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Molecular Cell Biology Core Concept Master Cheat Sheet

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.

Energy of activation (Ea) = the free energy necessary to start a reaction.

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

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05: Protein Structure and Function 07: DNA Structure and Function
• Antibody: A specific protein that interacts with a foreign • Nucleoside: Compounds with a ribose or deoxyribose and a
substance (antigen) in a specific way. base. Base includes four types G, C, A and T (or U).
• Beta-sheet (ß-sheet): A sheet like structure formed by the • Nucleotide: Compounds with a ribose or deoxyribose, a base
interaction between two or more extended polypeptide and a phosphate group, it is the basic building unit for DNA
chains. (monomers of DNA).
• Cytoskeleton: The filamentous skeleton, formed in the • Pyrimidines: A type of base, including both cytosine and
eukaryotic cytoplasm that is largely responsible for thymidine.
controlling cell shape. • Purines: A type of base, including both guanine and
• Dalton: A unit of mass equivalent to the mass of a adenine.
hydrogen atom (1.66 x 10-24 g) • Tm: Melting temperature of DNA. DNA is a double helix
• Disulfide Bridge: A covalent linkage formed between two molecule, when heated, the two strand separate from each
cysteine-SH groups either in the same polypeptide chain or other (melting) and the absorbance at 260 nm increases.
in different polypeptide chains. When half of the DNA is in single strand status, the
• Enzyme: A molecule, most often a protein that contains a temperature is called the DNA’s Tm.
catalytic site for a biochemical reaction. • Denature: The hydrogen bonds break between the two
• Globular protein: A folded protein that adopts an strands of the DNA molecule, can be caused by heat or pH.
approximately globular shape. May also be called soluble • Renature: The denatured DNA restore the double helix
proteins. structure and re-form hydrogen bonds.

Residue n Residue n+1


R2

R1 R3
Peptide bond

06: Gene and Chromosomes


• Karyotype: A complete set of all metaphase chromosomes
in a cell. Species-specific and is used for genetic diagnosis. 08: Transcription, Translation and The
• G band and Q band: Bands shown on chromosomes after Genetic Code
various treatments and staining technique. Same • mRNA: A messenger between DNA and protein, made from
chromosome from one specieis always show same banding DNA template (transcription) and then directs the protein
pattern. synthesis.
• FISH: fluorescence in site hybridization. A fluorescence • tRNA: Transfer RNA, carry amino acid to protein synthesis
labeled DNA fragment (probe) is hybridized to a site.
chromosome therefore a gene can be located to a • rRNA: Structure RNA of ribosomes where proteins are
chromosome. synthesized.
• Nucleosome: A bead-string structure formed by DNA and • microRNA: miRNA, have mismatch to mRNA, but they bind
histones, the basic DNA structure in a chromatin. to mRNA, leading to mRNA degredation or block mRNA
• Chromatin: The general structure of any chromosome, the translation.
basic units is nucleosomes. • Template strand: The transcribed DNA strand, with
• Chromatid: One-half of a replicated chromosome. sequence complementary to mRNA sequence.
• Histone: structure proteins for nucleosome, including H1, • Non-template strand: Not transcribed, sequence is identical
H2A, H2B, H3 and H4 types. to mRNA, also called coding strand.
• Chromosome: The unit of inheritance with the basic • Promoter: A DNA sequence having a regulatory function
structure of arms, a centromere and two telomeres. over the transcription of an adjacent gene, and to which RNA
• Euchromatin: Chromatin region stained lightly, usually are polymerase binds prior to transcription.
lightly packed and transcriptionally active.
• Heterochromatin: Chromatin region stained dark, usually
are heavily packed and transcriptionally inactive.
• Telomere: The DNA-protein strucuture at the ends of each
chromosome plays critical role in DNA replication and aging. miRNA

Dicer

Degredation Block Translation

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09: Control of Gene Expression in 11: Recombinant DNA Technology
Prokaryotes • Recombinant DNA: a DNA molecule that is made from two
• Promoter: A DNA sequence having a regulatory function different sources and often manipulated in a test tube and a
over the transcription of an adjacent gene, and to which host cell.
RNA polymerase binds prior to transcription. • cDNA: complementary DNA, the DNA synthesized from a
• Pribnow Box: A conserved promoter sequence located at- mature mRNA template. cDNA is often used to clone genes.
10 position of mRNA, usually is TATAA, also called TATA box, • Genomic DNA: DNA isolated from organisms, containing all
the function is for transcription factor binding. DNA in the genome of a cell or an organism.
• Operon: consist of two or more adjacent coding regions • PCR: polymerase chain reaction, a molecular biology
that are controlled by the same transcription factors. technique using DNA polymerase, template DNA and primers
• Polycistronic: The structure genes of an operon are to synthesize specific DNA fragments.
transcribed as a single mRNA molecule containing multiple • Restriction Endonuclease: an enzyme that cuts double-
genes. stranded DNA within the molecule.
• Structure genes: The genes in an operon that encodes the • DNA vector: an agent that can carry a DNA fragment into a
enzymes necessary for a metabolic pathway. host cell and ensure its replication and sometimes,
• Regulatory genes: The genes in an operon that play expression.
regulatory roles, acting as either repressors or activators. • Cloning vector: A vector that carries DNA into a host cell for
• Cis-acting element: DNA sequences in the vicinity of the replication.
structural portion of a gene that are required for gene • Expression vector: A vector that carries DNA into a host
expression. Operator sequence and promoter sequence are cell and express the DNA into its final protein product.
cis-acting elements.
• Trans-acting elements: Factors that bind to the cis-acting
sequences to control gene expression, for example, RNA
polymerase, TFs, repressors. Digest with same restriction enzyme BamH I

Sticky ends
TrpR p o TrpL TrpE TrpD TrpC TrpB TrpA
Anneal

mRNA
mRNA
no Trp, seal with DNA ligase

no bind

Repressor R Trp synthesis


Recombinant DNA

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

Shot Gun Sequencing


Exon Intron
Sequence Assem bly

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13: Membrane Structure 15: Cellular Energetics
• Membrane Structure: Maintains and protects cellular • Glycolysis: Glycolysis is a pathway in which a molecule of
contents, provides for electrochemical gradients, dynamic glucose is oxidized into two molecules of pyruvic acid.
and flexible enough to allow cell shape changes and cell Glycolysis takes place in the cytosol of the cell.
movements, supports membrane bound proteins, which are • Electron Transport: a series of redox reactions take place,
involved in cell signaling and growth and differentiation. in which one molecule is reduced (gains an electron) and the
• Phospholipids: make up the major portion of membranes next is oxidized (gives up an electron). At each step, a Proton
in cells. They are Amphipathic molecules, which means they (H+ atom) is pumped across the mitochondrial membrane,
have both a hydrophobic (water fearing) and a hydrophilic creating the concentration gradient used by the enzyme ATP
(water loving) component. Synthase.
• Phospholipid Bilayer: By forming a bilayer, the • NADH: is an important electron transporter in the respiratory
hydrophobic tails can interact with each other and the chain enzyme complexes. NADH is the reduced form of
hydrophilic heads can interact with water molecules in the NAD+, and NAD+ is the oxidized form of NADH.
surrounding fluid. • Oxidative Phosphorylation: involves the phosphorylation of
• Cell Membrane: is made up of phospholipids, glycolipids, ADP to form ATP. These reactions depend on the H+ proton
cholesterol and proteins. A cell membrane is approximately gradient that is created during the events of the respiratory
5 nm thick and is a fluid dynamic structure. chain. ATP Synthase is an enzyme also known as the F0F1
• Cholesterol: is very prominent in the membranes of cells; it ATPase.
inserts itself within the bilayer. Cholesterol enhances the • Photosynthesis: utilizes the energy from sunlight to
permeability-barrier properties of the cell membrane. eventually form hexose, sucrose and starch along with
oxygen. These reactions begin with the absorption of light
photons, and then involve electron transport and, ultimately,
carbon dioxide metabolism.

14: Membrane Transport


• Membrane Transport: Molecules that are small and
hydrophobic can pass through the cell membrane by passive
diffusion, down their concentration gradient i.e, oxygen and 16: Intracellular Compartments
carbon dioxide. • Intracellular Compartments: Cells contain many special
• Facilitated Diffusion: is carried out by a carrier protein or compartments, known as organelles. There are many crucial
channel protein and transports the molecule passively, down enzymatic and non-enzymatic processes necessary for cell
its concentration gradient. survival that take place in or on lipid membranes.
• Active Transport: is the process by which a carrier protein, • Nuclear Protein Import: Proteins that are targeted for the
also known as a pump, facilitates the movement of a nucleus contain a nuclear localization signal. Nuclear import
molecule against its concentration gradient. This process receptors bind the nuclear localization signal portion of the
requires metabolic energy from ATP hydrolysis. protein and facilitate its transport into the nucleus.
• Na+-K+ Pump: utilizes the energy released from ATP • Intracellular Protein Transport: There are 3 main ways in
hydrolysis to transport Na+ and K+ ions against their which proteins are transported within cells: (A) Gated
concentration gradients. This pump is responsible for the transport, (B) Transmembrane transport and (C) Vesicular
membrane electrical gradient inside relative to outside the transport.
cell. • Posttranslation Translocation: Proteins are imported
• Ion Channels: Exist in either an open or closed state. The through multi-subunit protein complexes, known as
different types of channel proteins are: (A) Voltage-gated translocators; both the insertion of the protein into the
channels, (B) Ligand-gated and (C) Nucleotide-gated translocator and the exit on the opposite side of the
channels. membrane requires energy.

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17: Intracellular Vesicular Traffic 19: Cell Signaling Pathways
• Molecular Mechanisms of Coated Vesicles: Most vesicles • Cell Communication: Cells interpret incoming signals in
bud off from a region of the membrane that has a unique order to: secrete molecules, move location and proliferate
protein coat (cage). There are 3 different types of protein into new cells.
coats used by cells: (A) Clathrin-coated, (B) COPI-coated • Forms of Signaling: Secreted molecules can mediate 3
and (C) COPII-coated vesicles. forms of signaling: Paracrine - secreted molecules can
• COPI and COPII-Coated Vesicles: COPI-coated vesicles diffuse a short distance in the extracellular matrix and then
transport cargo from the cis end of the golgi complex to the be taken up by adjacent cells, Autocrine - secreted
endoplasmic reticulum (ER), called retrograde transport. molecules can act on the cell they were released from and
COPII-coated vesicles transport cargo from the endoplasmic Endocrine: molecules secreted into the bloodstream, which
reticulum to the golgi complex, called anterograde are then carried to the target cells and diffuse out into the
transport. tissue.
• ER-Golgi Transport: Proteins that are targeted for the • G-protein Linked Cell-Surface Receptors: G-protein
golgi complex are packaged into COPII-coated vesicles. receptors exist in the plasma membrane of many cell
Vesicles bud from special ER regions, called RE exit sites; types; they have an extracellular domain - where the
these sites usually do not contain ribosomes. receptor binds molecules outside of the cell and initiates the
• Golgi-Lysosome Transport: Mannose 6-phosphate (M6P) signal transduction and an intracellular domain - interact
is a lysosomal sorting signal. Proteins that are destined to with G proteins and stimulate their activation through
reside in the lysosome, such as lysosmal hydrolase, are binding of ATP.
tagged with a M6P. • G-protein: Shutting off the Signal: After the G-protein
activates cyclic AMP, it hydrolyses GTP into GDP and is then
returned to an inactive state.

18: Cellular Communication


• Chemical signal: Cell signals are often chemicals.
• Paracrine signal: local signals that can only influences the
neighboring cells, such as neuron transmitters. 20: Cytoskeleton and Cellular Motility
• Endocrine Signal: Specialized cells release molecules • Cytoskeleton: provides dynamic structure and support for
(often hormones) into blood vessels of circulatory system, cells, which is reorganized frequently, and provides and
hormones move to distant target cells. maintains cell shape.
• Signal receptors: often membrane proteins that can bind • Cytoskeleton Functions: facilitates intracellular movements
signal molecules from cell surface except for intracellular including: Vesicle Transport, and Chromosome Segregation.
receptors, which is localized in cytosol. • Actin Filaments: also known as microfilaments are
• RTK: receptor tyrosine kinase, numerous typs but oftern organized into bundles just underneath the plasma
include receptors for growth factors. It has intrinsic tyrosine membrane. Actin filaments, along with motor proteins such
kinase activity and is capable of self activation by as myosin, are reorganized as cells change their shape and
phosphorylation and dimerization. move.
• GPCR: G-protein coupled receptors, usually has 7 • Intermediate Filaments: are made up of various
transmembrane domain and has an intracellular domain to intermediate filament proteins including: keratins, vimentin,
bind signal molecule and a cytosol domain to bind G protein. neurofilament proteins and nuclear lamins, and share the
• G Protein: A huge class of proteins that bind to guanine same long rope-like structure and are prominent around the
nucleotide GDP and GTP, usually hetertrimers and associate nucleus and extend out towards the periphery of the cell.
with GPCR or cytosol side of cell membrane. Upon signal • Microtubules: are long, hollow tube-like cylinders, which are
binding by a GPCR, it undergoes a conformational change made up of the protein tubulin, and are involved in vesicle
and hydrolizes GTP to activate the downstream targets. and organelle movement within cells. ·

Signal

Receptor
Reception

Cell
Transduction
membrane

Transducer

Effector
Response

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21: The Cell Cycle and Programmed Cell 23: Cancer
Death • Cancer: The general name for over 100 medical conditions
• Cell Cycle: The Cell Cycle is made up of 4 distinct phases: involving uncontrolled and dangerous cell growth.
(1) Gap 1 (G1), (2) S Phase, (3) Gap 2 (G2) and (4) M • Oncogenesis: process of initiation of tumors (cancer) in an
Phase (Mitosis). organism.
• G1: In cells that are actively cycling through the cell cycle, • Tumor: tissue composed of cells that deviate from normal
G1 is when the cell monitors its environment and size. program of cell division and differentiation.
During this time the cell grows. • Benign tumor: tumor cells remain together in a single
• S Phase: In order for a cell to divide successfully, it must mass and do not invade or disrupt surrounding tissues.
copy its entire DNA to be able to supply 2 daughter cells. • Malignant tumor: tumor cells invade and disrupt
During S phase, (synthesis phase) a cell must copy its surrounding tissues (and are diagnosed as cancer).
chromosome and the entire DNA it contains. • Metastasis: spread of malignant tumor cells throughout the
• Mitosis: Mitosis involves the dividing of the nucleus and body (typically through the blood and lymphatic system).
the surrounding cell. Mitosis occurs after the successful • Cell cycle: proliferating cells undergo G1, S, G2 and M
replication of the cell’s DNA. During mitosis, the parent phase for cell division, the process is controlled by a set of
DNA and copied DNA must be separated. Following this proto-oncogenes and tumor suppressor genes.
event, the cytosol and cell membrane divide during • Differentiation: Cells reduce proliferation and become
cytokinesis. certain type of cell performing certain function.
• Programmed Cell Death: Programmed cell death is a Differentiation correlates with loss of ability to proliferate.
mechanism used by the body to remove unwanted cells as • Stem cell: cells divide without undergoing differentiation,
part of normal development, injury and disease. It is the and capable of self-renewal.
deliberate suicide of a cell that is highly regulated and
quite different from necrosis, which includes inflammation
and accidental cell death. A family of proteolytic enzymes CANCER DUE TO ACTION OF DNA REPAIR GENES
called caspases mediates programmed cell death. These
caspases are stored in cells as inactive pre-caspases Mutagens or
Malignant
Transformation
DNA Replication
Mutated DNA
Repair genes
Proto-oncogene CELL
PROLIFERATION DNA damages

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

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