Download Biological Molecules

Lecture 3: Biological Molecules
Background
Integral themes in biological systems exemplified by macromolecules:
1.
There is a natural structural hierarchy of structural level in biological organization.
2.
Due to the interactions among subunits at lower organizational levels, new properties emerge as
you move up the structural hierarchy.
3.
Form fits function.
Polymers—large molecules consisting of many identical or similar subunits connected together
A.
Macromolecules are polymers.
Terms:
Polymer—large molecules consisting of many identical or similar subunits connected together
Monomer—subunit or building block of a polymer
Macromolecule—large organic polymer
1.
Four classes of macromolecules in living organisms
a.
Carbohydrates
b.
Lipids
c.
Proteins
d.
Nucleic acids
2.
Small set of monomers is the basis for an immense variety of polymers
a.
All macromolecules are constructed by 40-50 different monomers
b.
Diversity results from the unique combination of these subunits
How are macromolecules formed?
Terms:
Polymerization—chemical reactions that link two or more small molecules to form larger molecules
with repeating structural units
Condensation Reaction—polymerization reaction which form covalent links producing net removal of
a water molecule for each covalent bond formed
Hydrolysis—reaction that breaks covalent bonds between monomers by the addition of a water
molecule
Condensation Reaction
1.
2.
3.
4.
During the reaction, one monomer loses a hydroxyl ion (OH-) and the other loses a hydrogen
ion (H+).
Water production is indirect (process will be discussed during metabolism lecture).
Process requires energy.
Process requires biological catalysts or enzymes.
Hydrolysis
1.
Hydrogen from water bonds to one monomer, hydroxyl to the adjacent monomer.
Carbohydrates
Carbohydrates—organic molecules made of sugars and their polymers
1.
Monosaccharides—monomer building block of carbohydrates
2.
Polymers are made by condensation reactions
3.
Carbohydrates are classified by the number of simple sugars they contain
Monosaccharides
Monosaccharides are simple sugars in which C, H, and O occur in the ratio of 1:2:1 (CH2O).
1.
Major nutrient source for cells; glucose is the most common
2.
Photosynthetic organisms produce glucose from CO2, H2O and sunlight
3.
Energy is stored in sugar’s chemical bonds and this energy is harvested by cellular respiration
4.
Other organic molecules are made from the carbon skeletons of sugars
5.
Sugars are the monomer used to make di- and polysaccharides
Characteristics of sugars
1.
An –OH is attached to each carbon except one, which double bonded to an oxygen
a.
Aldehyde--double bonded oxygen is on the terminal carbon (e.g., glucose)
b.
Ketone-- double bonded oxygen is within the carbon skeleton (e.g., fructose)
2.
Carbon skeleton varies in size from three to seven carbons.
Classification
# of Carbons
Example
Triose
3
Glyceraldehyde
Pentose
5
Ribose
Hexose
6
Glucose
3.
4.
Sugars have asymmetric carbons which allow the formation of enantiomers (e.g., glucose and
galactose).
a.
Small differences in spatial arrangement between isomers affect molecular shape which
confers distinctive biochemical properties.
In aqueous solutions, many monosaccharides form ring structures. The ring structure is
favored in chemical equilibrium.
Disaccharides
Disaccharides are double sugars that consist of two sugars joined by a glycosidic linkage.
Glycosidic linkage—covalent bond formed by a condensation reaction between two sugar monomers
(e.g., maltose).
Disaccharide
Monomers
Maltose
Glucose + Glucose
Used in beer fermentation
Lactose
Glucose + Galactose
Present in milk
Sucrose
Glucose + Fructose
Table sugar
Polysaccharides
Polysaccharides are macromolecules that are polymers of a few hundred or thousand monosaccharides.
1.
Formed by enzyme mediated condensation reactions
2.
Important biologically
a.
Energy storage—starch and glycogen
b.
Structural support—cellulose and chitin
Storage polysaccharides
1.
Starch—glucose polymer; storage polysaccharide in plants
a.
Helical glucose polymer with  1-4 linkages
b.
Storage granules in plants called plastids
c.
Simplest form: amylose (unbranched)
d.
Amylopectin—branched polymer
e.
Grains and potatoes are a common source
2.
Glycogen—glucose polymer; storage polysaccharide in animals
a.
Large glucose polymer ( 1-4 and  4-6 linkages) with a higher degree of branching
than amylopectin
b.
Stored in muscle and liver
Structural Polysaccharides
1.
Cellulose—linear unbranched polymer of glucose ( 1-4 and  4-6 linkages)
a.
Structural component of plant cell walls
b.
Differs from starch based on the nature of its glycosidic linkages ( vs. )
c.
Differences in glycosidic linkage result in unique three-dimensional shapes and physical
properties
d.
Hydrogen bonding between cellulose molecules forms bundles called microfibrils that
reinforce the cell wall
e.
Can not be digested by animals; no enzyme to digest the  1-4 linkage
2.
Chitin—structural polysaccharide that is a polymer of an amino sugar
a.
Exoskeleton of arthropods
b.
Cell walls of some fungi
c.
Nitrogen containing group replaces –OH on carbon 2
Lipids
Lipids are a diverse group of water insoluble organic compounds. They dissolve in nonpolar solvents.
Important groups include fats, phospholipids and steroids.
Fats
Fats are macromolecules constructed from glycerol (a three carbon alcohol) and fatty acid (carboxylic
acid).
Glycerol (structure)
Fatty acid (structure)
1.
Composed of a carboxyl group on one end and an attached hydrocarbon chain (“tail”)
2.
Carboxyl functional group (“head”) has properties of an acid
3.
Hydrocarbon tail usually consists of an even number of carbons (16-18 are common)
4.
Nonpolar C-H bonds make the molecule hydrophobic and not water soluble
5.
Ester bond—bond formed between the –OH group on glycerol and the carboxyl group
6.
Each of glycerol’s three OH’s can form ester bonds
7.
Triaclyglycerol—a fat composed of three fatty acids bonded to one glycerol by ester linkages
8.
Characteristics:
a.
Insoluble in water
b.
Variation is due to the fatty acid composition
c.
Fatty acids in a fat may be the same or vary
d.
Fatty acid vary in length
e.
Fatty acids may vary in the number and position of double bonds
Saturated Fat
Unsaturated Fat
No double bonds in the fatty acid tail
Has double bonds (one or more)
Carbons in skeleton are bonded with
Carbon double bond does not allow close
maximum number of H’s
packing at room temperature
Solid at room temperature
Liquid at room temperature
Butter, lard, grease
Olive, corn or peanut oil
9.
Functions:
a.
Energy storage (C-H bond is energy rich)
b.
Take up less space than carbo’s; therefore more compact reservoir for energy storage
c.
Insulation
d.
Cushioning
Phospholipds
Phosholipids contain glycerol, two fatty acids and a phosphate group and usually a small chemical
group attached to the phosphate group.
1.
Third glycerol carbon is attached to a negatively charged phosphate group
2.
There is usually a small (usually charged or polar) molecule attached to the phosphate group
3.
Phospholipids can be quite diverse based on the nature of the fatty acids and phosphate
attachements
4.
Contain both a hydrophobic and hydrophilic group which affects its interaction with water
5.
Form micelles—tails away from water, heads towards
6.
Major component of cell membranes; bilayer with head towards aqueous environments and
tails held together by interactions between tails
Steroids
Lipids have four fused rings of carbon with various functional groups attached.
Cholesterol is a common steroid. It is a precursor for other steroids including sex hormones and bile
acids.
Proteins
Polypeptide chain—polymers of amino acids arranged in particular linear sequences and linked by
peptide bonds.
Proteins are macromolecules that consist of one or more polypeptide chain organized in threedimensional space.
1.
Proteins makeup 50% of cellular dry weight
2.
Functions:
a.
Structural support
b.
Storage
c.
Transport (e.g., hemoglobin)
d.
Signaling (e.g., neurotransmitters)
e.
Signal transduction (e.g., receptors)
f.
Movement (e.g., contractile proteins)
g.
Defense (e.g., antibodies)
h.
Catalysis of biochemical reactions
3.
Vary extensively in structure
4.
Comprised of 20 amino acids
Amino Acids
Proteins are made up of amino acids. Amino acids (most) consist of an asymmetric carbon, called the
alpha carbon, which is covalently bonded to:
1.
2.
3.
4.
Hydrogen atom
Carboxyl group
Amino group
Variable R group—this is specific to each amino acid and confers that amino acid’s unique
properties
At biologically relevant pH’s, both the amino and carboxyl group are ionized.
Amino acids can exist in three ionic states. The state is determined by the pH of the solution.
1.
Cation (-NH3+)
2.
Zwitterion (-NH3+, COO-)
3.
Anion (COO-)
Amino acids can be grouped by the properties of their side chains.
1.
Nonpolar side groups (hydrophobic); less soluble in water
2.
Polar side groups (hydrophilic); soluble in water
a.
Uncharged polar
b.
Charged polar
(i)
Acidic side groups; Dissociated carboxyl group gives this group a negative
charge
(ii)
Basic side groups; amino group with an extra proton gives this group a positive
charge
Polypeptide chains are polymers formed from amino acids monomers by peptide bonds.
Peptide bond—covalent bond formed by a condensation reaction that links the carboxyl group of one
amino acid to the amino group of another
1.
2.
3.
4.
Polarity—peptides have ends:
a.
N-terminus—amino group end
b.
C-terminus—carboxyl group end
Backbone—repeating sequence of N-C-C-N-C-C-N
Length—from a few monomers to thoussands
Unique linear sequences
Conformation of a protein confers function
Protein conformation is the three-dimension shape of a protein.
Native conformation is the functional conformation found under normal physioogical conditions.
1.
Occurs spontaneously, usually due to hydrophobic interactions
2.
Enables recognition and bonding between proteins and other molecules
3.
Stabilized by chemical bonding and weak interactions between neighboring parts of the protein
molecule
4.
Conferred by the linear organization of the amino acids
Levels of protein structure
1.
2.
3.
4.
Primary
Secondary
Tertiary
Quaternary (two or more polypeptide chains)
Primary
Primary structure is the unique sequence of amino acids.
1.
Determined by genes
2.
Slight change in primary sequence alters protein conformation and function
3.
Sequencing
a.
Developed by Sanger
(i)
Complete digest to determine relative proportion of aa’s
(ii)
partial digest and overlap mapping to determine sequence
Secondary
Secondary structure is the regular coiling and folding of a peptide backbone.
Types:
1.
Alpha helix
2.
Beta pleated sheet
Tertiary
Tertiary structure is the three-dimensional shape of a protein. Results from folding of R groups and
their interactions with the aqueous environment.
Covalent and weak interactions contribute to tertiary structure.
Weak interactions:
a.
Hydrogen bonding between polar side groups
b.
Ionic bonds between charged side chains
c.
Hydrophobic interactions between nonpolar side chains in a proteins interior
Covalent linkage:
a.
Disulfide bridges; strong bond that reinforces conformation
Quaternary structure
Interaction between and among several polypeptide chains
Nucleic Acids
Genes, an organism’s heritable units, are comprised of nucleic acids.
Types of nucleic acids:
1.
Deoxyribonucleic acid (DNA)
a.
Makes up genes that indirectly direct protein synthesis
b.
Contain information for its own replication
c.
Contains coded information that programs all cell activity
d.
Replicated and passed to next generation
e.
In eukarotic cells, it is found primarily in the nucleus
2.
Ribonucleic acid (RNA)
a.
Functions in the synthesis of proteins coded for by DNA
b.
Messenger RNA (mRNA) carries encoded genetic message from the nucleus to the
cytoplasm
c.
Information flow:
DNA  RNA  Protein
d.
Sequence:
(i)
In the nucleus, genetic message is transcribed from DNA into RNA
(ii)
RNA moves into the cytoplasm
(iii) Genetic message is translated into a protein
Nucleic acids are polymers of nucleotides linked together by condensation reactions.
Nucleotide—building block of nucleic acids; comprised of a five-carbon sugar covalently bonded to a
phosphate group and a nitrogenous base.
1.
2.
3.
Pentose--5-carbon sugar
a.
Two types:
(i)
Ribose—found in RNA
(ii)
Deoxyribose—found in DNA; lacks -OH group on carbon 2
Phosphate—attached to carbon 5 of the sugar
Nitrogenous base; two families:
a.
b.
Pyrimidine—six member ring comprised of carbon and nitrogen
(i)
Cytosine (C)
(ii)
Thymine (T); only found in DNA
(iii) Uracil (U); only found in RNA
Purine—five member ring fused to a six member ring
(i)
Adenine (A)
(ii)
Guanine (G)
Functions of nucleotides:
1.
Monomer for nucleic acids
2.
Energy transfer (e.g., ATP)
3.
Electron receptors in enzyme controlled redox reactions (e.g., NADPH)
Nucleic acids
1.
Formed by phosphodiester linkages; bond between the phosphate of one nucleotide and the
sugar of another
2.
Backbone consists of repeating pattern of sugar-phosphate-sugar-phosphate
3.
Varying nitorgenous bases are attached to the backbone
4.
Genes are represented by linear sequence of nitrogenous bases which in turn is the unique code
for linear sequence of amino acids in a protein.
Inheritance is based on the replication of the DNA double helix
1.
DNA consists of two nucleotide chains wound in a double
2.
Sugar-phosphate backbone is on the outside of the helix
3.
The polynucleotidee strands of DNA are held together by hydrogen bonding between paired
nucleotide bases and by van der Wall attraction between stacked bases
4.
Base pairing rules:
a.
A always with T
b.
G always with C
c.
In RNA, A always with U
5.
The two strands are complementary and can serve as templates for new complementary strands
6.
Most DNA molecules are long (often thousands or millions of bases)