Download Ch 3 Biochemistry Notes

Chapter 3 Biochemistry
Organic Molecules- The Building
Blocks of Life
I. What is an Organic Compound?
• Contains carbon atoms that can be
covalently bonded
– to other carbon atoms
– and to other atoms (like Hydrogen, Oxygen,
Nitrogen, Sulfur, etc)
• Carbon has 4 electrons in its
outmost electron shell. How
many sites does it have to form
covalent bonds?
4
A. Carbon Bonding
4 sites
Since it has
to covalently bond to other
atoms, a carbon atom works well as a basic
building block – it combines in a variety of ways
to form:
1. Chains- c-c-c-c
2. Branched Chain
3. Ring Forms
c-c-c-c
c-c
c
c
c-c
4. single, double & triple bonds
c-c
c=c
c=c
Chains, Branched, Ring forms
Each line represents a single covalent bond
Methane is the simplest carbon compound1 Carbon & 4 hydrogen atoms
Other simple organic molecules
• Butane
cyclohexane
B. Functional groups
See page 52 in your textbook for more on functional groups
Example of adding a hydroxyl group –
makes ethane into an alcohol-
Example of adding an amino group
- makes methane or ethane into-
C. Sizes of Molecules
1. Monomers- small simple molecules
2. Polymers- complex molecules
formed when monomers are bonded to
each other
3. Reactions to build/ break
down molecules
• Condensation Reaction- when 2
monomers join together- a water is
released
(an H from 1 end and an OH from the other end
are cut loose when the monomers join.)
• Hydrolysis Reaction– when polymers
are broken back down- they need a water
added.
Hydrolysis of sucrose
D. Energy from ATP
• Life needs a constant supply of energy
• Chemical bonds store energy.
• Food molecules are the $1,000 dollar bills of energy
storage. They function as fuel molecules, storing large
quantities of energy in a stable form over long
periods of time.
• One molecule that living things use to store energy is
in the bonds of the ATP (Adenosine Triphosphate)
molecule
Adenosine Triphosphate
Adenosine Triphosphate:
Blue = ribose (a 5-carbon sugar)
Green = adenine (a nirtogenous base) Yellow = phosphate groups
Energy is stored in covalent bonds joining the phosphate groups (yellow).
The ATP-ADP Cycle. Energy is
needed for the formation of ATP and
is released as the ATP is converted
back to ADP and phosphate.
III. 4 Classes of Organic
Molecules
• Built from carbon (C), hydrogen (H) and
nitrogen (N)- in different ratios
• Each group has distinct properties
• Each organic molecule group has small
molecules (monomers) that are linked to
form a larger organic macromolecule
(polymers) made of three to millions of
monomer subunits.
A. Carbohydrates - the most important energy
source for cells
• General formula [CH2O]n - where n is a number
between 3 and 6. Ex- glucose= C6H12O6
• Carbohydrate functions
– in short-term energy storage (such as sugar)
– as intermediate-term energy storage (starch for plants
and glycogen for animals)
– as structural components in cells
• (cellulose in the cell walls of plants and many protists)
• chitin in the exoskeleton of insects and other arthropods.
1. Monosaccharides - single sugar
units
2. Disaccharides - formed by linking
two monosaccharides.
3. Polysaccharides - formed by
linking many sugar units together
• starch, glycogen, and cellulose are
three common polysaccharides
Polysaccharide
Storage Polysaccharides
1.
Starch - the storage carbohydrate in plants
- formed by linking many glucose units using dehydration
synthesis;
– a
– b
2.
amylose - straight chain carbohydrate - up to 1000 glucose
amylopectin - branches of 24-36 glucose off main
Glycogen -storage carbohydrate in animals -
glycogen is more extensively branched than amylopectin to
increase the efficiency of storage.
(Why?; glycogen is stored in liver and muscle; humans store enough
glycogen for about 1 day; the levels of blood glucose and
glycogen are controlled by insulin and glucagon. Insulin promotes
the storage of glucose while glucagon promotes its release.)
Structural Polysaccharides
1. Cellulose - the structural sugar of the plant
cell wall; about 50% all organic carbon in biosphere is
tied up in cellulose. Globally plants produce 1011 t
cellulose per year
2. Chitin - the structural component in the
exoskeleton of arthropods. It is also found in the
fungal cell wall rather than cellulose as in plants.
Structure of cellulose
Humans consider cellulose to
be roughage – why?
Cellulose Fibers from Print Paper (SEM x1,080). This image is copyright Dennis Kunkel at
www.DennisKunkel.com, used with permission.
B. Proteins
• Important in biological systems as control and
structural elements.
– Control functions carried out by enzymes and hormones.
– Structural proteins function in the cell membrane, muscle tissue,
etc.
• The amino acid is the building block of proteins
– an amino end (NH2)
– a carboxyl end (COOH).
– The R indicates the variable component (R-group) of
each amino acid.
• All living things (and even viruses) use various
combinations of the same twenty amino acids.
1. Amino Acid
*Amino acids are linked together by joining
the amino end of one molecule to the
carboxyl end of another.
*Removal of water allows formation of a type
of covalent bond known as a peptide bond.
2. PEPTIDE BONDS
Some examples of proteins
• Antibodies: they recognize molecules of invading
organisms.
• Receptors: part of the cell membrane, they
recognize other proteins, or chemicals, and inform
the cell... 'The Door Bell'.
• Enzymes: assemble or digest.
• Neurotransmitters and some hormones: Trigger
the receptors... (the finger on the door bell...)
• Channels, and pores: holes in the cell membrane
(with or without a gate). Usually, filter the flow...
Structure Of Proteins
1. Primary structure - the specific sequence of
amino acids;
2. Secondary structure - H-bonds cause
segments of the protein to be coiled or folded
α-helix
pleated sheet
3. Tertiary structure - results from interactions
between amino acid side chains
4.
Quaternary structure – multiple sub- groups
Denaturation :
Disrupting native (or natural) conformation;
(if denaturation not too great the protein
may return to its native conformation)
Proteins can be denatured in several ways.
1.
2.
3.
4.
5.
pH
Salt
heat
different solvent
chemical treatment
3. Enzymes
•
•
•
•
Organic molecules that act as catalysts
Essential to cell functions
Most (not all) enzymes are proteins.
Enzymes & substrates ( the reactant
being catalyzed) fit together like a “lock
& key”
• Fit shapes reactants to weaken bonds so
that less energy is needed for reaction.
C. Lipids
• Long-term energy storage.
• Generally insoluble in polar substances
such as water.
• Secondary functions of lipids are as
structural components
– phospholipids are the major building block in
cell membranes
– "messengers" (hormones) play roles in
communications within and between cells.
1. Structure of
Fatty Acids
• The carboxyl head is
polar- therefore it is
HYDROPHILIC –
water loving
• The hydrocarbon CH2
units are
HYDROPHOBICwater fearing
(not water soluble).
Fatty acids
• Can be saturated (meaning they have as many
hydrogens bonded to their carbons as possible)
• Unsaturated (with one or more double bonds
connecting their carbons, hence fewer
hydrogens).
• A fat is solid at room temperature, while an oil is
a liquid under the same conditions. The fatty
acids in oils are mostly unsaturated, while those
in fats are mostly saturated.
2. Triglycerides
• Triglycerides are composed of three fatty
acids (usually) covalently bonded to a 3carbon glycerol.
Fats and oils function in energy storage.
• Animals convert excess
sugars into fats.
• Most plants store excess
sugars as starch,
although some seeds and
fruits have energy stored
as oils (e.g. corn oil,
peanut oil, palm oil,
canola oil, and
sunflower oil).
– Fats yield 9.3 Kcal/gm,
while carbohydrates yield
3.79 Kcal/gm. Fats store
six times as much energy
as glycogen.
Diets & Fat Intake
• Attempts to reduce the amount of fats present in
specialized cells known as adipose cells that
accumulate in certain areas of the human body.
• By restricting the intakes of carbohydrates and
fats, the body is forced to draw on its own stores
to makeup the energy debt.
• The body responds to this by lowering its
metabolic rate, often resulting in a drop of "energy
level."
• Successful diets usually involve three things:
decreasing the amounts of carbohydrates and fats;
exercise; and behavior modification
3. Phospholipids
• One fatty acid is
replaced with a
phosphate.
• The negative charge(s) of the phosphate makes
the “head” of the phospholipid hydrophilic.
The long, hydrocarbon tail is non-polar and,
therefore, hydrophobic.
•
*The water loving edge of the molecule orients
toward water- the inside and outside of the cell.
*The water fearing edges of the molecule orient
toward each other to make a lipid “bilayer”
- the construction of the cell membrane.
4. Cholesterol and steroids:
• Structure is a lipid with 4
carbon rings with various
functional groups attached
• Cholesterol has many
biological uses, such as its
occurrence in the cell
membranes, and its role in
forming the sheath of
some neurons. Excess
cholesterol in the blood
has been linked to
atherosclerosis, hardening
of the arteries.
• Steroids are mainly used
as hormones in living
things
•Structure of four steroids. Image from Purves et al., Life:
The Science of Biology, 4th Edition, by Sinauer
Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.
D. Nucleic Acids
•Function - informational molecules –
heredity/genetic, protein synthesis, and energy
•A nucleotide is formed from a 5 carbon
sugar, a phosphate and a nitrogen base.
•Polymers formed by linking together long
chains of nucleotide monomers.
3 Nucleic Acids
1. DNA-deoxyribonucleic acid
Double strand of nucleotides
Double Helix shape
• RNA-ribonucleic acid
Single strand nucleotides
1. ATP -Adenosine Triphosphate
Structure of DNA
double strand of nucleotides
Structure of tRNA -single strand of nucleotides
RNA differs from DNA in the
following ways:
• RNA is single stranded while DNA is
double stranded.
• RNA has a sugar called ribose while
DNA has a sugar called deoxyribose.
• RNA has the base uracil while DNA has
the base thymine.
How DNA & RNA work together
• DNA(deoxyribonucleic acid) is the genetic material.
• It functions by storing information regarding the
sequence of amino acids in each of the body’s
proteins.
• This "list" of amino acid sequences is needed when
proteins are synthesized.
• Before protein can be synthesized, the instructions in
DNA must first be copied to another type of nucleic
acid called messenger RNA.
•
3 types RNA
• Messenger RNA, or mRNA.
– carries the code for building a protein from the nucleus to
the ribosomes in the cytoplasm. It acts as a messenger.
• Transfer RNA or tRNA.
– picks up specific amino acids in the cytoplasm & brings
them into position on ribosome where they are joined
together in specific order to make a specific protein.
• Ribosomal RNA or rRNA –place for protein synthesis
How a protein is built