Cell Biology - Ch.2

Front 1

5 Basics of Cell Chemistry

Back 1

1. Carbon

2. Water

3. Selectively Permeable Membranes

4. Polymerization (synthesis) of small molecules.

5. Self-Assembly

Front 2

Carbon

Back 2

Chemistry of the cell is the chemistry of carbon.

Chemistry (Organic) of Carbon containing compounds.

Backbone of biologically important molecules.

Front 3

Fundamental properties of Carbon

Back 3

Valence of four.

Outermost electron orbital missing for electrons.

Atoms may share electrons by covalent bonds.

Front 4

Different types of bonds

Back 4

Front 5

Carbon containing molecules are stable

Back 5

Carbon valence and low atomic weight - provide versatility and stability for carbon containing molecules.

Bond energy provide stability.

Bond energy - amount of energy required to break 1 mole of such bonds.

Stability - large energy required to break C-C bonds (83 kilocalories per mol).

Front 6

Diversity of Carbon Molecules

Back 6

The tetravalent nature of the carbon atom provides great diversity, especially for biological molecules.

Linear or circular molecules.

With hydrogen - forms hydrocarbon.

Hydrocarbons are insoluble in water.

Front 7

Simple Hydrocarbon Molecules

Back 7

Front 8

Oxygen, Nitrogen, Phosphorus, and Sulfur.

Back 8

Part of functional groups.

Functional groups confer water solubility and chemical reactivity on the molecules.

Phospholipid molecules with hydrocarbon tails provide non aqueous nature of the membrane.

Front 9

Common Functional Groups

Back 9

Provide physical and chemical properties - water solubility and chemical reactivity.

Front 10

Carbon can form Stereoisomers

Back 10

Tetrahedral structure - geometric symmetry.

Asymmetric carbon atom.

Two configurations.

Front 11

Water - Unique Properties

Back 11

Polarity

Cohesiveness

Temperature-stabilizing Capacity

Solvent

Front 12

Water - Polarity

Back 12

One part partial negative and partial positive charge because O's more electronegative atom draws electrons towards that region.

Uneven distribution old charge within a molecule.

Front 13

Water - Cohesiveness

Back 13

H²O molecule affinity for each other by Electronegative (Oxygen) and Electropositive (Hydrogen) charges.

Front 14

Water molecules are polar

Back 14

Oxygen atom in the water molecule is negative.

Draw electrons towards it.

Leaving the other end (+) charge top draw Hydrogen atoms.

Front 15

Water molecules are cohesive

Back 15

Electronegative oxygen atom if one molecule associated with the electropositive hydrogen atom of the adjacent molecules.

Property of Hydrogen bonds - being broken and reformed.

ICE - Hydrogen bonds - extensive and rigid.

Cohesivenes accounts for surface tension, high boiling point, high specific heat, high heat of vaporization, etc.

Front 16

High Temperature Stabilizing Capacity

Back 16

Due to Hydrogen bonding between adjacent water molecules - provide this property.

Specific Heat - amount of heat absorbed by a substance/gram to raise 1° Centigrade.

High heat of Vaporization - energy required to convert one gram of liquid into vapor.

Front 17

Specific Heat

Back 17

Amount of heat absorbed by a substance/gram to raise 1° Centigrade.

Front 18

High heat of Vaporization

Back 18

Energy required to convert one gram of liquid into vapor.

Front 19

Water - An Excellent Solvent

Back 19

Solvent - Fluid.

Solute - substance dissolved in the solvent.

Solute's Affinity

Hydrophobic - water fearing.

Hydrophilic - water loving.

Front 20

Selectively Permeable Membranes (Part 1)

Back 20

Membrane - hydrophobic permeability barrier consisting of

Phospholipids

Glycolipids

Membrane proteins

Sterols

- Cholesterol (animal cell)

- Phytosterol (plant cell)

- Ergosterol (fungus)

Front 21

Selectively Permeable Membrane (Part 2)

Back 21

Most membrane cells are not simply hydrophobic or hydrophilic.

Amphipathic

Phospholipid molecules of two

long nonpolar tails.

Front 22

Basic structure of lipid bilayer

Back 22

Front 23

Membranes and Membrane Structures Visual

Back 23

Front 24

Membrane - Selectively (Part 1)

Back 24

Hydrophobic interior - permeable to nonpolar molecules.

- Impermeable to most polar molecules and ions.

Cellular constituents - polar or charged - no affinity to interior.

Charge on an ion and hydration sphere - determines the permeability of a membrane.

Front 25

Membrane - Selectivity (Part 2)

Back 25

Hydrophilic Channel - specialized transmembrane protein.

Carrier Protein - binds a solute/molecule and transport across.

Transport - ions, proteins, solutes, gases regulated by cellular needs - selectively permeable.

Front 26

Essentials of Synthesis by Polymerization

Back 26

Cellular Structure - Ribosomes, Chromosomes, Membranes, Cell Walls etc. are all made up of linear polymers known as Macromolecules.

Macromolecules - Nucleic Acids (DNA and RNA), Polysaccharides (Glycogen, Starch, and Cellulose), Proteins.

Front 27

Macromolecule Hierarchy

Back 27

Level 1 - Small Organic Molecules

Level 2 - Macromolecules

Level 3 - Supramolecular Structures

Level 4 - Organelles and other Structures.

Level 5 - The Cell

Front 28

Macromolecule Hierarchy - Level 1

Back 28

Water soluble Organic molecules obtained from the other cells or synthesized from simple nonbiological molecules.

- Carbon dioxide, Ammonia, or Phosphate ions.

Front 29

Macromolecule Hierarchy - Level 2

Back 29

Biological Macromolecules - polymerization of organic molecules.

- Nucleic Acids (DNA, RNA), Proteins, Polysaccharides.

Front 30

Macromolecule Hierarchy - Level 3

Back 30

Assembly of supramoleculer structures – Cell wall, membranes, chromosomes.

Front 31

Macromolecule Hierarychy - Level 4

Back 31

Intercellular structures.

- Organelles

Front 32

Macromolecule Hierarchy - Level 5

Back 32

The Cell

Front 33

Synthesis of Biomolecules - Polymerization

Back 33

Macromolecules

- building blocks of cellular components; mitochondria, membranes, chromosomes, and ribosomes.

- Linear and Branched

Linear - DNA, RNA, Proteins.

Starch, Cellulose, and Glycogen.

Front 34

General Principal of Macromolecule

Back 34

Macromolecules that are responsible for most of the form and order characteristic of living systems are generated by the polymerization of small organic molecules.

Front 35

Three Important Macromolecules

Back 35

Proteins

Nucleic Acids

Polysaccharides

Front 36

Three Important Macromolecules - Protein

Back 36

Kind of Macromolecule - Informational.

Examples - Enzymes, Hormones, and Antibodies.

Repeating Monomores - Amino Acids.

# of kinds of Repeating Units - 20

Front 37

Three Important Macromolecules - Nucleic Acids

Back 37

Kind of Macromolecule - Informational.

Examples - DNA and RNA.

Repeating Monomores - Nucleotides.

# of kinds of Repeating Units - 4 in DNA and 4 in RNA.

Front 38

Three Important Macromolecules - Polysaccharides

Back 38

Kind of Macromolecule - Storage: Structural

Examples - Starch, Glycogen: Cellulose

Repeating Monomores - Monosaccharides: Monosaccharides

# of kinds of Repeating Units - One or a few:One or a Few

Front 39

Macromolecule - Basic Synthesis

Back 39

1. Stepwise Polymerization

2. Condensation Reaction

3. Activated Monomer

4. Carrier Molecule

5. Energy Retirement

6. Directionality

Front 40

1. Stepwise Polymerization

Back 40

Macromolecules are always synthesized by the stepwise polymerization of similar or identical small molecules called monomers

Front 41

2. Condensation Reaction

Back 41

Addition of each monomeric units occurs with the removal of a water molecules.

Front 42

3. Activated Monomer

Back 42

Monomeric units must be in activated form before condensation to occur.

Front 43

4. Carrier Molecule

Back 43

Activation involves coupling of the activated monomer to a carrier molecule.

Front 44

5. Energy Requirement

Back 44

Energy to couple monomers to the carrier molecule is provided by ATP, Adenosine Triphosphate.

Front 45

6. Directionality

Back 45

Macromolecules have a inherent directionality. It means that the two ends of the polymers are chemically different from each other.

Front 46

Activation

Back 46

Amino acids are activated by linking to carrier molecule transfer RNA (tRNA)

Polysaccharides are synthesized from sugar molecules which are activated by derivatives of nucleotides

ADP for starch and UDP for Glycogen

Nucleic Acid Synthesis – No carrier molecule because ATP and GTP are high-energy molecules

Front 47

Protein Folding Requirements

Back 47

Information needed to specify the folding of macromolecules and their interactions to form more complicated structures with specific biological function is inherent in the polymers themselves.

Front 48

Many proteins self assemble

Back 48

Immediate product of amino acid polymerization is polypeptide.

To become proteins - bonding and folding is required to acquire a three-dimensional structure for biological activities.

Molecule Chaperones - required for protein folding.

Front 49

Denature and Renaturing

Back 49

Front 50

Self Assembly:

Strict vs. Assisted

Back 50

Strict Self Assembly - no factors are required.

Assisted Self Assembly - Chaperones are required.

Front 51

Non-covalent Folding Interactions

Back 51

Hydrogen Bonds - electronegative to electropositive.

Ionic Bonds - electrostatic

Van der Walls Interactions - weak interactions between atoms.

Hydrophobic - nonpolar groups in a macromolecule.

Front 52

Virus Self Assembly

Back 52

Complex of proteins and nucleic acids (DNA or RNA).

Not functional until it meets its host.

Invade and infect living cells.

Utilized host's cellular machinery.

Reproduce its progeny in the host cell to produce virion.

Front 53

Tobacco Mosaic Virus

Back 53

Plant Virus with rod like particle

- 18 nm diameter, 300 nm length.

Genome - RNA of 6395 nucleotides (6.3 kilobase).

2130 copies of single kind polypeptide.

Polypeptide 158 Amino Acids - Coat Protein.

Front 54

Heinz Fraenkel-Conrat

Back 54

In vitro assembled RNA and protein components with functional virus.

Regenerated the virus particles.

First demonstration that the components on complex biological systems can reassemble into functional entities without external information.

One strain of virus RNA can be mixed with other strain of viral protein - infective.

Front 55

Tobacco Mosaic Virus (TMV) Structural Model

Back 55

Front 56

TMV Self Assembly

Back 56

Basic unit consists of two-layered disc of coat protein

Each layer has 17 identical subunit

Each disc initially a cylindrical structure

Conformational changes occur

Tighten the helical shape to interact with 102 nts. of RNA

Front 57

Self Assembly Limitations

Back 57

Information required to specify configuration lies in the macromolecule/polymer.

This allow the self-assembly systems achieve stable 3D configurations without additional information.

Some systems –depends on Additional information which is supplied by a pre-existing structure

The ultimate structure arises NOT by assembling the components (But by Ordering) into the matrix of an existing structure.

Examples –Membranes, cell walls, chromosomes.

Front 58

Cellular Advantages to Self Assembly (Part 1)

Back 58

Chemical Specificity

Efficiency of Assembly

All structure found in organisms synthesized from 30 small precursor molecules.

Polymers/macromolecule derived from different kind of condensation reactions.

Front 59

Cellular Advantages to Self Assembly (Part 2)

Back 59

Quality control issues – QC exerted at every step of the synthesis of polymers.

If a defective part – discarded at early stage of the assembly.

Front 60

Self Assembly Hierarchy

Back 60

Monomers < polymers < simple molecules < complex molecules < supramolecular assembly < organelles cells < tissue < organ < body of condensation reactions