 A genome is the entirety of the genetic material of a

cell or an organism
 The genome comprises coding sequences (genes) and non-
coding sequences
 E. coli: ~ 4,300 genes
 Homo sapiens: ~20,000 genes

 A gene is expressed when its functional product is

manufactured and present in the cell in an active
form.
 Not all genes are expressed all the times:
 Constitutive genes
 Expressed all the times
 Controllable genes
 Expressed only in particular situations
 Prokaryotes:
 Lactose metabolism
 Tryptophan metabolism
 Eukaryotes: All cells contain the whole
genome. Genes are selectively expressed:
 Response to pathogens
 Control of cell cycle
 Development
https://www.youtube.com/watch
?v=SMtWvDbfHLo
 Eukaryotic RNA polymerase binds to basal promoters. Basal
promoters always contain the TATA box. However RNA
polymerase alone cannot initiate transcription of a gene.
 It is dependent upon the binding of transcription factors at
the promoter. Transcription factors are protein that bind DNA
and/or other transcription factors and allow or block the
binding of RNA polymerase.
 Some transcription factors are the same for ALL proteins
others are quite specific. Only when a complete initiation
complex is assembled on a promoter, RNA polymerase can
bind and initiate transcription.
TATA Box
 Core transcription complex

TFIID TATA-binding protein (TBP) Other transcription factors

associated proteins (TAFs)

TAFs
TATA TBP

Promoter-proximal
element
Start site
Promoter
RNA
Polymerase II
Binding of specific
activators
Different enhancers may
control expression in
different tissues
https://www.youtube.com/watch
?v=SMtWvDbfHLo
 Signal Transduction SIGNALING CELL Signal

Pathways in 1
molecule
Plasma
Receptor
Eukaryotes 2 protein membrane

3
1. Signaling cell secretes signaling molecule
(ie. hormone). The signal could also be a TARGET CELL
molecule on the surface of another cell. Relay
2. Signaling molecule binds and activates a proteins
specific receptor
3. Activated receptor activates relay protein
Transcription factor 4
#1, which gets activated and in turn
(activated)
activates relay protein #2 and so on…
4. At the end of the pathway a transcription
factor will be activates NUCLEUS
5. Activated transcription factor translocates
into the nucleus and promotes DNA
transcription of target gene(s) 5 Transcription
mRNA
New
protein

6
Translation
Proteins Along a Signaling Pathway Are
Activated by Phosphorylation

REMEMBER?????
 To any given stimulus there is usually a complex set
of responses coordinated by the proteins expressed
by the cell.
 Example: response to injury
 To any given stimulus there is usually a complex set
of responses coordinated by the proteins expressed
by the cell.
 Example: response to injury;
 Repair wound-Cells must divide, thrombin must be
activated, platelets must reach the wound site, cells
surrounding the wound must divide, new blood vessels
must be rebuilt..
 Fight infection-White blood cells must reach the site of
infection, blood vessels dilate, infectious agents must be
recognized, phagocytosed and carried to the LN, white
blood cells need to change shape, cytokines and
chemokines must be secreted….
Toll-Like Receptors Receptors
 RNA interference employs miRNAs (micro,
interfering RNA) to “turn off” genes in eukaryotes.
 miRNAs are small (~20 bases) single-stranded
regulatory RNAs capable of interfering with the
translation of messenger RNAs that contain either
complete or partial complementarity.
 RNA interference can also employ another kind of
interfereing RNAs, siRNAs. In this lecture we will
only cover miRNAs.
Chromosome

Gene for
miRNA
 1. Transcription of micro-RNA genes produces an 80 base molecule that folds into a
stem-loop structure called pre-mi-RNA
2. The pre-mi-RNA is transported to the cytoplasm
3. In the cytoplasm double stranded RNA is recognized by the enzyme Dicer
4. Dicer cuts the pre-mi-RNA into small fragment of single stranded RNA generating
(si) RNAs
5. (si) RNAs block expression of homologous genes in two ways:
a. Form a complex with mRNA through imperfect complementary base binding
and block translation
b. Form a complex with mRNA through perfect complementary base binding and
target the RNA for degradation

NB. Micro RNAs are also used by cells to interfere with viral gene expression.
 Specific genes
 Spliced introns
 Some miRNAs are encoded by specific genes and are
transcribed as ~80 bases long molecules of RNA that
fold into a specific three-dimensional structure
(stem-loop). The 3D molecule is then processed to
give rise to the single stranded interfering RNA
 The human genome has approximately 1,000 genes
for micro-RNAs
 siEbola-3 LNP treatment confers survival and reduces viral load.

EP Thi et al. Nature 000, 1-4 (2015) doi:10.1038/nature14442