1. Microbial genetics
Bio 433
By
Dr. Mona Othman Albureikan

2. The relationship between genotype and phenotype
• Genotype refers to the complete
genetic makeup of an organism.
• Phenotype refers to the expression of a
gene or genes carried by an organism.
• Genotype directs phenotypic
expression, but since all genes are not
expressed all of the time, genotype is
not always expressed as phenotype.

3. • Two examples are lactose
catabolism in E. coli and
ecophenotypic expression
of pigment in Serratia
marcescens.
The relationship between genotype and phenotype

4. • E. coli only produces the
enzyme b-galactosidase
(lactase) when lactose is
present.
• When lactose is depleted or not
present, the sequence of genes
controlling enzyme production
is shut down.
The relationship between genotype and phenotype

5. • S. marscescens produces the
red pigment (Prodigiosin)
when incubated at a
temperature range between
25 and 30 oC.
• When incubated at 37 oC, the
pigment is not produced or
produced very little.
The relationship between genotype and phenotype

6. Transcription (Transcription unit)
The structure of gene

7. • A promoter is a region of DNA that initiates transcription of a particular
gene.
• Promoters are located near the transcription start sites of genes, on the same
strand and upstream on the DNA (towards the 5' region of the sense strand).
Transcription (a promoter)

8. • In eukaryotes, they are found at -30, -75, and -90 base pair.
• In prokaryotic, approximately -10 and -35 nucleotides upstream from
the transcription start site.
Transcription (a promoter)

9. • A transcription terminator is a section of nucleic acid sequence that marks
the end of a gene or operon in genomic DNA during transcription.
Transcription (a promoter)

10. Transcription
• Transcription is the first step of gene xpression.
• The template for transcription is DNA.
• The product of this process is messenger RNA (mRNA).
• The enzymes responsible for transcription in both prokaryotic and
eukaryotic cells are called DNA-dependent RNA polymerases, or
simply RNA polymerases.

11. • Transcription proceeds in the nucleus in eukaryotics ; in the cytoplasm
in procaryotes.
• The mechanism of transcription has parallels in that of DNA
replication.
• Unlike DNA replication, in which both strands are copied, only one
strand is transcribed.
Transcription

12. • The strand that contains the gene is called the sense strand, while the
complementary strand is the antisense strand.
• The mRNA produced in transcription is a copy of the sense strand,
but it is the antisense strand that is transcribed.
Transcription

13. Four different type of RNA can be transcribed from DNA:
1. Primase - primer RNA used to initiate DNA replication.
2. Messenger RNA (mRNA) - used to carry the instructions about polypeptide
structure to the site of translation.
3. Ribosomal RNA (rRNA) - part of the ribosome, used in the construction of
polypeptides.
4. Transfer RNA (tRNA) - carry amino acids to the site of translation.

14. The three steps of transcription

15. Steps of Transcription
• Transcription begins when an RNA polymerase binds to a promoter
site on the 5' to 3' DNA.

16. • A small polypeptide portion of the RNA polymerase molecule called
the sigma factor recognizes the promotor site sequence.
• A short leader sequence of about 10 DNA nucleotides separates the
promoter from the actual gene sequence.
Steps of Transcription

17. • The RNA polymerase molecule untwists and separates the hydrogen
bonds between the two DNA nucleosides.
• Triphosphate ribonucleotides (rATP, rUTP, rGTP and rCTP) are joined
to their complementary bases on the DNA (A-U, G-C).
Steps of Transcription

18. • As the growing mRNA strand is synthesized, it detaches from the
DNA.
• This process continues until
RNA polymerase reaches
a terminator sequence of guanines
and cytosines, followed by
a repeating sequence of adenines.
Steps of Transcription

19. Steps of Transcription
• Since guanine forms three hydrogen bonds
with the cytosine on the DNA template, it
takes longer for the RNA polymerase to
join these.

20. • A loop forms in the guanine-rich portion of mRNA, putting strain on the
adenine-rich portion behind it, causing the molecule to separate from the
DNA strand and releasing the RNA polymerase.
Steps of Transcription

21. • Another way transcription is terminated is
called Rho-dependent, since it depends on a
protein called Rho, located near the end of
the mRNA transcript.
• The Rho protein moves along the mRNA
until the termination sequence is reached,
separating the DNA strand from the mRNA
transcript and the RNA polymerase enzyme.
Steps of Transcription

22. Transcription (termination)
Termination (a hairpin loop terminator) - type 1 terminator;
• RNA moves pass the inverted
repeats and transcribes the
termination sequence.
• Because of the inverted repeat
arrangement ➔ RNA synthesized
forms a hairpin loop structure.
• Hairpin loop makes the RNA
polymerase slow down and eventually stops.

23. Termination (a hairpin loop terminator) - type 1 terminator
• RNA polymerase can not continue
attached to DNA.
• RNA polymerase dissociate.
Transcription (termination)

24. Transcription (termination)
Termination (Rho-dependent terminator) – type 2 terminator
• Terminator is a sequence rich
in C (C-rich) and poor in G (G-poor).
• Terminator DOES NOT form
a hairpin loop.
• Rho (protein) binds to C-rich sequence
upstream of the termination site.

25. Eukaryotic transcription differs from that of bacteria
in several ways:
1. RNA synthesis in eukaryotes occurs primarily in the nucleus, with the
exception of RNA produced in the mitochondrion or chloroplast.
2. Eukaryotes have three different types of nuclear RNA polymerase,
one for the synthesis of mRNA, one for the major rRNA gene and one
for tRNA and smaller rRNA molecules.

26. 3. At least five different transcription factor proteins assist the binding
of eukaryote RNA polymerase to promoter sequences (bacteria only use
a single sigma factor).
- These are removed following initiation of transcription and replaced by
proteins called elongation factors (not found in bacteria).
Eukaryotic transcription differs from that of bacteria
in several ways:

27. A sigma factor (σ factor)
• A sigma factor (σ factor) is a protein needed only for initiation of RNA
synthesis. It is a bacterial transcription initiation factor that enables
specific binding of RNA polymerase to gene promoters. The specific
sigma factor used to initiate transcription of a given gene will vary,
depending on the gene and on the environmental signals needed to
initiate transcription of that gene.

28. Eukaryote mRNA undergoes RNA processing (pre-
translational modification) prior to translation:
a. The 5' end of the mRNA transcript
has a guanine nucleotide added during
elongation. This is called capping.
b. At termination, proteins remove the
mRNA transcript and adds 200
adenines to the 3' end. This is
called polyadenylation.

29. c. Capped and polyadenylated mRNA is
called premessenger RNA, since it contains
intervening sequences of RNA that do not code
for the placement of amino acids. These "junk"
sequences are called introns and they separate
usable portions called "expressed" sequences
or exons. Introns are removed from the mRNA
by small rRNA molecules
called spliceosomes or "ribozymes."
Eukaryote mRNA undergoes RNA processing (pre-
translational modification) prior to translation:

30. - Prokaryotes often exhibit concurrent RNA transcription.
- In this process several RNA
polymerase molecules attach to the
initiation sequence one after
another forming a polyribosome complex.
- In this way, multiple copies of the same mRNA molecule can be made from
the same gene or set of genes.
Transcription (Prokaryotes )

31. References
 Molecular Genetics of Bacteria ( 4th Edition ) (2013), Larry Snyder , Joseph E. Peters , Tina M. Henkin , Wendy
Champness ISBN 10: 1555816274 ISBN 13: 9781555816278.
 Molecular Genetics of Bacteria, 5th Edition, by Jeremy W. Dale, Simon F. Park ,April 2010, ©2010.
 Genetics of Bacteria, Sheela Srivastava,(2013) ISBN: 978-81-322-1089-4
 Microbial Genetics. (1994). Jones and Bartlett Series in Biology. Jones and Bartlett Publishers, Inc.; 2nd
edition, ISBN-10: 0867202483, ISBN-13: 978-0867202489, 484 pages.
 Microbial genetics. (2008). Jones and Bartlett series in biology
Series of books in biology. David Freifelder, publisher, Jones and Bartlett, 1987. 601 pages.
 Molecular Biology: Genes to Proteins Hardcover . (2007). Burton E. Tropp, Publisher: Jones & Bartlett Publishers; 3
edition, ISBN-10: 0763709166, ISBN-13: 978-0763709167, 1000 pages .