Structure and Function of DNA and Human

Genome
Dr. Avinash Rawal
Learning Objectives
• Summarize the basic chemical composition of a nucleotide:
nitrogenous base, phosphate and deoxyribose sugar
• Recall the 4 nitrogenous bases of DNA: Adenine, Guanine, Cytosine
and Thymine
• Explain the difference between purine and pyrimidine bases and list
which bases are purines and which are pyrimidines
• Synthesize the complementary DNA strand for a given DNA sequence
• Explain Chargaff's rule and use it to calculate composition of a DNA
strand
• Explain the relationship between DNA composition and melting
temperature
• Describe the features of the DNA strands and the DNA double helix
 Learning Objectives
• Describe the experiments that allowed us to conclude DNA is the hereditary
material for cells
• Outline the central dogma of molecular biology
• Explain how prokaryotic DNA is packaged and differentiate this from how
eukaryotic DNA is typically packed
• Recall the basic composition of a nucleosome
• Explain the relationship between nucleosomes and nuclease digestion
patterns
• Define the 10 nm and 30 nm fibers
• Describe how nucleosomes are packaged up to give rise to the 30 nm solenoid
fiber
• Describe how the solenoid fiber is further packaged to give rise to looped
chromatin domains
• Explain how the state of DNA differs at different points of the cell cycle (i.e.
Learning Objectives
• Describe the structure of DNA during interphase
• Describe the structure of DNA during mitosis
• Explain the purpose of centromeres and their role in cell division
• Define the kinetochore
• Describe DNA telomeres structure and explain their purpose
• Outline how DNA telomeres are made
• Describe the technique of karyotyping including its purpose, how it is
performed, and the types of cells commonly used
• Explain what is meant by epigenetics
• List examples of types of epigenetic modifications that occur in
humans
• Define heterochromatin and euchromatin
Learning Objectives
• Recognize the site of DNA methylation in humans
• Discuss the effect that DNA methylation has on gene expression
• Explain Fragile X disorder and how it results from inappropriate
methylation
• Recognize the clinical presentation of Fragile X disorder
• Define what is meant by Barr bodies and X-inactivation and the role
DNA methylation plays in the process
• Describe the major modifications that occur to core histone proteins
and their effect on gene expression
• Explain how HDACs and HATs affect the expression of DNA
Learning Objectives
• Describe the basic features of a human gene and the function of each part
• Describe the types of DNA sequences that are part of the human genome
(single copy, repetitive, etc.)
• Explain what is meant by single copy DNA and its role in the cell
• Explain what is meant by tandem repeat sequences and their role in the
cell
• Explain what is meant by interspersed DNA repeats and their role in the
cell
• Explain what is meant by transposable elements and how this relates to
interspersed DNA repeats
• Explain how retrotransposons copy themselves
• Describe how retrotransposons can cause DNA mutations
• Explain what is meant by pseudogenes
DNA
• DNA or deoxyribonucleic acid is a cell’s
instruction manual
• It encodes all the genetic information
necessary to produce a functional organism ATC G
• It is the heredity material ournitrogenousbases

• DNA is a repeating macromolecular

structure made up of nucleotide subunits
• Each nucleotide in the chain is made of a
sugar (deoxyribose), a phosphate, and a
nitrogenous base (either adenine,
thymine, guanine or cytosine)
The Nitrogenous Bases
AsGold
Mnemonic Pure
• Purines (Adenine and Guanine): nitrogenous bases with two rings

Mnemonic PyramidCUT
• Pyrimidine (Thymine and Cytosine): nitrogenous bases with a single
ring
 Single Strand:
The Structure of DNA
• So each chain consists of a backbone of
sugar and phosphates alternating. Each
sugar has a nitrogenous base attached si 3
• The final structure incorporates two single
chains held together by hydrogen bonds
between the nitrogenous bases Two Strands held together by hydrogen bonds
• A bonds to T (2 Hydrogen bonds) between nitrogenous bases:
• G bonds to C (3 Hydrogen bonds)
• The two strains run antiparallel to one 3 5
another
• In other words, one strand is starting with the
phosphate (aka 5’ end) at the end of the
chain, the other has the sugar (aka 3’ end)
• The ultimate result is the double helix
structure
Terminology: 3’ and 5’ ends
• The phosphate end is referred to as the 5’
end
ÉI
• The –OH end on the sugar is referred to as
the 3’ end
• This nomenclature is based on organic
chemistry numbering of the 5 carbons that
make up the deoxyribose sugar
• Also, thanks to the predictable pairings of A
with T and C with G, if we are given the
sequence of one strand of DNA we can
determine the other
Which of the following sequences is complementary
for this DNA sequence

5'-CTCGTACCGTTA –3’ ?

A. 5'-TAACGGTACGAG-3‘
B. 5'-CTCGTACCGTTA-3‘
C. 5'- ATTGCCATGCTC-3‘
D. 5'-GAGCATGGCAAT-3'
 Lookforvideosaboutthis
Chargaff’s Rule
• Since in a double helix of DNA, adenine always pairs with thymine and
guanine always pairs with cytosine, if information is given about one
base, we can calculate the others
• Chargaff’s Rule: A=T and G=C, Hence, the # of purines= # of pyrimidines
(A+G=T+C)
• So we can predict % of other bases if given a % of one base
• Example: If a DNA sample from an organism has 21% guanine
• It has 21% cytosine (G=C)
• A+T = 100- 42= 58%
• A = 29% and T=29%
• Also, if % bases do not match Chargaff’s rule, then the DNA structure is not
a complete double stranded structure
• So it might be or have regions that are single stranded
Chargaff’s Rule Practice Question

If a DNA sample from an organism has 23% adenine,

what percent of the sample is cytosine?
A. 23%
B. 46%
C. 69%
III
Halfcytosineguanine
D. 27% IE
jy54
E. 44%
Composition of DNA and Melting Temperature
EEE
• We can make the two strands of DNA come apart
with enough energy
• One way this can be done is by heating up the DNA
• However, how much heat is required to separate the
strands (aka melt the strands) depends on the
composition
• This is because A and T have two hydrogen bonds
connecting them and so require less energy to
separate that G and C which have three hydrogen
bonds between them
• Using this information, we can roughly determine
which DNA strands have the highest melting
temperature
• So higher G-C content means higher melt temperature
 Final 3D Structure of DNA: Double Helix
• Using the data available at the time,
Watson and Crick developed a model of
DNA that persists to this day: the double
helix
• Characteristics of DNA double helix:
2 nm
• Major groove
• Minor groove
• Antiparallel orientation of two DNA strands
• Complementary strands
• Pyrimidine-purine pairing
• T with A, C with G
How did we discover DNA is the heredity
material?
Griffith’s Experiment
• Was working with two strains of Streptococcus
pneumoniae: one virulent (S) and one avirulent
(R)
• Infecting a mouse with strain S caused it to die
while infecting with R would lead to mouse
surviving
• Griffith also noted that killing the S strain and
injecting it also failed to kill the mouse
• However something very surprising happened
when the killed S and live R strains were
injected together: the mouse died and Griffith
was able to recover live S strain from the dead
mouse
• His conclusion: something in the killed S strain was
able to change the live R strain into S strain leading
to the mouse’s death
• However since Griffith injected the entire killed
S bacteria, he had no idea what part of the
bacterial cell was causing this “transformation”
Avery, MacLeod and McCarthy’s Experiment:
Follow up from Griffith’s Results
• In order to see which part of the killed S cells
were responsible for transforming the bacteria,
Avery et al. did a follow up experiment where
they took the S cell extract and treated it with
various enzymes to remove components:
• In condition one, they added proteinases to degrade
the protein
• In condition two, they added ribonucleases to
degrade the RNA
INA YEN ProA • In condition three, they added deoxyribonucleases to
degrade the DNA
• After this, they added the extracts to the R killed
cells to see if they could still get live S cells
• They were able to see the transformation in all
conditions except for when they added the
deoxyribonuclease
• Conclusion: DNA was responsible for
transforming the R cells into S cells
Thanks to their efforts and others, today we
understand the role of DNA and the nucleus in the
central dogma of molecular biology
DIA

ii

19
 Packaging DNA inside the Nucleus
• Each human cell contains approximately 6 billion base pairs that make
up our 46 individual chromosomes

• So how do our cells organize and manage our huge DNA molecules?
• How do we fit all this DNA into a cell?
• How to does the cell provide access to the parts being actively used for
making proteins?
Prokaryotic DNA & Packaging
• Prokaryotes package DNA in bacterial
chromosomes and plasmids
• Bacterial chromosomes: Circular DNA molecule,
containing some bound proteins, that is localized
in a special region of the bacteria called the
nucleoid
• Negatively supercoiled
• folded into extensive loops held by RNA and proteins
• Bacterial plasmids: small, circular molecules of
DNA that carry genes for both their own
replication and one or more cellular function
• Four classes of E. Coli plasmids Image:
• F (fertility) factors https://www.ck12.org/book/ck-12-biology-advanced-
concepts/section/11.5/
• Col (colicinogenic) factors
• R (resistance) factors
• Cryptic plasmids

21
 Eukaryotes package DNA in chromatin and June13ᵗʰ202
chromosomes in ofourcells DNA everynucleus
a 7andahalffeet

• Chromatin: DNA-protein-RNA fibers that make up

chromosomes; constructed from nucleosomes spaced
regularly along a DNA chain
• Chromosome: DNA molecule, complexed with
histones and other proteins, and RNA, that becomes
condensed into a compact structure at the time of
mitosis or meiosis

mm

22
The packaging of DNA inside the nucleus
• DNA is first wound up around
proteins known as histones to give
O rise to a structure known as a
nucleosome (beads on a string)
• Gives rise to a 10 nm fiber
• These nucleosomes are then
packed together to form
chromatin fibers
• Gives rise to a 30 nm fiber aka
solenoid fiber
• These fibers can be further
condensed when cells divide (aka
mitosis and meiosis) to give rise to
chromosomes
Structure of a Nucleosome
• Nucleosomes consist of DNA wound
around proteins known as histones
• Histones are small, positively charged
proteins
• This allows them to readily interact with the
negative DNA phosphate backbone
• Thus they consist of a high amount of amino
acids Lysine and Arginine
• Humans have 5 abundant histones: H1,
H2A, H2B, H3 and H4
• H2A, H2B, H3 and H4 are core histones
• This is the structure that the DNA wraps around
• H1 is a linker histone
• This protein binds linker DNA outside the
nucleosome structure
Structure of a Nucleosome

• The histone core is an octomer

consisting of 2 subunits each of
H2A, H2B, H3 and H4
• Contain 147 base pairs of DNA
wrapped 1.67 turns around a
histone core
 DNA associated with nucleosomes is more
resistant to nuclease digestion
• DNA wrapped around histones is
more resistant to digestion via
nucleases while the linker DNA is
very sensitive
• Partial digestion of chromatin
generates 200 bp ladder ->
evidence that proteins are
clustered at 200 bp intervals
• We typically see this sort of laddering
inside cells undergoing apoptosis (as
nucleases degrade DNA during this
process)
• More intense digestion gives rise to
fragments around 145-147 bps
long
From Nucleosome to Solenoid Fiber
• Histone protein H1 binds to linker DNA
and serves to compact the DNA
further
• When H1 attaches, the structure is
known as a chromatosome which
consists of 166 base pairs of DNA
wrapped around the histone core and
held in place by H1 (a linker histone)
• This structure is able to condense
further to give rise to the 30 nm fiber
• H1 is essential for the 30 nm fiber
formation
Packing up the Solenoid Fiber

• The solenoids can be folded into

loop domains averaging 50-100
kb in length
• Looped domains are attached to
the chromosomal scaffold
 DNA Packaging and the Cell Cycle
• DNA will change its state
of condensation at certain • During interphase, a
points in the cell’s lifecycle cell’s typical state where
growth and protein
synthesis are occurring,
• During mitosis, when cells the DNA is at its most
divide to form daughter
cells, the chromatin decondensed as
condenses to its most chromatin
condensed state appearing
as chromosomes
1stGI
2ndSphase
Organization of an interphase chromatin Transcriptionally
active DNA,
decondensed to 10
nm fiber form
Figure 4-57 Molecular
Biology of the Cell (©
Garland Science 2008)

• Interphase chromatin is folded into a series of loop

domains, each containing 50,000-100,000 nucleotide pairs
of double-helical DNA condensed into a 30-nm fiber.
• The chromatin in each loop is further condensed through
poorly understood folding processes that are reversed when
the cell requires direct access to the DNA packaged in the
loop.
 Further Condensation: Chromosomes
during mitosis and meiosis
anyoudesistengrate• DNA is replicated during interphase,
cellmembrane resulting in two copies of each
si
throughphosphorylation
chromosome.
• Metaphase chromosomes consist of
two identical sister chromatids, held
together at the centromere
• Microtubules of the mitotic spindle
attach to the centromere, and the two
sister chromatids separate and move
to opposite poles.
• Then the nuclear membrane re-forms,
and the chromosomes decondense.
• Each daughter nuclei contains one
copy of each parental chromosome.
 Centromere
• The centromere is a specialized
region of a chromosome that helps
ensure the correct distribution of
duplicated chromosomes to
daughter cells during mitosis.
• Centromeres are DNA sequences to
which proteins bind, forming a
kinetochore.
• Spindle microtubules bind to the
kinetochore.
• Proteins associated with the
kinetochore act as “molecular
motors” to drive the movement of
chromosomes along the spindle
fibers.
Metaphase Chromosome

34
Figure 4-71 Molecular Biology of the Cell (© Garland Science 2008)
 Telomeres
• Telomeres are sequences at the ends
of chromosomes, and are required for
the replication of linear DNA
molecules.
• The sequences are similar among
eukaryotes, with repeats containing
clusters of G residues on one strand.
• They are repeated hundreds or
thousands of times and end with a 3ʹ
overhang of single-stranded DNA.
• The telomere sequences of some
organisms (including humans) form
loops at the ends.
• They bind a protein complex (shelterin)
that protects the chromosome termini
from degradation.
Telomeres
• The ends of linear chromosomes can’t be
replicated by DNA polymerase.
• Instead, telomerase, which uses reverse
transcriptase activity, replicates telomeric DNA
sequences.
• Maintenance of telomeres appears to be
important in determining the lifespan and
reproductive capacity of cells.
• Studies of telomeres and telomerase may provide
new insights into aging and cancer.
 Karyotyping
Cell
• Karyotyping allows us to Iainamanita
examine chromosomes in a cell EE
• Common cell types karyotyped
• T lymphocytes from blood
• Chorionic villi
• Amniotic fluid
• The cells are grown in tissue
culture and arrested in mitosis
by microtubule disrupting
drugs
• Synchronize and enrich for
a population of cells in
mitosis
Karyotype from a male patient with Down syndrome, showing
• Hypotonic lysis to release three copies of chromosome 21. From Thompson & Thompson
chromosomes
Summary: Eukaryote DNA Packaging in the Nucleus

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cannot
you
 11nm 30nm
2nm

700nm
300nm

1400nm
Sperm Nucleus Structure and Chromatin
Packaging
• The chromatin within a sperm cell is
organized differently compared to a
somatic cell
• Histone-rich chromatin located
towards the periphery
• Protamine-rich chromatin located
towards the center
• Some regions of the sperm chromatin
replaces histones with protamines
• Protamines are small, arginine-rich,
nuclear proteins
• Allows for enhanced packaging into
toroid (doughnut loop-shaped)
structures
• Makes the chromatin more compact
for packaging in the sperm head

Top image from: Zini and Libman, CMAJ August 29, 2006 175 (5) 495-500; DOI:
Toroid
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Bottom image from: William Steven Ward, Am J Clin Exp Urol 2018;6(2):87-92 www.ajceu.us /ISSN:2330-
1910/AJCEU0075900,
https://pdfs.semanticscholar.org/1147/a321ab07e4921ee420803567d8ca4a37c263.pdf
 Epigenetic Modifications and Regulation of
Gene Expression
• Epigenetic: The term that refers to any
factor that can affect gene function without
change in the genotype
• Some typical epigenetic factors involve
alterations that change genome structure
and affect gene expression without
changing the primary DNA sequence:
• DNA methylation,
• Chromatin structure
• Histone modifications
• Transcription factor binding
• Side Note: As you learn more about
gene expression and protein
production you will appreciate that
there are lots of levels of regulation
for this process, not just those we will
discuss here that are epigenetic
 Euchromatin vs Heterochromatin
• Euchromatin is genomic DNA that is • Heterochromatin
chromatin that
is highly folded
is usually
more loosely packed and diffuse. transcriptionally inactive
• Most of transcriptionally active genes • Heterochromatin is highly organized and
are in euchromatin. unusually resistant to gene expression
• Transcriptionally active genes often • DNA is packaged so tightly that transcription is
inhibited
have acteylated histones associated • DNA in heterochromatin is often
with their DNA methylated on cytosines in CpG
• During interphase the euchromatin is sequences
decondensed and distributed • During interphase, heterochromatin
throughout the nucleus. remains highly condensed and is
transcriptionally inactive
DNA Methylation
• Methylated DNA is often associated with
heterochromatin
• Major site of Methylation in mammals
including humans is on cytosine of 5’-CG-3’,
usually in 5’ noncoding sequences
• Methylation patterns are inherited after DNA
replication
• X-chromosome inactivation – one of the X
chromosomes in cells from females is highly
condensed, transcriptionally inactive
heterochromatin
• The inactive X chromosome:
• Barr body
• The Barr body is extensively methylated
• So generally speaking, methylation of DNA is
associated with turning off gene expression
aka gene silencing
Disease of Inappropriate DNA Methylation:
Fragile X Disorder aka Martin-Bell Syndrome
• Disorder related to a mutation in
FMR1 gene
• FMR1 is located on the X
chromosome so disease is inherited
in a X-linked dominant fashion
• This disorder is also an example of
a trinucleotide repeat disease (a
disease caused by an inappropriate
number of repeats in a gene)
• The mechanism of disease is due
to inappropriate DNA methylation
 Fragile X (aka Martin-Bell Syndrome)
• Within the promoter of the FMR1
gene is a region that consists of
repeated CGG sequences
• These repeats are normal and don’t
cause any issues with FMR1 expression
• A problem occurs however if the CGG
region becomes too large (aka too
many CGG repeats)
• Once the CGG repeats >200, it triggers
the cell to consider these CGGs
methylation sites and so it
hypermethylates the FMR1 promoter
• This methylation silences the FMR1 gene
and so it is not expressed
• Since FMR1 is required for various
functions in the body, its absence causes
the syndrome Fragile X disorder
 Fragile X Syndrome (Martin-Bell Syndrome) GG
● Clinical features
• Intellectual Disability
• Delayed language development, autistic behavior
• Coarse facial features (long and narrow face, prominent
forehead, jaw, big ears)
• Macroorchidism: Testicles grow to a total average volume of
50 ml (normal 15 to 20 mL) in adulthood (rarely occurs before
puberty)
• Deep plantar creases
• Beyond average height and head circumference
• Mitral valve prolapse: can lead to mitral regurgitation
• Hyperactivity
• Focal seizures

Clinical features due to absence of FMR1 protein (an RNA-binding

protein)
• FMRP is an RNA-binding protein that associates with
polyribosomes to suppress the translation of proteins from its RNA Macroorchidism
targets.
• These targets appear to be involved in cytoskeletal structure, synaptic
transmission, and neuronal maturation, and the disruption of these Deep plantar creases
processes is likely to underlie the mental retardation and learning 46
abnormalities seen in fragile X patients.
 Histone Modifications
• The core histones are covalently retuit c Fátiositivoconnegativo
p
modified at many different sites on Histone Core Tails:
their tails The Modification Sites
• Acetylation is associated with increased
in transcription
• Loosen chromatin packaging and
allow transcription factor
interactions
• Phosphorylation
• Methylation of histones can either
increase or decrease gene expression
depending on which amino acids are
methylated and how many methyl groups
are added
• Loss of H1 leads to unfolding of the
30 nm fiber
Histone Acetylation
• Acetylation of lysine residues on histones weakens the DNA-histone interactions and
makes the DNA more accessible to factors for transcription
• Histone acetyl transferases (HATs) catalyze the acetylation of histone
• Histone deacetylase (HDAC) removes the acetyl groups
• Associated with gene silencing
Closed structure: decreased gene expression

Open structure: increased gene expression

 June17ᵗʰ2024

Composition of the Human Genome

 Firstfemaleinourplanet AfricaUtopia
from
was
Human Genome Nuclear Genome:
• The human genome is contained within two distinct compartments: the nucleus
and the mitochondria.
• The mitochondrial DNA contains 37 genes that are essential for normal
mitochondrial function and is exclusively of maternal origin.
• The human nuclear genome contains the bulk of the genome and consists of up
to 23 different chromosomes
• 22 autosomes
• X & Y sex chromosomes
• Males and females have two copies of each of the autosomes
• Males have one X and one Y chromosomes Mitochondrial Genome:
• The X chromosome came from the mother
• The Y chromosome came from the father
• Females have two X chromosomes
• One from each parent
• Chromosomes 13, 14, 15, 21 & 22 are special,
• they are autosomal acrocentric chromosomes
isnotcentral
centromere
 Structure of a Human Gene

DNA

RNA
PYotein

getsynthesizedinthe
Ribosomes nucleolus
• A human gene consists of:
• A promoter region (5’ Regulatory Region) • Exons
• Regulates the timing and amount of expression of a • Protein coding sequences within the gene
particular gene, specifically how much mRNA is made • Introns
• Located in the 5’ end • Sequences between exons that are removed from the
mature mRNA
• NOT made into mRNA • 3’UTR
• 5’ UTR • Contains regulator regions that affect gene expression
• Responsible for recruiting ribosome to make RNA into and export
protein • Made into RNA but not into protein
• Located downstream from promoter and upstream (5’ • 3’ Regulatory Sequences
side) of gene • Can also be other regulatory sites in the 3’ end of the
• Made into mRNA but not into protein gene that are not made into RNA
 Organization of the Human Genome
• Genetic linkage analysis and
physical mapping of cloned
genomic and cDNA sequences
established maps of the
human genome, which
provided a background for
genomic sequencing.
• A major surprise from the Only 1-2% of our genome
human genome sequence actually encodes proteins
was the unexpectedly low
number of genes: only 20,000
to 25,000.
• But alternative splicing in
human genes allows a
single gene to specify
more than one protein.
• So what is in the human About 90% of an
average human
genome? gene consists of
introns.
Single Copy Elements

• Only 1-2% of DNA sequences codes for proteins, but 75% of DNA is
transcribed into RNA.

• Single copy DNA à Present once, or very few times in the genome.

• About 50% of the genome, and includes the 1.5% that are genes

• Shorter stretches of DNA (generally kb sized)

Repetitive Sequences
• Tandem repeats: Multiple copies arranged next to each other in a
row
• 10-15% of mammalian genome
• Alpha Satellite DNA, minisatellite & microsatellite
• Abundant in centromeres and telomeres
• Interspersed repeated DNA: This type of DNA is scattered around the
genome
• A large portion of interspersed repeated DNA: the Alu family
• Transposable elements (self replicating molecular parasites)
Tandem Repeats
Example of a
Microsatellite

• Tandem repeats (One repeat follows after another) – approx. 10% of

genome
• Tens, to tens of thousands of times; come in families
• Examples of Tandem Repeats found in Human DNA:
• a-satellites
• 171bp sequence – repeats up to 1M+ bp in length
• Found near centromeres; suspected to be important for spindle attachment
• Minisatellites
• 14 to 500bp long – repeats in the low thousands of bp
• Microsatellites
• 1 to 13bp long – repeats in the low hundreds of bp
• Note: Repeat expanded in Fragile X CGG is an example of a microsatellite
 Interspersed Repeats
• 2 important families make up significant proportion of genome and implicated
in genetic diseases
• Both families are retrotransposons—their transposition is mediated by
reverse transcription. So they are capable of self replication
• SINE (short interspersed elements) e.g. Alu family
• ~300 bps length
• Members of family related but not identical
• 500,000 Alu family members in genome
• Make up several percent of DNA
• Arose by reverse transcription of small RNAs
• Including tRNAs and RNAs involved with protein transport
• LINE (long interspersed elements) e.g. L1 family
• Long repeats (upto 6 kb)
• 100,000 copies per genome
• Plentiful in some regions, sparse in others
• Transpositionally active
• Can encode for reverse transcriptase

Reverse Transcriptase makes a complementary DNA product using an RNA template!!!

Transposable elements
• Nearly half the human genome consists of
repetitive elements that have replicated and moved
through the genome by RNA or DNA intermediates.
• Some may help regulate gene expression, but most
appear not to make a useful contribution to the
cell.
• Transposable elements have, however, played a
major role in stimulating gene rearrangements that
have contributed to the generation of genetic
diversity.
How retrotransposons copy themselves and disperse
in the genome:
• Transposition by the L1 element (red) begins when
an endonuclease attached to the L1 reverse
transcriptase (green) and the L1 RNA (blue) nicks
the target DNA at the point at which insertion will
occur.
• This cleavage releases a 3’-OH DNA end in the
target DNA, which is then used as a primer for the
reverse transcription step shown.
• This generates a single-stranded DNA copy of the
element that is directly linked to the target DNA.
• In subsequent reactions, further processing of the
single-stranded DNA copy results in the generation
of a new double-stranded DNA copy of the L1
element that is inserted at the site of the initial
nick
 Medical Importance of Interspersed Repeats
• Alu and L1 sequences have been implicated as the cause of mutations
in hereditary diseases by retrotransposition
• Retrotransposition events may account for up to 1 in 500 mutations
• Repeats may insert into a gene and disrupt function
• If there is insertion of ~300 bps, most likely it is an Alu insertion
• Transposition of LINEs and SINEs occur during the development of several types
of non-inherited cancer.

59
 thisapparently
Won'taskquestionsabout hastloslides
Pseudogenes
• Pseudogenes are nonfunctional segments of DNA that resemble functional genes.
Pseudogenes can arise in two ways:
• Duplication of a segment of DNA results in the transfer of a block of DNA to a new
location in the genome.
• Duplication by reverse transcription of an mRNA, followed by integration of the cDNA
copy into a new chromosomal site.
• Duplication of a gene by reverse transcription usually yields an inactive gene copy called a
processed pseudogene—they lack introns and the normal sequences that direct
transcription.