalent bonds with as many as 4 different atoms
3. carbon atoms can form bonds with each other
4. carbon atoms can form long chains
B. An organic molecule derives its overall shape from the arrangement of the carbon atoms that form
the backbone, or skeleton, of the molecule
C. Hydrocarbons
1. compounds consisting of only carbon and hydrogen
2. liquid fuels such as gasoline, diesel fuel, and heating oil are composed of hydrocarbons
IV. CARBOHYDRATES
A. Three kinds: monosaccharides, disaccharides, and polysaccharides
B. Monosaccharides - simplest carbohydrate – the monomers of carbohydrates
1. called simple sugars - are ready energy for living organisms (can be used as an energy
source very quickly)
2. examples.- glucose, fructose, galactose, ribose, deoxyribose
3. Formula (CH2O)n where n = 3 - 8
4. they always contain the -OH (hydroxyl) functional group
5. they always contain either an aldehyde group or a ketone group
a. if it contains an aldehyde group, it is called an aldose
b. if it contains a ketone group, it is called a ketose
6. Monosaccharides contain between 3 and 8 carbons, and are named according to how many
carbons they contain
a. triose - 3 C
c. pentose - 5 C
b. tetrose - 4 C
d. hexose - 6 C
7. Monosaccharides can either be in a straight chain form & or in a ring form
8. Glucose
Page 38
a. C6H12O6
b. is an aldose and a hexose
c. Function of glucose: as an energy source
During cell respiration, the energy in glucose is used to make energy for an
organism's cells to use
9. Ribose & Deoxyribose
a. Function: are a structural part of (they are found in) nucleotides, which are
components of DNA and RNA
b. they are pentose sugars
C. Disaccharides - dimers of monosaccharides (two monosaccharide residues bonded together)
1. Are formed by a Condensation (Dehydration Synthesis) Reaction, which covalently bonds
the two monosaccharides together
2. The bond between the 2 monosaccharides is called a glycosidic linkage
3. Function
a. to store energy short term
b. when the two monosaccharides are needed for energy, the bond is broken, (through
a hydrolysis reaction) and each monosaccharide enters cell respiration
BIOCHEMISTRY, P. 3
CARBOHYDRATES CONTINUED:
D. Polysaccharides
1. long chains of monosaccharides, with each two monosaccharides being bonded together by
a condensation reaction
2. Functions of polysaccharides
a. storage/transport of monosaccharides
b. structural
3. Some are storage/transport forms for sugar
a. are made (condensation reaction) when there is a surplus of sugar in the organism
b. are broken (hydrolysis reaction) when there is a lack of sugar in the organism
c. Two kinds
1) starch - found in plant cells
2). glycogen - found in animal cells; stored in the liver
when glucose is needed by body, the hormone glucagon stimulates the
liver to turn glycogen to glucose
4. Some are structural forms of sugar
a. cellulose
P. 38, Figure 3.8b
1) found in plants
2) its monomers align in parallel fashion (H bonds), forming fibers
3) accounts for plant rigidity because chains link together by hydrogen
bonds to form fibers
b. chitin - found in exoskeleton of arthropods and cell walls of fungi P. 39, Fig 3.10
6. Directionality – the nature of the bonding between carbohydrate subunits determines their
relative orientation in the carbohydrate, which then determines the secondary structure
of the carbohydrate
V. LIPIDS
A. 4 Functions of lipids
1. Structural function = component of membranes - they separate aqueous compartments
2. Energy storage function
3. Hormones
4. Body insulation
B. “Monomers” (we use this terms loosely) of Lipids = Fatty acids
1. are made of a long chain of hydrocarbons (C-H bonds) with a carboxyl (COOH) group at
one end
2. are either saturated or unsaturated
p.40, Figure 3.11
a. saturated
1) the chain is filled with H atoms (the bonding possibilities are complete for
all carbons)
2) contain all single bonds
3) common in animals
b. unsaturated
1) the chain is not filled with H atoms, so their is room for more H atoms
2) contain double or triple bonds
3) common in plants
BIOCHEMISTRY, P. 4
LIPIDS CONTINUED:
3. One end is hydrophilic and the other end is hydrophobic
a. hydrophilic
1) means water loving - this end will dissolve in water
2) this is the carboxyl end
3) this end is polar
b. hydrophobic
1) means water fearing - this end will not dissolves in water but will dissolve in
nonpolar organic compounds
2) this is the hydrocarbon end
3) this end is nonpolar
D. Polymers (lipids) – monomers are held together by a ester linkage
1. Tricylglycerol - fats (formerly known as triglyceride)
P. 40, Figure 3.12
a. one fat molecule = 3 fatty acids covalently bonded to 1 glycerol
b. formed by dehydration synthesis reaction
c. function - energy storage - this energy is not as easy for the body to use as the
carbohydrates
2. Phospholipids
P. 41, Figure 3.13
a. contains: phosphate group, glycerol, 2 fatty acids
b. are formed by replacing a fatty acid of a fat molecule with a phosphate group (so it
only has 2 fatty acids)
c. has a hydrophilic head and a hydrophobic tail
1) phosphate group and glycerol = the hydrophilic head
2) hydrocarbons = hydrophobic tail
d. forms the structural basis of cell membrane - hydrophobic tails are touching each
other
3. Glycolipids
a. contains: carbohydrate chain, glycerol, 2 fatty acids
b. phosphate group of phospholipid is replaced by a short carbohydrate chain (which is
hydrophilic)
c. are also important part of cell membranes
4. Steroids - this is the weird group
a.4 rings of carbon - do not resemble lipids structurally
b. Types
1) cholesterol - component of cell membranes and brain and nervous tissue
2) steroid hormones (chemical messengers b/w different parts of the body)
- ex. - estrogen, testosterone, cortisone
BIOCHEMISTRY, P. 5
VI. PROTEINS
A. Have a wide range of functions
1.
FUNCTION
EXAMPLES
structural
collagen, silk, microtubules
regulatory
hormone - insulin
contractile
actin, myosin
transport
hemoglobin, myoglobin
protective in blood
antibodies
membrane
antigens, membrane transport
enzymes
amylase, pepsin
2. In function - their diversity is tremendous
In structure - they are all polymers of amino acids
B. Monomers of protein - amino acids
1. Contains a carboxyl group (-COOH), an amino group (-NH2), a H atom, and a side chain
(called an R group) all attached to the same carbon (alpha carbon)
2. The R group differs from one amino acid to another - it makes each amino acid unique
3. Only 20 amino acids are used in living systems to build proteins
C. Formation of the polymers
1. Condensation (dehydration synthesis) reaction between carboxyl group of one
amino acid and amino group of another amino acid
2. This forms a nonpolar covalent bond forms between two amino acids that is called a
peptide bond
3. Protein molecules contain hundreds of peptide bonds linking any of the 20 amino
acids in different order to form different proteins
D. 4 levels of protein structure
1. Primary structure - unique sequence of its amino acid, in linear order – a polypeptide
This order of amino acids ultimately determines the protein’s shape and its ability to
perform its function
2. Secondary structure
a. a regular pattern of hydrogen bonds between amino acid residues
b. Comes in one of two forms:
1) alpha helix - hydrogen bonds hold helix coils in shape
2) beta-pleated sheet - hydrogen bonds hold neighboring strands of
sheets together
3. Tertiary structure - characteristic of overall 3-dimensional shape of the polypeptide
chain(s)
a. Is influenced by 4 types of interactions between R groups (which have different
properties)
1) Ionic bonds
2) H2 bonds
3) Disulfide bonds (covalent bonds b/w sulfur atoms of 2 cysteine residues)
4) Hydrophobic interactions (nonpolar R groups tend to stay together)
b. The interactions between the R groups determines the structure and function of that
region of the protein
4. Quaternary structure - interactions of 2 or more polypeptide chains to fit together in a
specific arrangement to form a complete, functional protein
BIOCHEMISTRY, P. 6
Proteins continued…
E. Directionality
Proteins have an amino end and a carboxyl end, and consist of a linear sequence of amino
acids connected by the formation of peptide bonds by dehydration synthesis between the
amino and carboxyl groups of adjacent monomers
F. Examples of Proteins
1. Structural Proteins
a. Fibrous proteins
1). Collagen - made by 3 polypeptides bound by hydrogen bonds into a triple
helix
- found in tendons, cornea covering, & skin
2). Keratin - found in nails, scales, feathers, hair
b. Globular proteins - used in cell division and cell wall framework
2. Hemoglobin
a. a globular protein composed of 4 polypeptide chains around a "heme" (iron
containing) molecule
b. Is found in red blood cells, and it carries oxygen to tissues
c. There are different kinds of hemoglobin. If a person has variety of different kinds
of hemoglobin, that could theoretically provide a wider range of functions
(because of the diversity in the types of hemoglobin molecules)
c. Sickle cell anemia
1) a disease caused by a single change in amino acid sequence
2) 1 glutamic acid is replaced by 1 valine
3) this causes change in the shape of the red blood cells so they can no longer
carry oxygen
3. Insulin
a. a globular protein that causes glucose to be transferred from the blood into cells
b. the pancreas releases insulin when the amount of sugar in the bloodstream is high
4. Enzymes
a. Protein molecules that act as catalysts (they speed up reactions)
b. Virtually responsible for all the chemical activities of living systems
c. they speed up chemical reactions, but remain unchanged themselves
G. Denatured = unfolded
1. This is when polypeptide molecules lose their shape because the environment isn’t correct
– because homeostasis is lost
2. If the polypeptide is only partially denatured, the polypeptide chains will fold, coil, join
together to reform original structure when they are returned to homeostasis
3. A denatured protein can't perform its function when it is denatured because it has lost its
Shape
VII. ENZYMES - VERY SPECIAL PROTEINS
BIOCHEMISTRY, P. 7
Pages 96-97
A. The importance of enzymes in metabolism
1. It is not enough for the molecules just to be present in a cell (the reaction won’t occur just
because the molecules are present)
2. In order for the molecules to react with one another, they must be close to one another and
must collide with enough force for them to react
3. The more stable a molecule's state, the more force that is required.
4. The force with which molecules collide depends upon their kinetic energy, which is
usually not very high within a cell
5. Enzymes help the molecules perform the chemical reactions, since the molecules alone
would take a long, long time (if ever)
B. HOW ENZYMES FUNCTION
1. ENERGY OF ACTIVATION - It is the minimum amount of energy that must be
possessed by the molecules in order for them to react with one another
2. Enzymes act as a CATALYST because they lower the activation energy required for a
reaction to occur by forming a TEMPORARY association with the molecules that are
reacting
3. SUBSTRATE - the molecule (or molecules) on which an enzyme acts – the reactant(s)
4. ACTIVE SITE
a. is a groove or pocket on the surface of the enzyme into which the substrate(s) fits
and where the reactions take place
b. it is formed by the folding of the enzyme
c. the active site's 3-dimensional shape and characteristics are complementary to that
of the substrate
5. THE INDUCED-FIT HYPOTHESIS
a. The binding between enzyme and substrate alters the conformation of the enzyme,
which induces (causes) a close fit between the active site and the substrate
b. This induced fit may put some strain on the reacting molecules and help the
reaction along
c. once the reaction has taken place, the enzyme releases the products of the reaction
and then catalyzes the next reaction
6. Other details
a. Enzymes are globular proteins
b. The enzyme itself is NOT permanently altered in this process
c. Because of enzymes, cells can carry out chemical reactions at great speed and at
comparatively low temperatures
d. Enzymes are typically effective in small amounts
e. Enzymes catalyze a SPECIFIC chemical reaction
f. Enzymes can be used over and over again
E. COFACTORS and COENZYMES
1. These are molecules that sometimes have to be present in order for an enzyme to perform
its function
2. Some enzymes only become active when all the appropriate cofactors or coenzymes are
present and bind to the appropriate sites on the enzyme
F. ALLOSTERIC INTERACTIONS
1. An allosteric interaction is a mechanism by which the enzyme can by activated or
inactivated
2. These interactions occur among enzymes that have at least 2 binding sites, one an the active
site and another, into which a second molecule (called the allosteric effector) fits.
3. The binding of the allosteric effector changes the shape of the enzyme molecule
and either temporarily activates or temporarily inactivates it
BIOCHEMISTRY, P. 8
IX. REGULATION of Enzyme Activity
Pages 98-99
A. It is important that the cell can control the rate of its reactions; otherwise, it would
overproduce products. This would waste energy and raw materials
B. COMPETITIVE INHIBITION
1. This is a type of regulation that occurs when a compound other than the substrate
temporarily occupies the active site of the enzyme, thus making it impossible for the
substrate to ocupy the active site
2. The inhibitory molecule must resemble the substrate in order for it to be able to
bind to the active site
C. NONCOMPETITIVE INHIBITION
1. This is a type of regulation that occurs when the inhibitory molecule binds to the enzyme at
a site other than the active site (the allosteric site).
2. This causes the enzyme to either become active or inactive (the opposite of whatever it
currently is)
D. Feedback Inhibition - this is a type of regulation that occurs when the last product in a
series of reactions acts as an inhibitor, inactivating the function an enzyme in its own pathway
E. Ways that cells regulate the rates of its reactions:
1. by regulating the concentrations of enzyme molecules, substrate molecules, and
cofactor molecules
2. some enzymes are produced only when they are needed
3. some enzymes are produced in an inactive form, & must activated before they can be used
4. Effects of changes in Temperature
a. An increase in temperature (to a point) INCREASES the rate of an enzymecatalyzed reaction
b. At a certain temperature (which is different for each enzyme, but is usually 100
degrees C) the temperature gets so high that the enzyme is moving so fast that
its H bonds are broken.
1) The enzyme loses its 3-dimensional tertiary structure and is said to be
DENATURED
2) The enzyme can not perform its function if it is denatured
3) Partially denatured enzymes can regain their shape and activity after being
cooled
4) There is a point where denaturation is irreversible
5. Effects of changes in pH
a. Each enzyme has an optimum pH, which is where the reaction will occur the
fastest
b. If the pH is much lower or much higher than that, the enzyme first works slower,
and then is denatured