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Chapter 23: Biological Chemistry
Biochemistry is the area of chemistry that focuses on the study of
compounds and processes occurring in living systems.
Important classes of biological compounds that we will be responsible for:
Carbohydrates: molecules composed of C, H and O in a 1 to 2 to 1 ratio
(carbohydrates play a role in providing nutrients to cells)
Lipids: a molecule with a large percentage of C and H atoms that produce
a non-polar substance (lipids are generally not soluble in water but would
be soluble in non-polar solvents)
Proteins: are polymers of amino acids (an amino acid has a NH2 group and
an CO2H group in the same molecule), proteins often act as the building
blocks of cells)
Nucleic Acids: are the molecules that carry genetic information, they are
polymers made from repeating phosphate, sugar, and a nitrogenous bases
(two major types are deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA))
Carbohydrates: molecules composed of C, H and O in a 1 to 2 to 1 ratio
(carbohydrates play a role in providing nutrients to cells)
Sugars (called saccharides) are carbohydrates
Sugars are broken into two categories: aldoses and ketoses
(the –ose ending is used to indicate that the molecule is a sugar)
An aldose contains an aldehyde carbonyl group in its open chain form
A ketose contains a ketone carbonyl group in its open chain form
A monosaccharide (called a simple sugar) contains a single aldose or ketose
molecule while a disaccharide molecule consists of two monosaccharide
molecules that join together. A polysaccharide contains many
monosaccharaides joined together into a chain,
Glucose is a aldahexose:
alda because of the aldehyde group,
hex because of 6 carbons,
-ose because it is a sugar
Ring formation in Glucose:
One of the lone pairs on an OH group (the one in red) will react with the
carbonyl carbon of the aldehyde (shown in blue) to form a six membered
ring that contains an oxygen atom (this ring is called a pyran).
The a and b symbols refer to the direction that the new OH group points
(up or down respectively) in the figure.
1) Fructose is a ketohexose:
keto because of the ketone group,
hex because of 6 carbons,
-ose because it is a sugar
Ring formation in fructose is similar
to what happens with glucose. The
difference is that the ketone carbon
is carbon 2 in the chain (the
aldehyde was carbon 1).
As a result, a five member ring
forms instead of the 6 that formed
with glucose.
2) The a form
3) The b form
Sucrose is a disaccharide that results when glucose and fructose undergo a
condensation reaction together. The condensation reaction is much like the
ring forming reaction of glucose except that water is expelled from the new
molecule.
Starch and Cellulose are both polysaccharides made of repeating glucose units
Starch uses a linkages and is digestible while Cellulose uses b linkages
and cannot be digested by humans
Lipids: because of their non-polar nature, lipids are not soluble in water, they
are said to by hydrophobic (water fearing).
Fats are important types of lipid. Fats consist of long chain fatty acids
(carboxylic acid) bound to a glycerol molecule (called a triglyceride).
A fat can be saturated (no C=C double bonds) or unsaturated (one or more
C=C double bonds)
Phospholipid a fat like molecule where one of the fatty acids of a triglyceride
has been replaced with a phosphate group
Steroid is a type of lipid that has a very specific ring structure-three six
membered rings fused together with a five member ring attached (see figure)
Cholesterol is another example of this type of lipid.
If a fat is reacted with water and base (a reaction called saponification) you
will produce fatty acids and glycerol.
Phospholipid bilayers: the long alkane like “tails” are non-polar and will dissolve
each other but will repel water (hydrophobic) while the phosphate head groups
are ionic and will be soluble in water (hydrophilic)
Cholesterol is another example of a lipid.
Amino Acids:
here are 20
essential
amino acids
that you need
in your diet.
Proteins are made of poly-amino acids
The amide link between the two amino
acids is called a peptide bond
The primary structure is simply listing the
order in which the amino acids occur in
the protein.
The secondary structure is the shape that
the polypeptide chain adopts (a helix or
pleated sheet)
The tertiary structure is the shape that
large section of the polypeptide adopt as
they fold or curl back on themselves
The quaternary structure is the shape that
occurs when multiple chains interact to
form a larger structure.
Hydrogen bonding, dipole-dipole, and
dispersion forces all play roles in
determining the shape.
Disulfide Bridges can also influence the shape of a protein.
When you get a perm, your hair is held in place while chemicals are added to help
the cysteine chains that are close together to form disulfide bridges. As a result,
the hair will remain in the shape that it was held after the perm. This will last until
the disulfide bridges naturally break down.
If you have very curly hair, the protein in your hair contains a more cysteine than
someone with straight hair. If you have your hair straightened, the chemicals they
use break apart the disulfide bridges and allow the hair to become straight. Over
time, the disulfide bridges will naturally start to reform and the hair will become
curly again.
Enzymes are proteins that act as catalysts.
The shape of the protein causes it to only catalyze a specific type of reaction
because only molecules with a very specific shape can interact correctly with the
enzyme. This is called the Lock and Key Enzyme Model.
After a substrate undergoes a reaction controlled by the enzyme, the enzyme
releases the products and is unchanged by the reaction.
Protein secondary, tertiary, and quaternary structure depend upon the environment
(temperature, pH, salt concentration, etc….). If the environment changes, the
protein will change shape and this can alter the ability of the protein to act as an
enzyme. This process is called denaturation.
Nucleic Acids: Chains of nucleotides containing a sugar bonded to a phosphate
and an organic base.
A nucleotide is one phosphate group bonded to the 5’ position on the sugar ribose
(or deoxyribose) which is then bonded to an organic base (called a nitrogenous
base).
In DNA, the polymer chain is
constructed of ester type linkages
between a phosphate group and the
OH groups of the sugar ribose
(note that the ribose is missing one
OH group and hence the name
deoxyribonucleic acid (DNA))
The phosphate backbone repeats
exactly the same throughout the
DNA molecule, the part that
changes so that the molecule can
carry genetic information is the
nitrogenous bases
A small section of DNA
Nitrogenous bases used in DNA and RNA (the red H indicates where the
base would be linked to the ribose backbone)
A small section of RNA
A small section of DNA
What single feature tells you which chain is RNA and which is DNA?
DNA is double stranded (the two strands run in opposite directions) which are
linked together by hydrogen bonding interactions occurring between the
nitrogenous bases. Here two representations are shown (famous a helix on the
right).
During DNA replication, the double stranded DNA molecule is separated
while the strand is copied.
DNA carries genetic information in the form of genes (large sections of the
DNA molecule that perform specific functions).
RNA has several uses and takes on different forms depending upon the use.
mRNA (messenger RNA) carries instructions for making proteins out into the
cytosol
tRNA (transfer RNA) transfers amino acids to the ribosome
rRNA (ribosomal RNA) becomes part of the ribosome where protein synthesis
takes place