Molecular Cell Biology Core Concept Master Cheat Sheet
O1: Introduction Molecular Cell Biology
• Molecular Biology is the study of the replication,
transcription, & translation of genetic material within a cell.
Manipulation of these processes is also known as molecular
biology or recombinant DNA techniques.
• Macromolecules- there are four main classes of
macromolecules: lipids, proteins, carbohydrates, and nucleic
acids.
• Deoxyribonucleic acid (DNA)- double helix chains of
paired bases containing thymine, cytosine, guanine, and
adenine.
• Ribonucleic acid (RNA)- the intermediate between DNA
and proteins.Proteins- chains of amino acids coded for by
genes in the DNA.
Transcritpion: DNA is transcribed into RNA and special
pairing of bases dictates which sequence is made.
02: The Cell
• Cell: The smallest unit of an organism that can live
independently.
• Cell Theory: an explanation of the role of cells in
relationship to living things. · Prokaryotic Cell: The
smallest unit of life for prokaryotic organisms such as
bacteria and other microbes.
• Eukaryotic Cell: The smallest unit of life for eukaryotic
organisms such as animals.
• Nucleolus: a “tiny nucleus” inside the nucleus, which
contains RNA.
• Nuclear Envelope: a protective layer, which surrounds the
nucleus.
• Nuclear Pore: holes in the nuclear envelope that allow the
nucleus to exchange information with the rest of the cell.
• DNA: a nucleic acid, an organic macromolecule.
• RNA: a nucleic acid, an organic macromolecule.
• Cytoplasm: the liquid space inside of a cell.
• Organelles: specialized cell structures, which perform
specific functions.
• Cell Membrane: a protective bilayer of lipids, which allows
the cell to maintain a stable internal environment.
Lysosome Nucleus
Ribosomes
Smooth
Endoplasmic
Reticulum
Mitochondria
Rough
Endoplasmic
Reticulum
Golgi Apparatus
Plasma Membrane
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03: Cells: The Chemical Foundations
• Organic chemicals: contain covalently bonded carbon
backbones.
• Isomers: chemicals with the same molecular formula but
different structural formulas.
• Buffers: solutions, which resist changes in pH upon addition
of small amounts of acid or base.
• Electrolytes: chemicals that release ions into solutions.
• pH: pH represents the concentration of hydrogen ions [H+]
in solution (scale 1-14, pH 7=neutral). pH = -log [H+]
• Acids: release H+ into solution, pH < 7
• Bases: release OH- that can combine with H+ to make
water, pH > 7
• Enzymes: proteins that serve as catalysts for biochemical
reactions.
• Entropy: a measure of a system's degree of disorder. It
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
Free energy Ea
Reactants + Enzyme
ΔG
Products
04: The Macromolecules
• Macromolecule: A molecule having a molecular weight in
the range of a few thousands to many millions.
• Functional group: The specific atom or group of atoms that
confers a particular chemical property on a biomolecule.
• Organic Compounds: Molecules containing covalently
bonded carbon backbones are called organic compounds.
• Monosaccharide: A carbohydrate consisting of a single
sugar unit.
• Disaccharide: A carbohydrate consisiting of two covalently
joined monosaccharide units.
• Polysaccharide: A linear or branched polymer of
monosaccharide units linked by glycosidic bonds.
Potential
l l
ABCD BACD
CABD DABC
Monomers
ABDC BADC A,B,C,D
CADB DACB
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 05: Protein Structure and Function
• Antibody: A specific protein that interacts with a foreign
substance (antigen) in a specific way.
• Beta-sheet (ß-sheet): A sheet like structure formed by the
interaction between two or more extended polypeptide
chains.
• Cytoskeleton: The filamentous skeleton, formed in the
eukaryotic cytoplasm that is largely responsible for
controlling cell shape.
• Dalton: A unit of mass equivalent to the mass of a
hydrogen atom (1.66 x 10-24 g)
• Disulfide Bridge: A covalent linkage formed between two
cysteine-SH groups either in the same polypeptide chain or
in different polypeptide chains.
• Enzyme: A molecule, most often a protein that contains a
catalytic site for a biochemical reaction.
• Globular protein: A folded protein that adopts an
approximately globular shape. May also be called soluble
proteins.
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.
• G band and Q band: Bands shown on chromosomes after
various treatments and staining technique. Same
chromosome from one specieis always show same banding
pattern.
• FISH: fluorescence in site hybridization. A fluorescence
labeled DNA fragment (probe) is hybridized to a
chromosome therefore a gene can be located to a
chromosome.
• Nucleosome: A bead-string structure formed by DNA and
histones, the basic DNA structure in a chromatin.
• Chromatin: The general structure of any chromosome, the
basic units is nucleosomes.
• Chromatid: One-half of a replicated chromosome.
• Histone: structure proteins for nucleosome, including H1,
H2A, H2B, H3 and H4 types.
• Chromosome: The unit of inheritance with the basic
structure of arms, a centromere and two telomeres.
• Euchromatin: Chromatin region stained lightly, usually are
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.
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07: DNA Structure and Function
• Nucleoside: Compounds with a ribose or deoxyribose and a
base. Base includes four types G, C, A and T (or U).
• Nucleotide: Compounds with a ribose or deoxyribose, a base
and a phosphate group, it is the basic building unit for DNA
(monomers of DNA).
• Pyrimidines: A type of base, including both cytosine and
thymidine.
• Purines: A type of base, including both guanine and
adenine.
• Tm: Melting temperature of DNA. DNA is a double helix
molecule, when heated, the two strand separate from each
other (melting) and the absorbance at 260 nm increases.
When half of the DNA is in single strand status, the
temperature is called the DNA’s Tm.
• Denature: The hydrogen bonds break between the two
strands of the DNA molecule, can be caused by heat or pH.
• Renature: The denatured DNA restore the double helix
structure and re-form hydrogen bonds.
08: Transcription, Translation and The
Genetic Code
• mRNA: A messenger between DNA and protein, made from
DNA template (transcription) and then directs the protein
synthesis.
• tRNA: Transfer RNA, carry amino acid to protein synthesis
site.
• rRNA: Structure RNA of ribosomes where proteins are
synthesized.
• microRNA: miRNA, have mismatch to mRNA, but they bind
to mRNA, leading to mRNA degredation or block mRNA
translation.
• Template strand: The transcribed DNA strand, with
sequence complementary to mRNA sequence.
• Non-template strand: Not transcribed, sequence is identical
to mRNA, also called coding strand.
• Promoter: A DNA sequence having a regulatory function
over the transcription of an adjacent gene, and to which RNA
polymerase binds prior to transcription.
miRNA
Dicer
Degredation Block Translation
 09: Control of Gene Expression in
Prokaryotes
• Promoter: A DNA sequence having a regulatory function
over the transcription of an adjacent gene, and to which
RNA polymerase binds prior to transcription.
• Pribnow Box: A conserved promoter sequence located at-
10 position of mRNA, usually is TATAA, also called TATA box,
the function is for transcription factor binding.
• Operon: consist of two or more adjacent coding regions
that are controlled by the same transcription factors.
• Polycistronic: The structure genes of an operon are
transcribed as a single mRNA molecule containing multiple
genes.
• Structure genes: The genes in an operon that encodes the
enzymes necessary for a metabolic pathway.
• Regulatory genes: The genes in an operon that play
regulatory roles, acting as either repressors or activators.
• Cis-acting element: DNA sequences in the vicinity of the
structural portion of a gene that are required for gene
expression. Operator sequence and promoter sequence are
cis-acting elements.
• Trans-acting elements: Factors that bind to the cis-acting
sequences to control gene expression, for example, RNA
polymerase, TFs, repressors.
TrpR p o TrpL TrpE TrpD TrpC TrpB
mRNA
mRNA
no Trp,
no bind
Repressor R Trp synthesis
10: Regulation of Gene Expression in
Eukaryotes
• Promoter: A DNA sequence having a regulatory function
over the transcription of an adjacent gene, and to which
RNA polymerase binds prior to transcription.
• Enhancer: a short region of DNA that can be bound with
proteins to promote expression of a distal or proximal gene.
• TATA Box: Binds to transcription factor for regulating gene
expression, usually within 30bp of the transcription start
site.
• Basal Transcription Factor: Transcription factors that are
required for all transcriptions, they unwind DNA and assist
RNA polymerase to bind to transcription initiation sites.
• Modulatory Transcription Factor: Transcription factors
that regulate time/space expression, may bind to enhancers
or to promoter regions to enhance or suppress gene
expression under certain conditions.
• DNA binding domain: A domain found in all transcription
factors, used to bind DNA, inclding three types: Zinc-finger,
HLH and leucine zipper.
• Zinc-Finger: A structure found in a number of transcription
factors, has repetitive two cystein and two histidine to bind a
Zn, and form a “finger” structure.
• Leucine-zipper: A structure found in a number of
transcription factors, characterized by leucine residue at
every other turn of helix, 7 amino acid apart.
TATA
Enhancer Promoter Box Transcription starts
Exon Intron
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11: Recombinant DNA Technology
• Recombinant DNA: a DNA molecule that is made from two
different sources and often manipulated in a test tube and a
host cell.
• cDNA: complementary DNA, the DNA synthesized from a
mature mRNA template. cDNA is often used to clone genes.
• Genomic DNA: DNA isolated from organisms, containing all
DNA in the genome of a cell or an organism.
• PCR: polymerase chain reaction, a molecular biology
technique using DNA polymerase, template DNA and primers
to synthesize specific DNA fragments.
• Restriction Endonuclease: an enzyme that cuts double-
stranded DNA within the molecule.
• DNA vector: an agent that can carry a DNA fragment into a
host cell and ensure its replication and sometimes,
expression.
• Cloning vector: A vector that carries DNA into a host cell for
replication.
• Expression vector: A vector that carries DNA into a host
cell and express the DNA into its final protein product.
Digest with same restriction enzyme BamH I
Sticky ends
TrpA
Anneal
seal with DNA ligase
Recombinant DNA
12: Genomics
• Genomics: the study of an organism's entire genome,
usually starts with whole genome sequencing.
• BAC: bacterial artificial chromosomes, which is based on F
plasmid and can tolerate large inserts, widely used in
genomic DNA library construction.
• BAC library: large genomic DNA fragments ligated into BAC
vectors.
• Shot gun sequencing: Genomic DNA from a BAC clone is
fragmented into smaller size, typically 1kb, and inserted into
a sequencing plasmid. These sequences are then assembled
based on the overlapping fragments.
• Sequence assembly: a computer-based approach to put
together all the genomic DNA sequence together, starting to
put together a BAC sequence first.
• Human Genome Project (HPG): Divided into two groups
based on different funding resource: public sector and Celera
private sector. The purpose is to obtain all genetic
information from humans.
• Functional Genomics: Use the sequence data to explore
how DNA and proteins work with each other and the
environment to create complex, dynamic living systems.
Procedure O verview
„ Step 1: BAC library Chrom osom e
construction
„ Step 2: Shot gun
sequencing
„ Step 3: Sequence
assem bly BAC library
Enhancer
Shot Gun Sequencing
Sequence Assem bly
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 13: Membrane Structure
• Membrane Structure: Maintains and protects cellular
contents, provides for electrochemical gradients, dynamic
and flexible enough to allow cell shape changes and cell
movements, supports membrane bound proteins, which are
involved in cell signaling and growth and differentiation.
• Phospholipids: make up the major portion of membranes
in cells. They are Amphipathic molecules, which means they
have both a hydrophobic (water fearing) and a hydrophilic
(water loving) component.
• Phospholipid Bilayer: By forming a bilayer, the
hydrophobic tails can interact with each other and the
hydrophilic heads can interact with water molecules in the
surrounding fluid.
• Cell Membrane: is made up of phospholipids, glycolipids,
cholesterol and proteins. A cell membrane is approximately
5 nm thick and is a fluid dynamic structure.
• Cholesterol: is very prominent in the membranes of cells; it
inserts itself within the bilayer. Cholesterol enhances the
permeability-barrier properties of the cell membrane.
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
carbon dioxide.
• Facilitated Diffusion: is carried out by a carrier protein or
channel protein and transports the molecule passively, down
its concentration gradient.
• Active Transport: is the process by which a carrier protein,
also known as a pump, facilitates the movement of a
molecule against its concentration gradient. This process
requires metabolic energy from ATP hydrolysis.
• Na+-K+ Pump: utilizes the energy released from ATP
hydrolysis to transport Na+ and K+ ions against their
concentration gradients. This pump is responsible for the
membrane electrical gradient inside relative to outside the
cell.
• Ion Channels: Exist in either an open or closed state. The
different types of channel proteins are: (A) Voltage-gated
channels, (B) Ligand-gated and (C) Nucleotide-gated
channels.
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15: Cellular Energetics
• Glycolysis: Glycolysis is a pathway in which a molecule of
glucose is oxidized into two molecules of pyruvic acid.
Glycolysis takes place in the cytosol of the cell.
• Electron Transport: a series of redox reactions take place,
in which one molecule is reduced (gains an electron) and the
next is oxidized (gives up an electron). At each step, a Proton
(H+ atom) is pumped across the mitochondrial membrane,
creating the concentration gradient used by the enzyme ATP
Synthase.
• NADH: is an important electron transporter in the respiratory
chain enzyme complexes. NADH is the reduced form of
NAD+, and NAD+ is the oxidized form of NADH.
• Oxidative Phosphorylation: involves the phosphorylation of
ADP to form ATP. These reactions depend on the H+ proton
gradient that is created during the events of the respiratory
chain. ATP Synthase is an enzyme also known as the F0F1
ATPase.
• Photosynthesis: utilizes the energy from sunlight to
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.
16: Intracellular Compartments
• Intracellular Compartments: Cells contain many special
compartments, known as organelles. There are many crucial
enzymatic and non-enzymatic processes necessary for cell
survival that take place in or on lipid membranes.
• Nuclear Protein Import: Proteins that are targeted for the
nucleus contain a nuclear localization signal. Nuclear import
receptors bind the nuclear localization signal portion of the
protein and facilitate its transport into the nucleus.
• Intracellular Protein Transport: There are 3 main ways in
which proteins are transported within cells: (A) Gated
transport, (B) Transmembrane transport and (C) Vesicular
transport.
• Posttranslation Translocation: Proteins are imported
through multi-subunit protein complexes, known as
translocators; both the insertion of the protein into the
translocator and the exit on the opposite side of the
membrane requires energy.
 17: Intracellular Vesicular Traffic
• Molecular Mechanisms of Coated Vesicles: Most vesicles
bud off from a region of the membrane that has a unique
protein coat (cage). There are 3 different types of protein
coats used by cells: (A) Clathrin-coated, (B) COPI-coated
and (C) COPII-coated vesicles.
• COPI and COPII-Coated Vesicles: COPI-coated vesicles
transport cargo from the cis end of the golgi complex to the
endoplasmic reticulum (ER), called retrograde transport.
COPII-coated vesicles transport cargo from the endoplasmic
reticulum to the golgi complex, called anterograde
transport.
• ER-Golgi Transport: Proteins that are targeted for the
golgi complex are packaged into COPII-coated vesicles.
Vesicles bud from special ER regions, called RE exit sites;
these sites usually do not contain ribosomes.
• Golgi-Lysosome Transport: Mannose 6-phosphate (M6P)
is a lysosomal sorting signal. Proteins that are destined to
reside in the lysosome, such as lysosmal hydrolase, are
tagged with a M6P.
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.
• Endocrine Signal: Specialized cells release molecules
(often hormones) into blood vessels of circulatory system,
hormones move to distant target cells.
• Signal receptors: often membrane proteins that can bind
signal molecules from cell surface except for intracellular
receptors, which is localized in cytosol.
• RTK: receptor tyrosine kinase, numerous typs but oftern
include receptors for growth factors. It has intrinsic tyrosine
kinase activity and is capable of self activation by
phosphorylation and dimerization.
• GPCR: G-protein coupled receptors, usually has 7
transmembrane domain and has an intracellular domain to
bind signal molecule and a cytosol domain to bind G protein.
• G Protein: A huge class of proteins that bind to guanine
nucleotide GDP and GTP, usually hetertrimers and associate
with GPCR or cytosol side of cell membrane. Upon signal
binding by a GPCR, it undergoes a conformational change
and hydrolizes GTP to activate the downstream targets.
Signal
Receptor
Reception
Cell
Transduction
membrane
Transducer
Effector
Response
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19: Cell Signaling Pathways
• Cell Communication: Cells interpret incoming signals in
order to: secrete molecules, move location and proliferate
into new cells.
• Forms of Signaling: Secreted molecules can mediate 3
forms of signaling: Paracrine - secreted molecules can
diffuse a short distance in the extracellular matrix and then
be taken up by adjacent cells, Autocrine - secreted
molecules can act on the cell they were released from and
Endocrine: molecules secreted into the bloodstream, which
are then carried to the target cells and diffuse out into the
tissue.
• G-protein Linked Cell-Surface Receptors: G-protein
receptors exist in the plasma membrane of many cell
types; they have an extracellular domain - where the
receptor binds molecules outside of the cell and initiates the
signal transduction and an intracellular domain - interact
with G proteins and stimulate their activation through
binding of ATP.
• 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.
20: Cytoskeleton and Cellular Motility
• Cytoskeleton: provides dynamic structure and support for
cells, which is reorganized frequently, and provides and
maintains cell shape.
• Cytoskeleton Functions: facilitates intracellular movements
including: Vesicle Transport, and Chromosome Segregation.
• Actin Filaments: also known as microfilaments are
organized into bundles just underneath the plasma
membrane. Actin filaments, along with motor proteins such
as myosin, are reorganized as cells change their shape and
move.
• Intermediate Filaments: are made up of various
intermediate filament proteins including: keratins, vimentin,
neurofilament proteins and nuclear lamins, and share the
same long rope-like structure and are prominent around the
nucleus and extend out towards the periphery of the cell.
• Microtubules: are long, hollow tube-like cylinders, which are
made up of the protein tubulin, and are involved in vesicle
and organelle movement within cells. ·
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 21: The Cell Cycle and Programmed Cell
Death
• Cell Cycle: The Cell Cycle is made up of 4 distinct phases:
(1) Gap 1 (G1), (2) S Phase, (3) Gap 2 (G2) and (4) M
Phase (Mitosis).
• G1: In cells that are actively cycling through the cell cycle,
G1 is when the cell monitors its environment and size.
During this time the cell grows.
• S Phase: In order for a cell to divide successfully, it must
copy its entire DNA to be able to supply 2 daughter cells.
During S phase, (synthesis phase) a cell must copy its
chromosome and the entire DNA it contains.
• Mitosis: Mitosis involves the dividing of the nucleus and
the surrounding cell. Mitosis occurs after the successful
replication of the cell’s DNA. During mitosis, the parent
DNA and copied DNA must be separated. Following this
event, the cytosol and cell membrane divide during
cytokinesis.
• Programmed Cell Death: Programmed cell death is a
mechanism used by the body to remove unwanted cells as
part of normal development, injury and disease. It is the
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
called caspases mediates programmed cell death. These
caspases are stored in cells as inactive pre-caspases
23: Cancer
• Cancer: The general name for over 100 medical conditions
involving uncontrolled and dangerous cell growth.
• Oncogenesis: process of initiation of tumors (cancer) in an
organism.
• Tumor: tissue composed of cells that deviate from normal
program of cell division and differentiation.
• Benign tumor: tumor cells remain together in a single
mass and do not invade or disrupt surrounding tissues.
• Malignant tumor: tumor cells invade and disrupt
surrounding tissues (and are diagnosed as cancer).
• Metastasis: spread of malignant tumor cells throughout the
body (typically through the blood and lymphatic system).
• Cell cycle: proliferating cells undergo G1, S, G2 and M
phase for cell division, the process is controlled by a set of
proto-oncogenes and tumor suppressor genes.
• Differentiation: Cells reduce proliferation and become
certain type of cell performing certain function.
Differentiation correlates with loss of ability to proliferate.
• Stem cell: cells divide without undergoing differentiation,
and capable of self-renewal.
CANCER DUE TO ACTION OF DNA REPAIR GENES
Mutagens or
Malignant
Transformation
DNA Replication
Mutated DNA
Repair genes
Proto-oncogene CELL
PROLIFERATION DNA damages

Repaired DNA

22: The Mechanics of Cell Division
• Mitosis: Mitosis involves the dividing of the nucleus and the
surrounding cell. Mitosis occurs after the successful
replication of the cell’s DNA.
• Prophase: the normally loosely packed chromatin is
condensed into the chromosome. The two centrosomes
(Mitotic Spindle) begin to extend microtubules, in
preparation for attaching to the chromosomes.
• Metaphase: the chromosomes are aligned at the center of
the cell at a region called the metaphase plate. Each of the
sister chromatids (2 per chromosome) are attached to
opposite poles of the mitotic spindle.
• Anaphase: There are many proteins that make up the
anaphase promoting complex. This complex plays a key role
in allowing the cell to successfully separate the sister
chromatids in the 2 future daughter cells.
• Cytokinesis: Eventually, as cytokinesis progresses, the
cleavage furrow deepens until the plasma membrane and its
contents are divided.
24: Immunology
• Immune System: It is a unique adaptive defensive system
that has evolved in vertebrates to protect them from
invading pathogenic microorganisms and cancer.
• Immunity: All those physiological mechanisms that endow
the animal with the capacity to recognize materials as
foreign to itself and to neutralize eliminate or metabolize
them with or without injury to its own tissues.
• Antigen: Any substance (usually foreign) that bind
specifically to an antibody or a T cell receptor.
• Antibody: A protein (immunoglobulin) that recognizes a
particular antigen and binds specifically to it.
• Innate immunity or native immunity: It is the resistance
to infections, which an individual possesses by virtue of his
genetic and constitutional make-up. It is not affected by
prior contact with microorganisms or immunization.
• Adaptive immunity or acquired immunity: It is the
resistance that an individual acquires during life, as distinct
from the inborn innate immunity. Adaptive immune
responses exhibit four immunological attributes: Specificity,
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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