1
BIO 302 - Lecture 09/05/2006
Basic Unit of Life: The Cell.
• All living organisms are composed of one or more cells.
• Performs two type of functions:
– Generate energy: chemical reactions necessary to maintain our life.– Passes the information for maintaining life to the next generation.
• Unicellular vs Multicellular
• Prokaryotes vs Eukaryotes
– What about virus (and phage)?
BIO 302 - Lecture 09/05/2006
Basic Unit of Life: The Cell.
Prokaryotes and Eukaryotes.
a) A membrane-bound nucleus is in eukaryotic cells and not in prokaryotes.
b) Eukaryotic cells contain membrane-bound organelles, while prokaryotes donot.
c) Prokaryotes have circular DNA molecules, while eukaryotes have linearchromosomes condensed with many proteins.
2
BIO 302 - Lecture 09/05/2006
Basic Unit of Life: The Cell.
Organelles
1. Nucleus : location of DNA and chromosomes.2. Endoplasmic reticulum : makes and modifies newly synthesized polypeptides;
synthesizes lipids.3. Golgi body (Dictyosome in plants) : modifies polypeptides, and sorts and ships proteins
and lipids for either secretion or for use inside the cell.
4. Mitochondria : produces ATP(chemical form of energy cells use).
5. Chloroplasts : site of photosynthesisin plants and algae.
6. Vesicles : functions such as transportor storage, and digestion.
7. Ribosomes : helps assemblepolypeptides during protein synthesis.
8. Cytoskeleton : confers shape to cellsand aids in the internal organization ofthe cell, allows cells and parts of cellsto move, and aids in the movement ofinternal structures.
BIO 302 - Lecture 09/05/2006
Macromolecules
Organelles and other structures of cells are made of polymerscalled “macromolecules”.
– Lipids and Polysaccharides• for structure / function of membranes and energy storage.
– Proteins• primary functional molecules of the cell: enzymatic,
regulatory & structural.
– Nucleic Acids (DNA & RNA)• involved in storage and transmission of information within the
cell.
3
BIO 302 - Lecture 09/05/2006
Macromolecules
• Lipids
a) A broad group of hydrophobic (insoluble in water) organic compounds.
b) Make up cellular membranes and define cells’ boundaries and organelles.
BIO 302 - Lecture 09/05/2006
Macromolecules
• Phospholipids
4
BIO 302 - Lecture 09/05/2006
Macromolecules
Proteins:
a) Large organic compounds that determine many organismalcharacteristics.
b) Proteins have different roles:(1) Enzymes(2) Hormones(3) Antibodies(4) Transcription factors(5) Structure(6) Movement(7) Regulation of cellular processes
c) Made of monomers called amino acids, of which there are twenty.Average protein contains around 350 amino acids.
BIO 302 - Lecture 09/05/2006
Macromolecules
Proteins: Amino Acids
(1) An amino (-NH2) group at one end.
(2) A carboxyl (COOH) group at one end.
(3) A carbon atom in the middle, calledthe α (alpha) carbon.
(4) A side group (called an R group) thatdetermines its characteristics.
5
BIO 302 - Lecture 09/05/2006
Macromolecules
Proteins: Amino Acids
• Peptide bonds link amino acids together by linking the carboxyl groupof one amino acid to the amino group on the next amino acid.
BIO 302 - Lecture 09/05/2006
Macromolecules
Proteins
• Amino acids can form three-dimensionalconformations that will ultimatelydetermine how the protein will fold andfunction.
• Proteins are folded and interact withsubstrates by:– Hydrogen bond– Ionic bond– Hydrophobic interaction– van der Waals association– Covalent bond
• Some molecules have the capacity to formseveral different types of weak bondssimultaneously or reversibly. This is theadvantage of weak bonds: They arereversible.
• Because molecules are always in motion,weak bonds are constantly breaking andreforming.
6
BIO 302 - Lecture 09/05/2006
Macromolecules
Proteins
• Amino acids can form three-dimensional conformations that willultimately determine how theprotein will fold and function.
• Hydrogen bond between amino acidbackbone.– α (alpha) helix
– β (beta) pleated sheet
BIO 302 - Lecture 09/05/2006
Macromolecules
Proteins: Three dimensional structures
7
BIO 302 - Lecture 09/05/2006
Macromolecules
Proteins: Amino Acids
(1) An amino (-NH2) group at one end.
(2) A carboxyl (COOH) group at one end.
(3) A carbon atom in the middle, calledthe α (alpha) carbon.
(4) A side group (called an R group) thatdetermines its characteristics.
BIO 302 - Lecture 09/05/2006
Macromolecules
Proteins: Amino Acids
Involved in chemical reaction.
Can form ionic bonds : Association between positively & negatively charged groups.Dependent upon pH, and salt concentration (salt ions can shield charged groups byforming their own ionic bonds).
They can also form hydrogen bonds.
8
BIO 302 - Lecture 09/05/2006
Macromolecules
Proteins: Amino Acids
Polar amino acids are overall uncharged,but they have uneven chargedistribution. They can form hydrogen bonds so they are called hydrophilic aminoacids.
Ser, Tyr and The - can be phosphorylated.
BIO 302 - Lecture 09/05/2006
Macromolecules
Proteins: Amino Acids
Hydrophobic interactions : Association of regions that are generallyuncharged & carbon-rich. Association of hydrophobic regions results inexclusion of water.
9
BIO 302 - Lecture 09/05/2006
Macromolecules
Proteins: Amino Acids
Cysteine can form disulfide covalent linkage
BIO 302 - Lecture 09/05/2006
Macromolecules
10
BIO 302 - Lecture 09/05/2006
Macromolecules
Nucleic Acids: DNA
a) Involved in storage and transmission of information within the cell.
BIO 302 - Lecture 09/05/2006
Macromolecules
Nucleic Acids: DNA
a) Involved in storage and transmission of information within the cell.b) Composed of units called nucleotides:
11
BIO 302 - Lecture 09/05/2006
Macromolecules
Nucleic Acids: DNAAdenine and guanine are double-ring structures called purines
Cytosine and thymine are single-ring structures called pyrimidines.
BIO 302 - Lecture 09/05/2006
Macromolecules
Nucleic Acids: DNA
a) Involved in storage and transmission of information within the cell.b) Made of units called nucleotides:c) Nucleotides are linked by phosphodiester bond. (5’ and 3’ of the
sugar).
12
BIO 302 - Lecture 09/05/2006
Macromolecules
Nucleic Acids: DNA
5’-TACG-3’
BIO 302 - Lecture 09/05/2006
Macromolecules
Nucleic Acids: DNA
13
BIO 302 - Lecture 09/05/2006
Macromolecules
1. Complementary Base Pairing.• Nucleotides always pair by hydrogen bonding.• A purine will always attach to a pyrimidine:
a) Adenine pairs with thymine with twohydrogen bonds.
b) Cytosine pairs with guanine with threehydrogen bonds.
2. The strands run opposite to each other,like opposite directions on a street(called antiparallel).
3. Hydrogen bonds help to hold the DNAdouble helix together so it does notseparate spontaneously. However, thetwo strands can break apart (ordenature) under several possibleconditions:a) High temperatures (near boiling) can break
hydrogen bonds, but the strands can reform(reanneal) at lower temperatures.
b) pH extremes (< 3 or > 10) can break hydrogenbonds.
c) Proteins can also break the double helix.
BIO 302 - Lecture 09/05/2006
Macromolecules
Nucleic Acids: DNA
DNA strands also held togetherby base stacking between pairsof neighboring bases.
14
BIO 302 - Lecture 09/05/2006
Macromolecules
Nucleic Acids: DNA
1. Negative charge (will move toward a + electrode!)
2. Denatured and renatured (nucleic acid hybridization).
3. Soluble in water.
4. Insoluble in ethanol.
5. Absorbs UV light.
6. Double-stranded DNA can be stained and amounts of DNA canbe measured using ethidium bromide.
BIO 302 - Lecture 09/05/2006
Ethidium bromide intercalates into the DNA double helix
EthBR fluoresces under UV light, enabling us to “see” DNA
no fluorescent color… fluorescent
Macromolecules
Nucleic Acids: DNA
15
BIO 302 - Lecture 09/05/2006
Macromolecules
Ribonucleic Acid: RNA
(1) The pentose sugars of thebackbone are ribose instead ofdeoxyribose.
(2) The base uracil (U) substitutesfor thymine (T), and pairs withadenine (A).
(3) RNA is a single strand, but canadopt different structure:
– Short nucleotide sequences canbase pair to form short double-stranded regions. It may be neededto maintain the RNA’s integrity.
– RNA can undergo folding withsecondary and tertiary structures.
.
RIBOSE
1
OHOCH2
H
H
OH
H
OH
H
OH23
4
5OHOCH2
H
H
OH
H
OH
H
H
1
23
4
5
2-DEOXY-RIBOSE
O N
H N
O
H
CH3
THYMINE
O N
H N
O
H
URACIL
RNA DNA
Molecular Differences between Ribonucleic Acid (RNA)& 2-deoxy-ribonucleic acid (DNA).
BIO 302 - Lecture 09/05/2006
Macromolecules
Ribonucleic Acid: RNA
(1) The pentose sugars of thebackbone are ribose instead ofdeoxyribose.
(2) The base uracil (U) substitutesfor thymine (T), and pairs withadenine (A).
(3) RNA is a single strand, but canadopt different structure:
– Short nucleotide sequences canbase pair to form short double-stranded regions. It may be neededto maintain the RNA’s integrity.
– RNA can undergo folding withsecondary and tertiary structures.
16
BIO 302 - Lecture 09/05/2006
Macromolecules
Ribonucleic Acid: RNA
(1) The pentose sugars of thebackbone are ribose instead ofdeoxyribose.
(2) The base uracil (U) substitutesfor thymine (T), and pairs withadenine (A).
(3) RNA is a single strand, but canadopt different structure:
– Short nucleotide sequences canbase pair to form short double-stranded regions. It may be neededto maintain the RNA’s integrity.
– RNA can undergo folding withsecondary and tertiary structures.
BIO 302 - Lecture 09/05/2006
Macromolecules
Ribonucleic Acid: RNA
(1) The pentose sugars of thebackbone are ribose instead ofdeoxyribose.
(2) The base uracil (U) substitutesfor thymine (T), and pairs withadenine (A).
(3) RNA is a single strand, but canadopt different structure:
– Short nucleotide sequences canbase pair to form short double-stranded regions. It may be neededto maintain the RNA’s integrity.
– RNA can undergo folding withsecondary and tertiary structures.