Gerald Karp Cell and Molecular Biology Fifth Edition

• • Scientific spectrum Cellular and Molecular Biology Reductionist Replaced by an equally strong appreciation for the beauty and complexity of the mechanisms underlying cellular activity

1. 1 The discovery of cells Robert Hook : mid-1600 s Anton van. Leeuwenhoek : animalcules M. Schleiden : 1830 s T. Schwann : 1839 R. Virchow : 1855 Cell Theory: 1. All organisms are composed of one or more cells 2. The cell is the structural unit of life 3. Cells can raise only by a division from a preexisting cell

1. 2 Basic properties of cells 1951 Johns Hopkins University: Dr. George Gey cultured first human cell line from He. La cell (Henrietta Lacks) that are being grown in the laboratory all around the world

Cells are highly complex and organized 1. Levels of cellular and molecular organization (same ancestor, only expression is different) 2. Cells possess a genetic program and the means to use it (3 x 1012 base pairs) 3. Cells are capable of producing more of themselves

4. Cells acquire and utilize energy 5. Cells carry out a variety of chemical reactions (metabolism) 6. Cells engage in numerous mechanical activities 7. Cells are able to respond to stimuli 8. Cells are capable of self-regulation (Fig. 1. 6) 9. Cells evolve

1. 3 Two fundamentally different classes of cells 3. 5 billion years: Cyanobacteria 1. 5 billion years: Eukaryotes

1. Characteristics that distinguish prokaryotic and eukaryotic cells

Types of prokaryotic cells • Archaea: thermophiles: halophils, thermophils (strain 121), acidophils, methanogens : CO 2 and H 2→CH 4) • Domain bacteria or eubacteria • Cynobacteria: PS and reduced N 2 to NH 3 • Use DNA sequence to study the species diversity (5000/millions species, 415 species in month)

Types of eukaryotic cells: cell specialization Differentiation

Six model organisms

The sizes of cells and their components

The human perspective The prospect for cell replacement therapy

1. 4 Viruses virion (outside the living cell) Viroids (RNA only, potato virus)

Experimental pathways The origin of eukaryotic cells • Prokaryotic cells: 2. 7 billion years old • Eukaryotic cells: ~1. 7 billion years • Both share similar genetic codes, enzymes, metabolic pathways, and plasma membrane • Common ancestor

Evolutionary relationships: compared nucleic acid sequence Chloroplast r. RNA, 16 S r. RNA from cyanobacteria, 18 S r. RNA from eukaryotic ribosome r. RNAs change very slowly over long periods of evolutionary time

Three Domains of Life Bacteria, Archaea, Eucarya

Gerald Karp Cell and Molecular Biology Fifth Edition Chapter 2 CHAPTER 2 Part 1

Chemical reaction Protein interaction, DNA replication, cell division Muscle movement: move a few molecules Transport the molecules and ions across the cell membrane DNA

2. 1 Covalent bonds An atom is most stable when its outmost electron shell is filled.

If two electron pairs are shared in molecular oxygen (O 2), the covalent bond is a double bond.

The electronegativity of an atom depends on two factors: 1. the number of positive charges in its nucleus (the more protons, the more electronegative) 2. the distance of the outer electrons from the nucleus ( the greater the distance, the less electronegative)

1. Polar and nonpolar molecules Unsymmetrical distribution of electrons

2. Ionization

2. 2 Noncovalent bonds (1 -5 kcal/mol) do not depend share electrons and goverened by a variety of weaker linkages, mediate dynamic interactions among molecules in the cells 1. ionic bonds 2. hydrogen bonds 3. hydrophobic interaction 4. van der Waals forces

• 1. ionic bonds 2. hydrogen bonds 3. hydrophobic interaction 4. van der Waals forces

The life-supporting properties of water

2. 1 covalent bond 2. 2 non-covalent bond 2. 3 Acids and Base 2. 4 The nature of biological molecules

• The chemistry of life centers around the chemistry of the carbon molecules • Back bones

2. 6 four types of biological molecules • • Carbohydrates Lipids Proteins Nucleic acids

Stereoisomerism glyceraldehyde

2. 6 four types of biological molecules • • Carbohydrates Lipids Proteins Nucleic acids

lipids 1. Fats 2. Steroids 3. phospholipids

The phospohlipid phosphatidylcholine

2. 6 Four types of biological molecules • Carbohydrates • Lipids • Proteins (10000 proteins in the cell, 450 amino acids in average polypeptide chain, titin contains 30, 000 amino acids) • Nucleic acids

The structure of proteins • Primary structure • Secondary structure • Tertiary structure Protein domains Dynamic changes within proteins • Quaternary

The structure of proteins • Primary structure (insulin aa sequence in 1950 s) rapid DNA sequencing can deduce the aa sequence, but problems existed) • Tertiary structure • Protein domains • Secondary structure Dynamic changes within proteins • Quaternary

Posttranslational modifications • Alterations of 20 basic amino acids (PTMs) to form other aa (Add p group for regulation of cell to become a normal or a cancer cell) • Molecular interactions • Shortening the life spin

The structure of proteins • • • Primary structure Secondary structure Tertiary structure Protein domains Dynamic changes within proteins Quaternary

The structure of proteins • Primary structure • Secondary structure • Tertiary structure (conformation of total protein, stabalized by non-covalent bond) • Protein domains • Dynamic changes within proteins • Quaternary

Types of noncovalent bonds maintaining the conformation of proteins

Spatial distinct modules fold independently: domains and have different functions (bind to DNA or other proteins) (How could it happen? One protein should only have one function? ) Fusion genes

• Dynamic changes within proteins • NMR: study the dynamic structure • Shift of H-bonds, movement of side chain, and full rotation of aromatic rings of tyrosine and phe • Important in protein function

The structure of proteins • Primary structure • Secondary structure • Tertiary structure (conformation of total protein, stabalized by non-covalent bond) • Protein domains • Dynamic changes within proteins • Quaternary (more than one chain, hydrophobic pitch connect each other)

Protein folding

The human perspective • Molecular chaperones (helper proteins) help unfolded or misfolded proteins to achieve their proper 3 -D conformations

• The role of molecular chaperons (helper proteins) : to prevent from interacting nonselectively with other molecules in the croweded compartments of the cell.

The emerging field of proteomics • 30, 000 genes from genomics study • Proteomics (proteome): organisms, particular tissue, cell, or cellular organelle • Study large numbers of proteins in a single experiment • High speed computer and biochemistry • More difficult to work with than DNA (different protein has different character, PCR for DNA, but proteins can not)

• Specific activity in vitro? • Function in cell replication or locomotion? • 3 D structure? Appear in which cell during development? And when? • Localization? • Modificationj? • How much and how long? Protein interaction? • Diseases?

Protein function • Protein microarrays (chips) • Microscopic-sized spots on glass microscope slide, each containing a protein sample

• PSA, PSA antibodies • Apply to other tests

Protein engineering • Find a protein which can bind surface of AIDS viral particle and remove it from the blood • Computer predicts the shape of such protein • Protein’s primary structure and tertiary structure must know • Folding problems

• Site-directd mutagenesis 1. Isolate an individual gene from human chromosome 2. Alter its information content precisely and synthesize the modified protein 3. thrombin (procoagulant and anticoagulant)

Structure-based drug design • Drug companies search new drugs from plants, fungi, micro-organisms or chemically synthesized. • Binding affinity with diseased proteins • Aspirin: anti-inflammatory due to inhibit cyclooxygenase-2 (synthesize prostagladins to promote inflammation, pain, and fever) • Prolonged using COX-2 can inhibit COX-1 and damage the lining of the stomach. • Isoleucine at position 523 in COX-1, a valine in COX 2 • Design a drug that bind COX-2 much greater affinity than COX-1 • COX-2 inhibitor: celebrex, vioxx

Protein adaptation and evolution

The structure of proteins • • • Primary structure Secondary structure Tertiary structure Protein domains Dynamic changes within proteins Quaternary