Cell and Molecular Biology (2141591)

Instructors: Pimpon Uttayarat, Ph.D. (Course Coordinator) Kanokporn Boonyasirichai, Ph.D.

Suwimol Jetawattana, Ph.D. Siraprapha Sanchatjate, Ph.D.

pu.cell2008@gmail.com

textBook: Molecular Biology of the Cell, 4th edition by Alberts et al. and also selected journal paper

Grading:

Homework 20% Midterm 30%

Class Participation 10% Final 30%

Presentation 10%

Textbook http://www.ncbi.nlm.nih.gov/books/

Search for the topic, e.g. cell organelles

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Cell and Molecular Biology Aug 14, 2010

Lecture 1:

Cellular biochemistry: pp 4-91 and pp 110-123 Cell structures and organelle function: Chapter 12 Protein structure and function: Chapter 3

IntroductionIntroduction

Each of the living creatures is merely a chemical system.

The chemistry of life is of a special kind:

First: It is based overwhelmingly on carbon compounds

organic chemistry

Second: Cells are 70% water life depends exclusively on

chemical reactions that take place in aqueous solution

Third: cell chemistry is enormously complex more

complicated than any other chemical system known

Fourth: it is dominated and coordinated by collections of

enormous polymeric molecules formed from chains of

chemical subunits

1. Cellular Biochemistry 1. Cellular Biochemistry

Chemical bonds

covalent: C-C, C-N, C-O

noncovalent: H-bonding, ionic interaction,

hydrophobic effect, VDW interaction

Building blocks: proteins, carbohydrates, lipids

and nucleic acids

Figure 2-9

This restriction is a major influence on the 3-D shape of many macromolecules

covalent bond: hydrocarbon covalent bond: hydrocarbon

Panel 2-1

Hydrocarbons are nonpolar and insoluble in water

resonance

12

3

covalent bond: C-O covalent bond: C-O

Panel 2-1

covalent bond: C-N covalent bond: C-N

Panel 2-1

-C-NH2

-C-NH-

O

Nitrogen in ring compounds: purine and pyrimidines

covalent bond: P bonds covalent bond: P bonds

Panel 2-1 Molecular Biology of the Cell, 4th edition

Bonds of Pi to OH, COOH, Pi

Phosphorylation of protein

The folded structures and macromolecular interactions that determine much of the cell biology are governed largely by noncovalent bonds and repulsion forces that have energy greater than kT but less than a typical covalent bond.

Non-covalent bonds have less than 1/20 the strength of a covalent bond

Panel 2-3 Molecular Biology of the Cell, 4th edition

• van der Waals interactions

• hydrogen bonds

• ionic interactions

• the hydrophobic effect

determined by the unusual chemical properties of water

Noncovalent bond Noncovalent bond

Bond energy

Figure 2-7 Molecular Biology of the Cell, 4th edition

Table 2-2 Molecular Biology of the Cell, 4th edition

Panel 2-3 Molecular Biology of the Cell, 4th edition

Ionic bonds in aqueous solutions

Noncovalent bond: ionic interaction Noncovalent bond: ionic interaction

Panel 2-3 Molecular Biology of the Cell, 4th edition

Example of ionic interaction Example of ionic interaction

Electrostatic attraction brings molecules together in cells

Panel 2-3 Molecular Biology of the Cell, 4th edition

Any molecules that can form hydrogen bonds to each other can alternatively form hydrogen bonds to water molecules. This is relatively a weak bond.

Noncovalent bond: hydrogen bond Noncovalent bond: hydrogen bond

Hydrogen bonds form when a hydrogen atom is “sandwiched” between two electron-attracting atoms (usually O or N)

Hydrogen bonds among H2O molecules Hydrogen bonds among H2O molecules

Each water molecules can form H-bond through its two H atoms to two other water molecules, producing a network in which H bonds are being continually broken and formed.

Because of these interlocking H bonds, water is liquid at RT with high boiling point and high surface tension and not a gas.

Panel 2-3 Molecular Biology of the Cell, 4th edition

Panel 2-3 Molecular Biology of the Cell, 4th edition

Oil is immiscible in water

Panel 2-2 Molecular Biology of the Cell, 4th edition

Hydrophilic molecules are readily dissolved in water.

Noncovalent bond: hydrophobic effect Noncovalent bond: hydrophobic effect

Amphiphilic molecules

Hydrophilic head

Hydrophobic tail

Panel 2-5 Molecular Biology of the Cell, 4th edition

micelle

Noncovalent bond: hydrophobic effect Noncovalent bond: hydrophobic effect

Hydrophobic effect drives phospholipids to aggregate and form lipid bilayers

Figure 2-22 Molecular Biology of the Cell, 4th edition

Figure 2-12 Molecular Biology of the Cell, 4th edition

Figure 2-17

5 > 1 mm

20 5-1000 nm

2 nm1000

100 ~ 100 um

Building blocks of cells Building blocks of cells

Figure 2-29

Figure 2-24

Amino acids are the subunits of proteins. All amino acids possess a carboxylic acid group and an amino group, both linked to a single carbon atom called -carbon.

Condensation reaction strings the building blocks together

Figure 2-65

amino acids proteins amino acids proteins

Proteins are polymers of amino acids joined head-to-tail by a peptide bond into a long chain that is then folded into a three-dimensional structure. A chain of amino acids is also known as polypeptide.

Figure 2-24Figure 3-24

Panel 2-4 Molecular Biology of the Cell, 4th edition

Monosaccharides that contain an aldehyde group are called

aldoses and those that contain a ketone group are called ketoses.

monosaccharides polysaccharides monosaccharides polysaccharides

Figure 2-19 Molecular Biology of the Cell, 4th edition

In a condensation (dehydration) reaction, hydroxyl groups on each monosaccharide forms a glycosidic bond with a loss of one water molecule. When a water molecule is added during hydrolysis, this newly formed disaccharide is broken into two monosaccharides.

Glycosidic bond ties monosaccharides together Glycosidic bond ties monosaccharides together

Large linear and branched molecules can be made from repeating sugar subunits. Short chains are called oligo saccharides and long chains are called polysaccharides. Glycogen is polysaccharides made entirely of glucose units.

Panel 2-4 Molecular Biology of the Cell, 4th edition

Panel 2-5 Molecular Biology of the Cell, 4th edition

fatty acids fatty acids

Panel 2-5

phospholipids are the major constituents of cell membranes phospholipids are the major constituents of cell membranes

Phosphate head

Fatty acid tail

glycerol

Fig. 10-1

triacylglycerols triacylglycerols

Panel 2-5

Other lipids Other lipids

Panel 2-5

A nucleotide consists of a nitrogen-containing base, a five-carbon sugar and one or more phosphate groups.

Panel 2-6 Molecular Biology of the Cell, 4th edition

Phosphate group makes nucleotide negatively charged.

The presence of hydroxyl group on the 2nd carbon of ribose differentiates RNA from DNA.

Bases are nitrogen-containing ring compounds. DNA and RNA are different in their bases.

nucleotides nucleic acids nucleotides nucleic acids

The sugar constituents of nucleic acids are five-carbon sugars that belong to the aldose type.

Panel 2-6 Molecular Biology of the Cell, 4th edition

sugars sugars

nomenclature

DNA: A T C G

RNA: A U C G

Panel 2-6 Molecular Biology of the Cell, 4th edition

bases bases

Nucleotides are joined together by a phosphodiester linkage between 5’ and 3’ carbons to form nucleic acids.

Panel 2-6 Molecular Biology of the Cell, 4th edition

The linear sequence is read in a one-letter code such as G-A-T-C from 5’ to 3’.

-H2O

nucleic acids nucleic acids

The synthesis of polysaccharides, proteins and nucleic acids

Key: condensation reaction to form macromolecules from small subunits (monomers) consumption of energy from nucleotide triphosphates to activate the monomers