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O1: Introduction Molecular Cell Biology 03: Cells: The Chemical Foundations
• Molecular Biology is the study of the replication, • Organic chemicals: contain covalently bonded carbon
transcription, & translation of genetic material within a cell. backbones.
Manipulation of these processes is also known as molecular • Isomers: chemicals with the same molecular formula but
biology or recombinant DNA techniques. different structural formulas.
• Macromolecules- there are four main classes of • Buffers: solutions, which resist changes in pH upon addition
macromolecules: lipids, proteins, carbohydrates, and nucleic of small amounts of acid or base.
acids. • Electrolytes: chemicals that release ions into solutions.
• Deoxyribonucleic acid (DNA)- double helix chains of • pH: pH represents the concentration of hydrogen ions [H+]
paired bases containing thymine, cytosine, guanine, and in solution (scale 1-14, pH 7=neutral). pH = -log [H+]
adenine. • Acids: release H+ into solution, pH < 7
• Ribonucleic acid (RNA)- the intermediate between DNA • Bases: release OH- that can combine with H+ to make
and proteins.Proteins- chains of amino acids coded for by water, pH > 7
genes in the DNA. • Enzymes: proteins that serve as catalysts for biochemical
reactions.
Transcritpion: DNA is transcribed into RNA and special • Entropy: a measure of a system's degree of disorder. It
pairing of bases dictates which sequence is made. increases with increasing disorder.
• Laws of thermodynamics: First Law: The total energy of
the universe is always conserved. Energy can neither be
created nor destroyed. Second Law: The universe tends
towards maximum disorder; the direction of all spontaneous
processes serves to increase the entropy of a system plus its
surroundings.
Enzymes act as catalysts to lower Ea, but they do not change ΔG.
No Enzyme
02: The Cell Free energy Ea
Reactants + Enzyme
• Cell: The smallest unit of an organism that can live
independently.
• Cell Theory: an explanation of the role of cells in ΔG
relationship to living things. · Prokaryotic Cell: The
smallest unit of life for prokaryotic organisms such as Products
bacteria and other microbes.
• Eukaryotic Cell: The smallest unit of life for eukaryotic
organisms such as animals.
04: The Macromolecules
• Nucleolus: a “tiny nucleus” inside the nucleus, which • Macromolecule: A molecule having a molecular weight in
contains RNA. the range of a few thousands to many millions.
• Nuclear Envelope: a protective layer, which surrounds the • Functional group: The specific atom or group of atoms that
nucleus. confers a particular chemical property on a biomolecule.
• Nuclear Pore: holes in the nuclear envelope that allow the • Organic Compounds: Molecules containing covalently
nucleus to exchange information with the rest of the cell. bonded carbon backbones are called organic compounds.
• DNA: a nucleic acid, an organic macromolecule. • Monosaccharide: A carbohydrate consisting of a single
• RNA: a nucleic acid, an organic macromolecule. sugar unit.
• Cytoplasm: the liquid space inside of a cell. • Disaccharide: A carbohydrate consisiting of two covalently
• Organelles: specialized cell structures, which perform joined monosaccharide units.
specific functions. • Polysaccharide: A linear or branched polymer of
• Cell Membrane: a protective bilayer of lipids, which allows monosaccharide units linked by glycosidic bonds.
the cell to maintain a stable internal environment.
Potential
l l
Lysosome Nucleus
ABCD BACD
Ribosomes
Smooth
CABD DABC
Endoplasmic
Reticulum
Monomers
ABDC BADC A,B,C,D
CADB DACB
Mitochondria
Rough
Endoplasmic
Reticulum
Golgi Apparatus
Plasma Membrane
R1 R3
Peptide bond
Dicer
Sticky ends
TrpR p o TrpL TrpE TrpD TrpC TrpB TrpA
Anneal
mRNA
mRNA
no Trp, seal with DNA ligase
no bind
12: Genomics
10: Regulation of Gene Expression in • Genomics: the study of an organism's entire genome,
Eukaryotes usually starts with whole genome sequencing.
• BAC: bacterial artificial chromosomes, which is based on F
• Promoter: A DNA sequence having a regulatory function
plasmid and can tolerate large inserts, widely used in
over the transcription of an adjacent gene, and to which
genomic DNA library construction.
RNA polymerase binds prior to transcription.
• BAC library: large genomic DNA fragments ligated into BAC
• Enhancer: a short region of DNA that can be bound with
vectors.
proteins to promote expression of a distal or proximal gene.
• Shot gun sequencing: Genomic DNA from a BAC clone is
• TATA Box: Binds to transcription factor for regulating gene
fragmented into smaller size, typically 1kb, and inserted into
expression, usually within 30bp of the transcription start
a sequencing plasmid. These sequences are then assembled
site.
based on the overlapping fragments.
• Basal Transcription Factor: Transcription factors that are
• Sequence assembly: a computer-based approach to put
required for all transcriptions, they unwind DNA and assist
together all the genomic DNA sequence together, starting to
RNA polymerase to bind to transcription initiation sites.
put together a BAC sequence first.
• Modulatory Transcription Factor: Transcription factors
• Human Genome Project (HPG): Divided into two groups
that regulate time/space expression, may bind to enhancers
based on different funding resource: public sector and Celera
or to promoter regions to enhance or suppress gene
private sector. The purpose is to obtain all genetic
expression under certain conditions.
information from humans.
• DNA binding domain: A domain found in all transcription
• Functional Genomics: Use the sequence data to explore
factors, used to bind DNA, inclding three types: Zinc-finger,
how DNA and proteins work with each other and the
HLH and leucine zipper.
environment to create complex, dynamic living systems.
• Zinc-Finger: A structure found in a number of transcription
factors, has repetitive two cystein and two histidine to bind a
Procedure O verview
Zn, and form a “finger” structure.
• Leucine-zipper: A structure found in a number of Step 1: BAC library Chrom osom e
transcription factors, characterized by leucine residue at construction
every other turn of helix, 7 amino acid apart. Step 2: Shot gun
sequencing
Step 3: Sequence
assem bly BAC library
TATA
Enhancer Promoter Box Transcription starts Enhancer
Signal
Receptor
Reception
Cell
Transduction
membrane
Transducer
Effector
Response
Repaired DNA
24: Immunology
• Immune System: It is a unique adaptive defensive system
22: The Mechanics of Cell Division that has evolved in vertebrates to protect them from
• Mitosis: Mitosis involves the dividing of the nucleus and the invading pathogenic microorganisms and cancer.
surrounding cell. Mitosis occurs after the successful • Immunity: All those physiological mechanisms that endow
replication of the cell’s DNA. the animal with the capacity to recognize materials as
• Prophase: the normally loosely packed chromatin is foreign to itself and to neutralize eliminate or metabolize
condensed into the chromosome. The two centrosomes them with or without injury to its own tissues.
(Mitotic Spindle) begin to extend microtubules, in • Antigen: Any substance (usually foreign) that bind
preparation for attaching to the chromosomes. specifically to an antibody or a T cell receptor.
• Metaphase: the chromosomes are aligned at the center of • Antibody: A protein (immunoglobulin) that recognizes a
the cell at a region called the metaphase plate. Each of the particular antigen and binds specifically to it.
sister chromatids (2 per chromosome) are attached to • Innate immunity or native immunity: It is the resistance
opposite poles of the mitotic spindle. to infections, which an individual possesses by virtue of his
• Anaphase: There are many proteins that make up the genetic and constitutional make-up. It is not affected by
anaphase promoting complex. This complex plays a key role prior contact with microorganisms or immunization.
in allowing the cell to successfully separate the sister • Adaptive immunity or acquired immunity: It is the
chromatids in the 2 future daughter cells. resistance that an individual acquires during life, as distinct
• Cytokinesis: Eventually, as cytokinesis progresses, the from the inborn innate immunity. Adaptive immune
cleavage furrow deepens until the plasma membrane and its responses exhibit four immunological attributes: Specificity,
contents are divided. Diversity, Memory, Self and non-self recognition.
Protect against
Bone
Bone
marrow
marrow
Immune
Immune Pathogens
Pathogens
Thymus
Thymus System
System
Bacteria
Bacteria
Lymphatic
Lymphatic
system
systemof
of Viruses
Viruses
ducts
ducts&&nodes
nodes
Protozoa
Protozoa
Multi-cellular
Multi-cellular
Spleen
Spleen parasites
parasites
Fungi
Fungi
Leucocytes
Leucocytes their
theirproducts
products