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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.

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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.

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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

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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.

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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.

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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

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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.

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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.

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BIO 302 - Lecture 09/05/2006

Macromolecules

Proteins: Amino Acids

Cysteine can form disulfide covalent linkage

BIO 302 - Lecture 09/05/2006

Macromolecules

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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:

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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).

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BIO 302 - Lecture 09/05/2006

Macromolecules

Nucleic Acids: DNA

5’-TACG-3’

BIO 302 - Lecture 09/05/2006

Macromolecules

Nucleic Acids: DNA

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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.

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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

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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.

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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.