Tuesday, February 07, 2006

Organic Molecules

Carbohydrates

Carbohydrate (saccharide)
A simple sugar (monosaccharide) or many simple sugars linked
together (polysaccharide)
• Used for energy storage and structural material

Monosaccharide (simple sugar)
A small organic molecule with the general formula CnH2nOn
• O–H is the main functional group on carbohydrates
√ The polar OH groups make carbohydrates hydrophilic
• The commonest monosaccharides are ring shaped molecules
• Most simple sugar names end in “-ose”
√ Examples: Glucose, fructose, galactose, ribose
• Glucose (C6H12O6) is the most abundant organic molecule on earth
√ Glucose is the main product of photosynthesis
√ Glucose is our “blood sugar”
√ Cells use glucose as their main energy source

Disaccharide
Two monosaccharides joined together
• Maltose = glucose + glucose
• Sucrose (table sugar) = glucose + fructose

Polysaccharides (complex carbohydrates)
A large number of glucose molecules joined together
• Used for energy storage (starch in plants, glycogen in animals)
• Used for structural material (cellulose in plants, chitin
in certain animals)

Energy storage polysaccharides:
All glucose molecules are in the same orientation
• Starch = A plant energy polysaccharide with little or no branching
of the glucose chain
√ Most abundant in grains, kernels, and storage roots
• Glycogen = An animal energy polysaccharide with frequent
branching of the glucose chain
√ Most abundant in liver and muscles

Structural polysaccharides:
Every other glucose molecule is upside down; no branching of
glucose chain
• This structure makes structural polysaccharides strong material
• Cellulose = A plant structural polysaccharide
√ Most abundant in plant fibers and wood
• Chitin = Structural polysaccharide in insects and shellfish
exonskeletons


Lipids

Lipids (fats, oils, wax, lard, etc.)
Hydrophobic macromolecules
• Lipid molecules are composed almost entirely of carbon and
hydrogen atoms
• Major functions: Energy storage, insulation, cell membranes

Fatty acids
Molecules containing a long hydrophobic tail and a carboxylic acid
• The building blocks of most lipids

Triglycerides (fats and oils)
Three fatty acids joined to a glycerol molecule
• Used for energy storage and insulation

Phospholipid
Two fatty acids and a phosphate-containing hydrophilic group
joined to a glycerol molecule
• The phosphate portion is called the hydrophilic “head”
• The two fatty acids are called the hydrophobic “tails”
O==================
hydrophilic hydrophobic
head tails
• Cell membranes are phospholipid bilayers
• The hydrophobic inside of the cell membrane stops most substances
from passing through

Steroids
Lipids with a backbone of 4 fused rings
• Steroids differ in the number and type of functional groups on the
steroid backbone.
• Examples: cholesterol, steroid hormones (estrogen, testosterone,
progesterone, corticosterone), vitamin D


Proteins

Proteins
Polymers of amino acids
• Proteins carry out all the tasks needed to keep the cell functioning
√ Examples: Chemical reactions, import/export of materials
• Each protein specializes in one specific task only
√ The protein performs the same task over and over
• The task each protein performs is determined by its amino acid
sequence
√ Changes in amino acid sequence can change a protein’s
function or stop it from doing any function
• There are four major protein types:
Receptors
Membrane transport proteins
Enzymes
Structural proteins

Receptors
Proteins in the cell membrane that detect molecules outside the cell
• Each receptor is highly specific to detect one and only one
type of molecule
• The molecule binds to the receptor’s binding site
• When a molecule is bound, the cell is “preprogrammed” to
perform some action in response


Binding site
The crevice in a protein where it binds its ligand (the molecule it works on)
• Each protein folds into a unique shape
• The binding site forms when the protein is folded correctly
• The binding site shape exactly fits the ligand’s shape
√ This “lock and key” fit makes the protein specific for its
ligand molecule and only its ligand molecule
√ The protein ignores all other molecules

Membrane transport proteins (also called carrier or channel proteins)
Proteins in the cell membrane that allow solutes to pass through the cell membrane
• Each transport protein is highly specific for only one solute molecule
type
√ The protein’s binding site gives it specificity

Enzymes
Proteins that carry out chemical reactions (“biological catalysts”)
• Some enzyme terms:
√ Active site = The enzyme’s binding site
√ Substrate = The reactants of the enzyme’s chemical reaction
– The enzyme’s ligand
√ Product = The product of the enzyme’s chemical reaction
• Each enzyme is highly specific to carry out one and only one
chemical reaction
√ Each enzyme is specific for only one reaction because
its active site fits only its substrate
• After releasing the product, the enzyme is unchanged and can repeat
the reaction on more substrate
• Most enzymes are named after the chemical they react with followed
by the ending “ase”
√ Examples: Lipase = An enzyme that reacts with lipids
Sucrase = An enzyme that reacts with sucrose


Cofactors
Non-protein substances that help enzymes bind their substrate
• Most vitamins and minerals are cofactors
• The cofactor sits in the enzyme’s active site
• Metal ions are common cofactors (examples: Fe3+, Mg2+, Zn+)
• Coenzymes = Organic cofactors
√ Example: Coenzyme A binds the acetyl substrate for enzymes
√ Coenzymes can transport the substrate between enzymes

Metabolic pathway
A series of enzymes that bring about large changes in substrate molecules by each individual enzyme making a small change.
• Substrate = the molecule that enters a metabolic pathway
• Endproduct = the molecule that exits a metabolic pathway
• Intermediates = all the molecules between the substrate and the
endproduct

Cycle
A circular metabolic pathway

Fibrous (structural) proteins
Rope-like proteins that provide strength and framework to tissues
• Examples:
√ Collagen = An extremely strong fibrous protein, abundant in
tendons and ligaments
√ Elastin = A stretchable (rubber band-like) fibrous protein
√ Keratin = A hard fibrous protein abundant in nails, hair, and
the skin

Amino acids
Small organic molecules with a backbone of an amine group, a central carbon, and a carboxylic acid.
• There are 20 amino acids. They differ only in the atoms attached to
the central carbon (the “side chain” or “R” group)
• R groups can be ionic, polar, or non-polar
• Each amino acid has a three letter abbreviation for its name
√ Examples: Met, Glu, Pro

Peptide bond
The covalent bond that joins amino acids together when they polymerize
• The amine of one amino acid joins to the carboxylic acid of another
amino acid
O

–C––N–

H


Polypeptide chain (“Polypeptide”)
Several amino acids joined together by peptide bonds
• Backbone of polypeptide = the chain of linked amino acid
backbones
• All backbones have an amine group at one end and a carboxylic acid
group at the opposite end

Protein
One polypeptide chain (or several polypeptide chains together) that carry out one function

Protein structure (shape or folding) can be described at 4 levels:
Primary structure
Secondary structure
Tertiary structure
Quaternary structure

Primary structure (1º)
The sequence of amino acids in the polypeptide chain
• Primary structure controls all other levels of protein folding
√ A change in even one amino acid can cause a protein to fold
incorrectly
Secondary (2º) structure
Areas of regular (patterned) folding of a polypeptide chain.
• Alpha helix = a coil shaped 2º structure
• Beta sheet = a zig-zag (back and forth) 2º structure

Tertiary (3º) structure
The folding together of the polypeptide’s secondary structures.

Quaternary (4º) structure
The folding together of several polypeptide chains into one functional protein.

Denaturation
Making a protein inactive by changing its shape
• Change in amino acid sequence
• Boiling
• Change in pH

Essential amino acids
Amino acids that an organism cannot make for itself and must therefore be obtained in the foods it eats.


Nucleic acids

Nucleic acids
DNA and RNA are the two types of nucleic acids
DNA is the genetic molecule (the “blueprints” of life)
Polymers of nucleotide monomers

Nucleotides
Small organic molecules made of …
• A phosphate group
• A five carbon sugar (ribose)
• A nitrogen-containing base

DNA (Deoxyribonucleic acid)
• The ribose in DNA is missing one oxygen atom
• The DNA nitrogenous bases are G, A, T, and C

RNA (Ribonucleic acid)
• The ribose in RNA has all oxygen atoms
• The RNA nitrogenous bases are G, A, U, and C

Nitrogenous bases
Ring-shaped molecules with backbones of nitrogen and carbon
atoms

Nucleic acids (RNA and DNA)
DNA is a polymer of DNA nucleotide monomers
RNA is a polymer of RNA nucleotide monomers
• Nucleotides are linked together by joining the ribose of one to the
phosphate of the next
√ Backbone of nucleic acid = the alternating phosphates and
riboses
√ 5’ end = the end of the backbone with a free phosphate
√ 3’ end = the end of the backbone with a free ribose
• The sequence of nitrogenous bases along the backbone holds the
genetic information

Complementary base pairing
Pairing of certain nucleotides by hydrogen bonds between their nitrogenous bases
• G complementary base pairs with C
• A complementary base pairs with T or U

Double stranded DNA
Two DNA strands running in opposite directions, joined together by complementary pairing between bases on opposite strands
• Double helix = the coil shaped structure that double stranded DNA
twists into
• Chromosomes are long pieces of double stranded DNA that hold a
cell’s genetic information

RNA strands
• RNA is single stranded
• Some RNA strands function as temporary (disposable) copies of the
DNA’s genetic information

Three special RNA molecules:

Adenosine Triphosphate (ATP)
The major energy delivering molecule of the cell
(“energy currency”)
• An RNA Adenosine nucleotide with 3 phosphates
• Energy requiring processes get energy out of ATP by splitting it to
adenosine diphosphate (ADP) and inorganic phosphate (P­i)

NADH and FADH2
RNA coenzymes that specialize in carrying high energy electrons
• Both carry hydrogen atoms along with the high energy electrons




Credit: http://lpc1.laspositascollege.edu/lpc/aedens/genbio/macromolecules.html

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