UMS Spring Semester 2014
Molecular genetics
 Definition(s)
 A reading frame is a sequence of nucleotides in DNA that contains no termination codon
and so can potentially translate as a polypeptide chain
 An ORF begins with a start codon and contains no stop codon for a distance long enough to
encode a protein
 EST is: A short sub-sequence of a cDNA sequence, they may be used to identify gene
transcripts, and are instrumental in gene discovery and gene sequence determination.
 comparative genomics: Analyzing & comparing genetic material from different species to
study evolution, gene function, and inherited disease.
Understand the uniqueness between different species
 Solitary genes: About 25-50 percent of the protein-coding genes are represented only once
in the haploid genome
 Duplicated genes: These genes are close but non-identical sequences that often are located
within 5-50 kb of one another called “gene family”
 Gene family: A set of duplicated genes that encode proteins with similar but not identical
amino acid sequences
 Low-complexity regions are often defined as regions of biased composition containing
simple sequence repeats
 Genetic linkage is the tendency of genes that are located close to each other on a
chromosome to be inherited together during meiosis.
 A chiasma (plural: chiasmata), in genetics, is thought to be the point where two
homologous non-sister chromatids exchange genetic material during chromosomal
crossover during meiosis (sister chromatids also form chiasmata between each other, but
because their genetic material is identical, it does not cause any change in the resulting
daughter cells)
 Single Nucleotide Polymorphisms (SNPs) in the human genome are the change of single
nucleotides at a particular loci.
 A single-base sequence variation between individuals at a particular point in the genome
called SNPs (pronounced as snip).
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Choose the right answer
1.
2.
3.
4.
A reading frame contains all the following except
(A) start codon
(B) stop codon
(C) termination codon
An open reading frames starts with
(A) AGT
(B) ATG
(C) TAG
(D) TAG
ORF is defined as a stretch of DNA containing at least
(A) 100 bp
(B) 200
(C) 210
(D) 300
By scanning for “Open Reading Frame” (ORF), the genes in bacteria and yeast have
been identified
(A) more than 90%
5.
(C) 85%
(D) 99%
ESTs represent partial sequences of cDNA clones (300 bp -> 700 bp)
(A) (300 bp -> 700 bp)
bp)
6.
(B) 90%
(B) (300 bp -> 500 bp) (C) (400 bp -> 700 bp)
(D) (500 bp -> 700
ESTs represent all the following except
(A) portions of expressed genes.
(B) m RNA
(C) protein portion
(D) c DNA
more than 700 mouse genes—have counterparts in the human genome,
7.
Solitary genes: are found only once in the haploid genome and represented about
(a) 25-50% of the protein-coding genes
(b) 15-50% of the protein-coding genes
( c) 25-70% of the protein-coding genes
8. By comparing the genome compositions between genomes, scientists can better
understand (a) the evolutionary history of a given genome
(b) genome composition
( c) portions of expressed genes
(b) genome sequence
9- Sequences like ATATATACTTATATA are called
( a) low-complexity
(b) high -complexity.
(c) intermediate-complexity.
10- the α globin and β globin families are existed on different chromosomes through
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(a) Transposition
(b) duplication
( c) mutation
11 Transposable elements (transposons) contains all the following except
(a) Long interspersed elements (LINEs)
(b) Short interspersed elements (SINEs)
(c) Long terminal repeats (LTRs)
(d) Dead transposons
(e) Simple sequence repeats (SSRs)
Simple sequence repeats (SSR )contains
(a)
(b)
(c)
(d)
One- to six-nucleotide sequences repeated hunderds of times
one- to twenty -nucleotide sequences repeated hunderds of times
One- to six-nucleotide sequences repeated thousands of times
Six to ten -nucleotide sequences repeated hunderds of times
Introns cutting and splicing recognized by
(A) (snRNPs)
(B) SNPs
(C) HnRNA
(D) S m RNA
Each cell in our bodies has about
(A) 7 feet of DNA stuffed into it
(B) 12 feet of DNA stuffed into it
(C) 10 feet of DNA stuffed into it
(D) 6 feet of DNA stuffed into it
Which of the following is corrects
When eukaryotic DNA is fragmented and centrifuged to equilibrium in a Cesium chloride
(CsCl) density gradient, the following are
( a) One band only observed
(a) One main and plasmid bands
( b) one main band and satellite band
(b) Multiple bands
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Microsatellite, also called
A)
B)
C)
D)
transposable elements 1-13 bp.
Interspersed repetitive DNA dispersed throughout the genome
Highly repetitive DNA
Coding sequence
( A,B,D) , (B,C,D), (C,D,E) , (A,B,C)
IF NO CROSSING OVER IN REGION BETWEEN THE TWO GENES
a) 100% Non-Recombinants
b) 100% Recombinants
c) 50% Non-Recombinants & 50% Recombinants
The units of distance are called map units (mu), They are also referred to as centiMorgans
(cM) , One map unit is equivalent to
A) 1% recombination frequency
b) 10% recombination frequency
c) I00% recombination frequency
The nucleus of a human cell contains between
a)
b)
c)
d)
30 000 and 40 000 genes.
30 000 and 50 000 genes.
20 000 and 40 000 genes.
10 000 and 30 000 genes.
The human genome is identical to everyone else's by
a)
b)
c)
d)
99.9%
79.9%
90.9%
95.9%
Human mtDNA is
a) double stranded DNA
b) single stranded circular DNA
c) closed double stranded circular DNA
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a) Complete the following
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
Both very short genes and long genes are missed by …………………….method
……………. is powerful method for identifying human by comparing the human
genomic sequence with that of the ……………. since human and mouse are sufficiently
related to have most genes in common
In short, the human and mouse genomes are remarkably similar not only in the
……………………………… but also at the level of ……………………………..
The Celera team found that much of mouse chromosome 16 corresponds to human
chromosome ……………………. which contains genes involved in
……………………………….
Genome composition is used to describe the make up of contents of a
………………….., which should include : ……………………., proportions of
………………………… and ……………………………. in details.
Each gene family could contain from a few to 30 members
The genomes of prokaryotes are contained in ……………………….., which are usually
………………………………………
In contrast, the genomes of eukaryotes are composed of multiple chromosomes, each
containing a linear molecular of DNA.
Genome composition is used to describe the make up of contents of
…………………….., which should include :…………………….., proportions of nonrepetitive ……………………………. and ………………………….
Many genes occur as ……………………, can be clustered on the
…………………………. or scattered throughout ……………………………..
Larger genomes are generated by increasing the number ……………………………..
constitutive heterochromatin are localized to …………………………and
………………………
Simple sequence repeats (SSR )contains …………………………-nucleotide sequences
repeated ………………………….of times
Six major types of noncoding human DNA have been described, ………………,
…………………………, ……………………), ………………….., ………………..and
………………………………………….
Complex genomes have roughly …………………….. more DNA than is required to
encode all the RNAs or proteins in the organism or have any apparent regulatory
function
16. Length of tandemly repeated DNA in bp of regular satellite
…………………….., mini satellite ………………………… and for microsatellite
………………………………
17. When eukaryotic DNA is fragmented and centrifuged to equilibrium in a Cesium
chloride (CsCl) density gradient two components are observed:
……………., most of the genomic DNA, density of ……………..with a G-C content
of ………………….
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 Satellite band, …………………… band DNA. : one or multiple miner bands; has the
buoyant density of …………………. with a G-C content …………………..




Microsatellite, also called as …………………………. 1-13 bp, ………………….
repetitive DNA …………………….. throughout the genome
Most eukaryotic chromosomes have short, species-specific sequences tandemly repeated
called ……………………………
chromosome lengths are maintained by ……………………… which adds repeats
without using the cell’s regular replication machinery.
The ends of eukaryotic chromosomes are formed by an enzyme called
……………………………….Telomerase an enzyme adds repeats of 3´ ends of
eukaryotic chromosomes
 The chiasmata become visible during the …………………………… of prophase I of
…………………………, but the actual "…………………………" of genetic material is
thought to occur during the previous …………………….. stage.

 Eukaryotes can have Nuclear genome, Mitochondrial genome, Eukaryotes can
have………………………genomes.
……………..,
…………………………..
and
……………………….
If
not
specified,
“genome”
usually
refers
………………………………….
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Correct the following
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
Scanning of the ORF is a good method to identify eukaryotic genes .
researchers at Celera Genomics in Rockville, Maryland, provide the strongest evidence
that many genes in humans is not present in mice
Fourteen genes on mouse chromosome 16 are not found in humans
Duplicated genes are close but non-identical sequences that often are located within 550 kb of one another called “gene family”
Much of mouse chromosome 20, corresponds to human chromosome 16 which
contains genes involved in Down syndrome and similar disorders.
Identical genes include: rRNA and globin genes , Non-identical genes include histones
Heterogeneous nuclear RNA hn RNA is a transcript before splicing is complete
Introns, translated intervening sequences in m RNA
Introns contain invariant 5’-GU and 3’-GA sequences at their borders
the simple-sequence DNAs repeats are localized near the centromers and secondary
construction of mouse chromosome
Most Simple-Sequence DNAs are Concentrated in Specific Chromosomal Locations.
Satellite DNAs Lie in euochromatin
~3/4 of the human genome consists of interspersed repetitive sequences
If no crossing over, the alleles of all genes located different chromosomes would be
inherited together
The number of linkage groups is equal to the number of genes of the species
15. Two genes that carry out independent assortment have recombination frequency of 50
% and are located homologous chromosomes or far apart on the same chromosome =
un-linked
16. Genes with recombination frequencies more than 50 % are on the same chromosome
17. Eukaryotes can have 2-4 genomes. If not specified, “genome” usually refers to the
nuclear genome.
18.
Human mtDNA consists of approximately 20.5 kb , 37 genes , it is closed single
stranded circular DNA
19.
Triallelic SNPs are known to occur at a very high frequency within the
human genome
20- Two strand crossing over counted as single crossover
21- Three strand counted as no crossovers
22- Four strand crossing over is the only one counted as a double crossover, result in 30%
recombinants and 70% non-recombinants.
23- One map unit is equivalent to 10% recombination frequency
24 Crossing over Occurs during interphase of meiosis, Non-sister chromatids of non
homologous chromosomes exchange DNA segments
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If no crossing over, the alleles of all genes located on the same chromosome would be inherited
dependently
IF NO CROSSING OVER IN REGION BETWEEN THE TWO GENES = 50% NonRecombinants
Give reasons
ORF is not a good method to identify eukaryotic genes .
-
due to the presence of multiple exons and introns,
Why we need to compare the genome
-
By comparing the genome compositions between genomes, scientists can
better understand the evolutionary history of a given genome
SNPs are being used for linkage studies in human genome
to track genetic diseases.
Individual 1
Individual 2
AGTCAGTCCTAGGA
AGTCAGACCTAGGA
Draw a diagram showing the use of EST in identifying genes
What are the main information Each EST must have?
1. • A sequence ID (ex. sequence-run ID)
2. • Location in respect of the poly A (3' or 5')
3. • The CLONE ID from which the EST has been generated
4. • Organism
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5. • Tissue and/or conditions
6. • The sequence
What are the main fields of the comparative genomics
Gene location
Gene structure , Gene characteristics

Gene structure ( Exon number, Exon lengths, Intron lengths, Sequence similarity)

Gene characteristics ( Splice sites, Codon usage, Conserved synteny )
What do you know about Alu elements
 (Short interspersed elements), Length = ~300 bp
 Repetitive: > 1,000,000 times in the human genome
 Alu elements are found in primates. Early in primate evolution, Alu transposition rate was
approximately one new jump in every live birth. Today, it is about one new jump in every
200 live births.

Constitute >10% of the human genome
 Found mostly in intergenic regions and introns
 Propagate in the genome through retroposition (RNA intermediates).
 Alu elements can be sorted into distinct families according to shared patterns of variation.
 At any given point in time, only one or several Alu “master copies” are capable of
transposing.
 All the millions of Alu elements have accumulated in a mere ~65 million years.
GENETIC AND EVOLUTIONARY EFFECTS OF TRANSPOSITION
1.
2.
3.
Duplicative transposition increases genome size
Bacterial transposons often carry genes that confer antibiotic or other forms of resistance.
Plasmids can carry such transposons from cell to cell, so that resistance can spread
throughout a population or an ecosystem
Gene expression may be altered by the presence of a transposable element.
- An insertion may eliminate the reading frame (phenotypic effects).
- A transposable element may contain regulatory elements (effects on
transcription of nearby genes).
- Transposable elements may contain
even if the element is in an intron).
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splice sites (effects on RNA processing
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4- . Transposable elements promote gross genomic rearrangement a
- directly (moving a DNA sequence from one genomic location to another).
- indirectly (as a result of transposition, two sequences become similar to one another so
that unequal crossing-over between them is possible).
Compare between
Non-repetitive DNA:
Intermediate
(Moderate) Repetitive
DNA:
Highly Repetitive DNA
once per genome “Single
copy
Disperse throughout the
genome in eukaryotes
Short repetitive DNA (<100 bp)
present up to 1 million times
DNA R=1 or 2
10<R<10,000
R (repetition frequency)
>100,000
eukaryotic genome
in the eukaryotic genome
Much information,
Little information,
Almost no information,
high complexity
moderate complexity
Found in prokaryotic and
eukaryotic
low complexity
Compare between the arrangement of coordinately controlled genes in prokaryotes and
eukaryotes
Prokaryotic
 Prokaryotic genes that are turned on
and off together are often clustered
into operons which are transcribed
into one mRNA molecule and
translated together
Eukaryotic
Eukaryotic genes coding for enzymes of a
metabolic pathway are often scattered over
different chromosomes and are individually
transcribed
Tandemly repetitive & Interspersed repetitive DNA
Proportion of mammalian DNA 10-15%
10
Proportion of mammalian DNA 25-40%
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The tandem repeat DNA are usually identical
The interspread repeat DNA are very similar
but not identical
Length of each repeated unit 1-10 bp
Length of each repeated unit100-10,000bp
Transposons
 Transposons  transposable elements
jump and interrupt the normal
functioning may increase or decrease
production of one or more proteins
 can carry a gene that can be activated
when inserted downstream from an
active romoter and vice versa
Retrotransposons
 Retrotransposons  transposable
elements that move within a genome by
means of an RNA intermediate,
 a transcript of the retrotransposon DNA
to insert it must be converted back to
DNA by reverse transcriptase .
SINEs =
LINEs =
Short interspersed repetitive sequence
Long interspersed repetitive sequence
SINEs are retrosequences
>5kbp
range in length from 75 to 500 bp.
< 500bp
•
< 105
Most abundant
Non-autonomous transposable elements (lacking
the ability to mediate their own transposition)
and their degenerate descendents
•
>10 5 copies Moderately Abundant
. Active or degenerate descendants of
transposable elements
SINEs do not possess any reading frame.
Thus, their retroposition must be aided by
other genetic elements.
Discuss the main advantages of using EST in identifying eukaryotic genome
 Fast & cheap (almost all steps are automated)
 • They represent the most extensive available survey of the transcribed portion of
genomes.
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 • There are necessary for gene structure prediction, gene discovery and genome
mapping:
 -> provide experimental evidence for the position of exons
 -> provide regions coding for potentially new proteins
 -> characterization of splice variants and alternative polyadenilation
 • Provide an alternative to library screening
 -> short tag can lead to a cDNA clone
 • Provide an alternative to full-length cDNA sequencing
 -> sequences of multiple ESTs can reconstitute a full-length cDNA
 • Single Nucleotide Polymorphism (SNP) data mining
Mention and describe the role of three types of regulatory DNA elements in eukaryotes
o Promoters – recognition sequences for binding of RNA polymerase
o
Enhancers – increase transcription of a related gene
o
Silencers – decrease transcription of a related gene
Insulators or boundary elements – block undesirable influences on genes
Describe where satellite DNA is found and what role it may play in the cell.
1) Satellite DNA Simple-sequence DNA (6% of the human genome), size 14 to 500 bp
2) highly repetitive DNA characterized by rapid rate of hybridization, consisting of short
unusual nucleotide sequences that are tandemly repeated 1000’s of times in large
clusters
3) In addition, multi-cellular eukaryotes have complex satellites with longer repeat units
mainly in heterochromatic region
4) It is found at the tips of chromosomes and the centromere (Centromeric
heterchromatin---necessary for separation of chromosome to daughter cells
5) Its function is not known, perhaps it plays a structural role during chromosome
replication and separation.
Describe the effects of transposons and retrotransposons
 Transposons  jump and interrupt the normal functioning may increase or decrease
production of one or more proteins
 can carry a gene that can be activated when inserted downstream from an active
promoter and vice versa
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 Retrotransposons  transposable elements that move within a genome by means of an
RNA intermediate, a transcript of the retrotransposon DNA to insert it must be
converted back to DNA by reverse transcriptase 
What is the main role of the following
a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
snRNPs catalyze the cutting and splicing reactions of introns
Promoters – recognition sequences for binding of RNA polymerase
Enhancers – increase transcription of a related gene
Silencers – decrease transcription of a related gene
Insulators or boundary elements – block undesirable influences on genes
enhancer blockers – prevent ‘communication’ between enhancers and unrelated
promoters
barrier sequences – prevent spread of heterochromatin combined
centromiric heterochromatin necessary for separation of chromosome to daughter cells
Telomere prevents chromosomes from shortening with each replication cycle
Genetic maps allow us to estimate the relative distances between linked genes, based on
the probability that a crossover will occur between them
k.
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UMS Spring Semester 2014
Fundamental of microeconomics ( Econ 260)
Section no: ……………………..
no
Name
Section time…………………………………
ID
Signature
UMS Spring Semester 2014
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Fundamental of microeconomics ( Econ 260)
Section no: ……………………..
no
15
Name
Section time…………………………………
ID
Signature
Ashgan Abougabal