Download Biochemistry: The Chemistry of Life

Biochemistry:
The Chemistry of Life
Unit A
Workbook p1-6
Biochemicals



Cells and the organelles in cells are made out of
organic molecules, known as biochemicals.
Organic molecules are those that contain carbon.
There are four types of biochemicals:
1.
2.
3.
4.
Carbohydrates
Lipids
Proteins
Nucleic acids
Chemical bonding

Chemical compounds are held together by
different types of bonds:
1.
2.
3.
Covalent bonds: when atoms share electrons
equally, strong bonding (ex: hold organic molecules
together).
Ionic bonds: one atom loses an electron another
gains an electron and these break apart easily.
Polar covalent: molecules with regions that have a
slight positive and slight negative natures
Water:




A polar, covalent, inorganic
molecule
Covalent: shares electrons
Inorganic: does not
contain carbon
Polar: The angle of the
molecule allows oxygen to
pull electrons from
hydrogen, creating a
slight -2 charge at the O
end, a slight +1 at each H.
+
+
__
Hydrogen Bonding:



A bond forming between the positive pole of
one water molecule and the negative pole of
another.
The negative O momentarily "sticks" to a nearby
positive H!
They are not very strong bonds
Cohesion vs Adhesion

Cohesion: the tendency of water to stick
together


Provides surface tension, helps pull water up tubes
Adhesion: the tendency of water to stick to
other surfaces

Helps water flow up small tubes (ie capillaries)
Three properties of water that make
it very important to living things:
1.
Universal solvent: many compounds dissolve
in water.

2.
Importance: Dissolved compounds can be brought
to cells (via sap or blood) or move about cell
cytoplasm.
Temperature Regulator: Large amounts of
energy are needed to raise temp of water.

Importance: Water bodies have stable
temperatures. Body temps can be maintained.
Transfer of heat from warm to cool body parts.
Three properties of water that make
it very important to living things:
3.
Lubricant: its abundance combined with its
properties of adhesion, cohesion, solvation
and heat capacity, make water an extremely
valuable lubricant


Example: water in saliva moistens food and
lubricates the esophagus during swallowing.
Importance: helps move materials from one area
of an organism to another with ease.
Acids, Bases and Buffers


Acids: molecules that dissociate to release a
hydrogen ion (H+1)
Bases: molecules that dissociate to release a
Hydroxide ion (OH-1)

Note: water is neither an acid or a base as it releases
both hydrogen and hydroxide ions in equal numbers.
So water is said to be neutral.
Acids, Bases and Buffers

pH: a measure of the free H+1 in a solution.



pH and the human body:




Can range from a low of 1 (acidic, more H+1 than OH-1) to a
high of 14 (basic, more OH-1 than H+1)
ph of 7 is neutral (equal amounts of H+1 and OH-1)
Muscle tissue: 7.35
Lungs: 7.38
Stomach: 2.5
Any large deviation in these values would hamper the
ability of the corresponding organ to function.

This is a major factor in the denaturing or breaking down of
enzymes necessary for chemical reactions
Acids, Bases and Buffers



Buffers prevent significant changes in pH and
maintain homeostasis.
They pick up or release hydrogen (H+1) ions or
Hydroxide (OH-1) ions to help maintain the
appropriate pH.
Example: bicarbonate ion HCO3-1 act in the
digestion and the circulatory system.
Macromolecules

Cells make their large molecules by joining small
organic molecules into chains called polymers.

Polymer = large molecule consisting of many identical
or similar molecular units strung together.

Monomer = individual units that serve as building
blocks of polymers.
Dehydration Synthesis

When these monomers
connect together to form
polymers, the reaction is
called dehydration
synthesis.

A bond is formed to join
two molecules and a
molecule of water is
released in the process.
Hydrolysis


The reverse reaction involving the addition of
water to break apart polymers into individual
unit molecules.
both hydrolysis and dehydration synthesis
require enzymes for the reactions to occur.
Carbohydrates


Literally means “hydrates of carbon”
Empirical formula: CH2O
Basically for every carbon atom you must have one
water molecule
 So if you have 5 carbons how many hydrogens and
oxygens would you have to have?
 10 hydrgens and 5 oxygens


Carbohydrates are typically classified according
to the number of saccharide (sugar) units they
have.
Monosaccharides




Composed of a single sugar unit
They are the simplest carbohydrates
Glucose: C6H12O6
Five carbon ring
Monosaccharides



Fructose: C6H12O6
Four carbon ring
Same chemical formula as glucose but different
placement of carbons in the ring.
Disaccharides



When monosaccharides undergo dehydration synthesis
to become a double sugar (two sugar units) they are
called disaccharides
Example: two glucose molecules will join to form a
double sugar, or disaccharide, called maltose.
Examples: sucrose, table sugar, is a disaccharide formed
by joining a fructose and a glucose in dehydration
synthsis
Polysaccharides
Polysaccharides are composed of three plus sugar
units.
Since it is formed from repeating units of another
molecule it is called a polymer.
There are four main kinds of polysaccharides:



1.
2.
3.
4.
Starch: storage of glucose in plants
Glycogen: storage of glucose in animals
Cellulose: cell walls
Chitin: exoskeletons of arthropods and cell walls in fungi
Starch


Starch is the storage form of sugar in plants. It is made
of amylose and amylopectin -- each thousands of
glucose units in length
A linear polymer that spirals and sometimes branches
Glycogen

Glycogen is the storage form of sugar in animals.
It looks like starch, but with more glucose many
branches attached.
Cellulose


Cellulose is a structural carbohydrate that forms cell
walls in plants. It is not digestible by either man or
other animals.
It is a linear sequence of glucose molecules.
Lipids:



Usually water insoluble (don’t mix freely with
polar solvents)
The second most important energy molecules
for animals
They include:
Fatty acids
 Neutral Fats
 Oils
 Steroids
 Waxes and other special molecules

Fatty Acids:




Non-polar chains of carbon
and hydrogen with a carboxylic
acid end.
The chains can vary from one
carbon to many.
Some fatty acids are saturated
(no double bonds between
carbons), full of hydrogens,
straighter shape
Some fatty acids are
unsaturated (have double
bonds between carbons), not
full of hydrogens and are
slightly twisted.
Fatty Acids:


Animal fatty acids tend to by more saturated and
more solid at room temperatures
While those fatty acids produced by plant tissues
are unsaturated, and tend to be more liquid at
room temp. (ie: vegetable oil)
Neutral Fats:

They are produced by dehydration synthesis of
one or more fatty acids with a glycerol (an
alcohol).
monoglyceride: one fatty acid on a glycerol
 Diglyceride: two fatty acids on a glycerol
 Triglyceride: three fatty acids on a glycerol

Phospholipids:
Polar group
Phosphate
Glycerol
Saturated
Fatty acid
Unsaturated
Fatty acid
Steroids



Nonpolar ring structures
Examples: sex
hormomes, estrogen,
testosterone
Notice the difference in
the double bonds
Estrogen
CH3
Testosterone
CH3
Steroids:
Cholesterol:
made by the liver
cells
Waxes


A combination of fatty acids and an alcohol
larger than glycerol.
Ex: ear wax
Proteins:
Made up of polymers of unit molecules called
amino acids
Functions:


1.
Functional: serve a particular function in body
reactions (ie enzymes, antibodies, transportation)

2.
Ex: Hemoglobin or a membrane protein
Structural: they form a particular structure fot the
body.

Ex: keratin (finger nails or hair) or collagen (connective
tissue)
Basic Amino Acid structure:
There
are twenty different amino acids
They all have the same basic structure.
The “R” group is different for each of
the amino acids
Peptide Bonds:



Proteins are formed by
the dehydration
synthesis of amino
acids.
When two proteins
bond together they form
a peptide bond and they
are now called a
dipeptide.
Peptide bonds are strong
covalent bonds
Peptide Bonds:


When three amino acids are held together by
two peptide bonds it is called a tripeptide.
Any more than three amino acids and it is called
a polypeptide.
Four levels of protein organization:

Primary: just the sequence of amino acids
Four levels of protein organization:

Secondary structure:
1.
2.
alpha helix: A spring like shape caused by the
attraction between H-bonds of every fourth amino
acid which causes the linear arrangement to take
on other shapes.
Beta pleated sheet:
Four levels of protein organization:

Tertiary Structure: 3-D shape





The shape is maintained by
various types of bonding between
the R-groups.
Covalent, ionic and hydrogen
bonding are all seen
Muscles and enzymes take on
these shapes
These proteins are sensitive to
changes in pH, temperature and
heavy metal ions.
Those that have lost their shape
due to exposure to these factors
are have been “denatured”
Four levels of protein organization:

Quaternary Structures:


Two or more polypeptides
(usually tertiary structures)
associate together to form a
particular shape with a
particular funciton
Example: hemoglobin
Nucleic Acids:

Separated into two types
1.
2.
Deoxyribonucleic Acid (DNA)
Ribonucleic Acid (RNA)
They are both polymers of unit molecules called
nucleotides. Each nucleotide is made up of a
1.
2.
3.
A sugar
A phosphate group
Nitrogenous base
DNA vs RNA
DNA:
 Sugar: Deoxyribose
 Nitrogenous Bases: Adenine (A), Thymine (T), Guanine
(G), Cytosine (C)
 Found only in nucleus
RNA:
 Sugar: Ribose
 Nitrogenous Bases: Adenine (A), Uracil (U), Guanine (G)
and Cytosine (C)
 Found in the nucleus and the cytoplasm
The phosphate group is the same for both DNA and RNA
DNA vs RNA
Nitrogenous base
Sugar
Phosphate group
Basic structure
of a nucleotide
Functions:
DNA
RNA
Function: along with
histone proteins, it forms
chromosomes, which
control cellular activity by
containing the instructions
for the synthesis of all
protiens
Function: there are three
types of RNA and they are
used to make ribosomes,
make messages from the
nucleus to ribosomes and
for the calling of particular
amino acids in protein
synthesis.
ATP


ATP stands for Adenosine triphosphate
It is an RNA nucleotide with an adenine base
and three phosphate groups attached to it.
Phosphate
groups
Adenine base
P
Ribose sugar
P
P
High energy bond
Review questions



Workbook page 6-9
Quiz next class (Wednesday) on proteins and
nucleic acids
Test next Wednesday all biochemistry