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Biology Revision Notes

Base pair
Two complementary nucleotides in an RNA and a DNA molecule that are held together by hydrogen bonds.
The Adenine – Thymine base pair is held together by 2 hydrogen bonds while the Guanine – Cytosine base pair is held together by 3 hydrogen bonds. That is also the reason why the two strands of a DNA molecule can be separated more easily at sections that are densely populated by A – T base pairs.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Cell cycle
The orderly sequence of events by which a cell duplicates its contents and divides into two.
A cell reproduces by performing an orderly sequence of events in which it duplicates its contents and then divides in two. This cycle of duplication and division, known as the cell cycle, is the essential mechanism by which all living things reproduce.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Specialized DNA sequence that allows duplicated chromosomes to be separated during M phase; can be seen as the constricted region of a mitotic chromosome.
The centromere is the chromosome region that attaches to a spindle fibre at metaphase of mitosis or meiosis and moves to the spindle pole at anaphase, pulling the rest of the chromosome behind it. It can often be distinguished microscopically at metaphase as a thin constriction in the otherwise thick condensed chromosome, and a point at which the chromosome is flexible and free to bend.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Complex of DNA and proteins that makes up the chromosomes in a eukaryotic cell.
Chromatin is a complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells. Under the microscope in its extended form, chromatin looks like beads on a string. The beads are called nucleosomes. Each nucleosome is composed of DNA wrapped around eight proteins called histones.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Chromatin-remodeling complex
Enzyme that uses the energy of ATP hydrolysis to alter the arrangement of nucleosomes in eukaryotic chromosomes, changing the accessibility of the underlying DNA to other proteins, including those involved in transcription.
Chromatin remodeling, an important facet of the regulation of gene expression in eukaryotes, is performed by two major types of multisubunit complexes, covalent histone- or DNA-modifying complexes, and ATP-dependent chromosome remodeling complexes.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Long, threadlike structure composed of DNA and proteins that carries the genetic information of an organism; becomes visible as a distinct entity when a plant or animal cell prepares to divide.
Humans have an additional pair of sex chromosomes for a total of 46 chromosomes. The sex chromosomes are referred to as X and Y, and their combination determines a person’s sex. Typically, human females have two X chromosomes while males possess an XY pairing. This XY sex-determination system is found in most mammals as well as some reptiles and plants.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Describes two molecular surfaces that fit together closely and form noncovalent bonds with each other.
The chemical molecules that make up DNA are known as nucleotide bases. There are four common types of bases: adenine (A), cytosine (C), guanine (G), and thymine (T). In the chemical “lock and key” fit, an A on one strand always pairs with a T on the other strand. As well, a C on one strand always pairs with a G on the other strand. The two strands are described as complementary to one another.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Deoxyribonucleic acid (DNA)
Double-stranded polynucleotide formed from two separate chains of covalently linked deoxyribonucleotide units. It serves as the cell’s store of genetic information that is transmitted from generation to generation.
Each nucleotide consists of three components:
• a nitrogenous base: cytosine (C), guanine (G), adenine (A) or thymine (T)
• a five-carbon sugar molecule (deoxyribose in the case of DNA)
• a phosphate molecule
• The backbone of the polynucleotide is a chain of sugar and phosphate molecules. Each of the sugar groups in this sugar-phosphate backbone is linked to one of the four nitrogenous bases.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Double helix
The typical structure of a DNA molecule in which the two complementary polynucleotide strands are wound around each other with base-pairing between the strands.
DNA structure DNA is made up of molecules called nucleotides. Each nucleotide contains a phosphate group, a sugar group and a nitrogen base. The four types of nitrogen bases are adenine (A), thymine (T), guanine (G) and cytosine (C). The order of these bases is what determines DNA’s instructions, or genetic code.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

One of the two main states in which chromatin exists within an interphase cell. Prevalent in gene-rich area, its less compacted structure allows access for proteins involved in transcription.
Euchromatin structure often contains unmethylated first gene exons. Histone modifications associated with active transcription include lysine acetylation and methylation. Typically, histone acetylation occurs at multiple lysine residues, most commonly on histones H3 and H4, and is usually carried out by a variety of histone acetyltransferase complexes (HATs) (Brown et al. 2000; Schuettengruber et al. 2007).
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Unit of heredity containing the instructions that dictate the characteristics or phenotype of an organism; in molecular terms, a segment of DNA that directs the production of a protein or functional RNA molecule.
A gene is the basic physical and functional unit of heredity. Genes are made up of DNA. Some genes act as instructions to make molecules called proteins. However, many genes do not code for proteins. In humans, genes vary in size from a few hundred DNA bases to more than 2 million bases.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Gene expression
The process by which a gene makes a product that is useful to the cell or organism by directing the synthesis of a protein or an RNA molecules with a characteristic activity.
Several steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation, morphogenesis and the versatility and adaptability of any organism.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Genetic code
Set of rules by which the information contained in the nucleotide sequence of a gene and its corresponding RNA molecule is translated into the amino acid sequence in a protein.
During translation, an mRNA sequence is read using the genetic code, which is a set of rules that defines how an mRNA sequence is to be translated into the 20-letter code of amino acids, which are the building blocks of proteins.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

The total genetic information carried by all the chromosomes of a cell or organism.
The genome is the entire genetic material of an organism. It is found in the nucleus of a cell, and is composed of a chemical called DNA . The study of the structure and function of the genome is called genomics .
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Highly condensed region of an interphase chromosome; generally gene-poor and transcriptionally inactive.
Compact and highly condensed form of chromatin. Heterochromatin is a tightly packed form of DNA or condensed DNA, which comes in multiple varieties. These varieties lie on a continuum between the two extremes of constitutive heterochromatin and facultative heterochromatin.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

One of a group of abundant highly conserved proteins around which DNA wraps to form nucleosomes, structures that represent the most fundamental level of chromatin packing.
Chromatin is composed of a cell’s DNA and associated proteins. Histone proteins and DNA are found in approximately equal mass in eukaryotic chromatin, and nonhistone proteins are also in great abundance. The basic unit of organization of chromatin is the nucleosome, a structure of DNA and histone proteins that repeats itself throughout an organism’s genetic material.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

An ordered display of the full set of chromosomes of a cell arranged with respect to size, shape, and number.
A karyotype is the number and appearance of chromosomes, and includes their length, banding pattern, and centromere position. To obtain a view of an individual’s karyotype, cytologists photograph the chromosomes and then cut and paste each chromosome into a chart, or karyogram, also known as an ideogram
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Large structure within the nucleus where ribosomal RNA is transcribed and ribosomal subunits are assembled.
The nucleolus is a distinct structure in the nucleus of the cell composed of filamentous and granular material. It is the site of synthesis and processing of ribosomal RNA and the assembly of this RNA with ribosomal proteins into ribosomal subunits.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Replication origin
Nucleotide sequence at which DNA replication is initiated.
DNA replication begins at a single origin of replication, and the two replication forks assembled there proceed (at approximately 500–1000 nucleotides per second) in opposite directions until they meet up roughly halfway around the chromosome
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Telomere gene
Repetitive nucleotide sequence that caps the ends of linear chromosomes. Counteracts the tendency of the chromosome otherwise to shorten with each round of replication.
Otherwise, cells might permanently arrest in the cell cycle, and attempts to “repair” the chromosome ends would have devastating consequences for genome integrity. This end-protection problem is solved by protein-DNA complexes called telomeres.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Disease caused by abnormal and uncontrolled cell proliferation, followed by invasion and colonization of body sites normally reserved for other cells.
The proteins involved in regulating cell division events no longer appropriately drive progression from one cell cycle stage to the next. Rather than lacking function, cancer cells reproduce at a rate far beyond the normally tightly regulated boundaries of the cell cycle. Cancer can be distinguished from many other human diseases because its root cause is not a lack of, or reduction in, cell function.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

DNA ligase
Enzyme that reseals nicks that arise in the backbone of a DNA molecule; in the laboratory, can be used to join together two DNA fragments.
DNA ligases are best known for their role in joining adjacent Okazaki fragments at the lagging strand of the replication fork; however, they are essentially involved in any process that requires sealing of phosphodiester bonds from the DNA backbone. Ligases catalyze the formation of phosphodiester bond between 3′OH and 5′phosphate on various substrates such as DNA nicks, DNA fragments with various lengths cohesive ends, DNA fragments with blunt ends and some.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

General term for an enzyme that catalyzes addition of subunits to a nucleic acid polymer.
Replication of genomic DNA is the primary function of DNA polymerases. Once the DNA is duplicated accurately, the cell can undergo division with each daughter cell receiving the complete genetic code of the organism. Polymerases responsible for DNA replication are complex multiprotein machines that can synthesize DNA with high speed, processivity, and fidelity.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

DNA repair
Collective term for the enzymatic processes that correct deleterious changes affecting the continuity or sequence of a DNA molecule.
DNA repair can be divided into a set of mechanisms that identify and correct damage in DNA molecules. There are two general classes of DNA repair; the direct reversal of the chemical process generating the damage and the replacement of damaged nucleotide bases.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

DNA replication
The process by which a copy of a DNA molecule is made.
Replication is the process by which a double-stranded DNA molecule is copied to produce two identical DNA molecules. DNA replication is one of the most basic processes that occurs within a cell. Each time a cell divides, the two resulting daughter cells must contain exactly the same genetic information, or DNA, as the parent cell. To accomplish this, each strand of existing DNA acts as a template for replication.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Homologous recombination
Mechanism by which double-strand breaks in a DNA molecule can be repaired flawlessly; uses an undamaged, duplicated, or homologous chromosome to guide the repair. During meiosis, the mechanism results in an exchange of genetic information between the maternal and paternal homologs.
Homologous recombination is an important pathway involved in the repair of double-stranded DNA breaks. Genetic studies form the foundation of our knowledge on homologous recombination. Significant progress has also been made toward understanding the biochemical and biophysical properties of the proteins, complexes, and reaction intermediates involved in this essential DNA repair pathway.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Lagging strand
At a replication fork, the DNA strand that is made discontinuously in short separate fragments that are later joined together to form one continuous new strand.
A lagging strand is one of two strands of DNA found at the replication fork, or junction, in the double helix; the other strand is called the leading strand. A lagging strand requires a slight delay before undergoing replication, and it must undergo replication discontinuously in small fragments.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Leading strand
At a replication fork, the DNA strand that is made by continuous synthesis in the 5′-3′ direction.
This continuously synthesized strand is known as the leading strand. Because DNA polymerase can only synthesize DNA in a 5′ to 3′ direction, the other new strand is put together in short pieces called Okazaki fragments. The Okazaki fragments each require a primer made of RNA to start the synthesis.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Mismatch repair
Mechanism for recognizing and correcting incorrectly paired nucleotides – those that are noncomplementary.
DNA mismatch repair (MMR) recognizes and repairs erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, and repair some forms of DNA damage. It plays an important role in maintaining genomic stability and cellular homeostasis. For example, MMR increases the accuracy of DNA replication by 20–400-fold in Escherichia coli.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

A randomly produced, permanent change in the nucleotide sequence of DNA.
Search Results
A gene mutation is a permanent alteration in the DNA sequence that makes up a gene, such that the sequence differs from what is found in most people. Mutations range in size; they can affect anywhere from a single DNA building block (base pair) to a large segment of a chromosome that includes multiple genes.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Nonhomologous end joining
A quick-and-dirty mechanism for repairing double-strand breaks in DNA that involves quickly bringing together, trimming, and rejoining the two broken ends; results in a loss of information at the site of repair.
Nonhomologous end joining (NHEJ) is a repair mechanism that directly ligates broken ends of DNA DSBs using a heterodimeric enzyme complex consisting of the proteins Ku-70 and Ku-80, the catalytic subunit of DNA protein kinase (DNA-PKCS), and XRCC4/ligase IV.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Okazaki fragment
Short length of DNA produced on the lagging strand during DNA replication. Adjacent fragments are rapidly joined together by DNA ligase to form a continuous DNA strand.
The lagging strand synthesis is done discontinuously. Okazaki fragments are initiated by creation of a new RNA primer by the primosome. To restart DNA synthesis, the DNA clamp loader releases the lagging strand from the sliding clamp, and then reattaches the clamp at the new RNA primer. Then DNA polymerase III can synthesize the segment of DNA.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

An RNA polymerase that uses DNA as a template to produce an RNA fragment that serves as a primer for DNA synthesis.

Primase is the name that has been given to the enzyme that synthesizes RNA primers. Primers are oligonucleotides that are complementarily bound to a DNA template and from which DNA polymerases elongate. Special proteins are responsible for loading primase at the origin of replication so that leading strand DNA synthesis can commence. In a subsequent step, other replication proteins cause primase to initiate DNA replication on the opposite lagging strand.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

The process by which DNA polymerase corrects its own errors as it moves along DNA.
DNA polymerase functions as a “self-correcting” enzyme that removes its own polymerization errors as it moves along the DNA.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Replication fork
Y-shaped junction that forms at the site where DNA is being replicated.
The double-stranded DNA of the circular bacteria chromosome is opened at the origin of replication, forming a replication bubble. Each end of the bubble is a replication fork, a Y-shaped junction where double-stranded DNA is separated into two single strands.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Replication origin
Nucleotide sequence at which DNA replication is initiated.
DNA replication begins at a single origin of replication, and the two replication forks assembled there proceed (at approximately 500–1000 nucleotides per second) in opposite directions until they meet up roughly halfway around the chromosome
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Ribonucleic acid (RNA)
Molecule produced by the transcription of DNA; usually single-stranded, it is a polynucleotide composed of covalently linked ribonucleotide subunits. Serves a variety of structural, catalytic, and regulatory functions in cells.
Ribonucleic acid (RNA) is a molecule similar to DNA. Unlike DNA, RNA is single-stranded. An RNA strand has a backbone made of alternating sugar (ribose) and phosphate groups. Attached to each sugar is one of four bases–adenine (A), uracil (U), cytosine (C), or guanine (G).
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Enzyme that elongates telomeres, synthesizing the repetitive nucleotide sequences found at the ends of eukaryotic chromosomes.
Telomerase. Some cells have the ability to reverse telomere shortening by expressing telomerase, an enzyme that extends the telomeres of chromosomes. Telomerase is an RNA-dependent DNA polymerase, meaning an enzyme that can make DNA using RNA as a template.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

A molecular structure that serves as a pattern for the production of other molecules. For example, one strand of DNA directs the synthesis of the complementary DNA strand.
DNA polymerases isolated from cells and artificial DNA primers can be used to start DNA synthesis at known sequences in a template DNA molecule.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Epigenetic inheritance
The study of mechanisms controlling gene expression that are independent of the DNA sequence itself.
Epigenetic mechanisms include DNA methylation, histone modifications, and noncoding ribonucleic acid regulation. Collectively, epigenetic mechanisms determine chromatin architecture, accessibility of genetic loci to transcriptional machinery, and gene expression levels.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Mobile genetic element
Short segment of DNA that can move, sometimes through an RNA intermediate, from one location in a genome to another; an important source of genetic variation in most genomes.
Examples of mobile genetic elements (MGE) and processes involved in intracellular mobility or intercellular transfer of antibiotic resistance genes.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

General name for short segments of DNA that can move from one location to another in the genome.
Since McClintock’s discovery, three basic types of transposons have been identified. These include class II transposons, miniature inverted-repeat transposable elements (MITEs, or class III transposons), and retrotransposons (class I transposons).
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Retrotransposon is a type of transposable element that moves by being first transcribed into RNA copy that is then reconverted to DNA by reverse transcriptase and inserted elsewhere in the chromosome.
Retrotransposons also move by a “copy and paste” mechanism but in contrast to the transposons described above, the copy is made of RNA, not DNA.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

RNA-containing virus that replicates in a cell by first making a double-stranded DNA intermediate that becomes integrated into the cell’s chromosome
In a double stranded RNA form, retroviruses infect a host cell with their genome, and then are reverse transcribed into double stranded DNA, with the DNA then integrated into the home cell genome.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Reverse transcriptase
Enzyme that makes a double-stranded DNA copy from a single-stranded RNA template molecule. Present in retroviruses and as part of the transposition machinery of retrotransposons.
Reverse transcriptase is an RNA-dependent DNA polymerase that was discovered in many retroviruses such as human immunodeficiency virus (HIV) and avian myeloblastosis virus (AMV) in 1970. Reverse transcriptases are commonly used to produce complementary DNA (cDNA) libraries from various expressed mRNAs and are also used to quantify the level of mRNA synthesis when combined with the polymerase chain reaction technique, called RT-PCR. Reverse transcriptase contains three enzymatic activities: (1) RNA-dependent DNA polymerase, (2) RNase H, and (3) DNA-dependent DNA polymerase.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Alternative splicing
The production of different mRNAs (and proteins) from the same gene by splicing its RNA transcripts in different ways.
Alternative splicing (AS) is a process by which exons can be either excluded or included in or from a pre-mRNA resulting in multiple mRNA isoforms. It plays a critical role in the regulation of gene expression and protein diversity in a variety of eukaryotes. In humans, approximately 95% of multi-exon genes undergo alternative splicing.
From: Methods in Enzymology, 2013

transposable elements
Can move to new positions within the same chromosome or even to a different chromosome
50% of our chromosomes

Model organism Maize
produce variably colored kernels

Because each kernel is an embryo produced from an individual fertilization, hundreds of offspring can be scored on a single ear, making maize an ideal organism for genetic analysis.

“dissociation” (Ds).
The first transposable element Barbara McClintock discovered was a site of chromosome breakage
are regulated by an autonomous element called “activator” (Ac)
typically located at site of breakage

can promote its own transcription
found in different location in different plants and animals

Insertion of Ds in the C gene
creates colorless corn cells

Excision of Ds from the C gene through the action of Ac in cells and their mitotic descendents
allows color to be expressed again, giving a spotted phenotype

c-m(Ds) is
unstable when Ac is present in the genome
where as
c-m(Ac) always unstable

autonomous elements
maize can inactivate a gene in which they reside, cause chromosome breaks, and transpose to new locations within the genome
perform these functions unaided

non autonomous elements
can transpose only with the help of an autonomous element elsewhere in the genome.

Short sequences called IS elements
Can move themselves to new positions
-Do not carry genes other than those needed for their environment

Bacterial IS
found in E.coli in the gal operon

Encode a protein called a transposase
begin and end with a short inverted repeat sequences that are required for their mobility

Aminoacyl-tRNA synthetase
During protein synthesis, an enzyme that attaches the correct amino acid to a tRNA molecule to form a “charged” aminoacyl-tRNA.
During elongation, aminoacyl-tRNAs are brought to a site on the ribosome containing the next codon to be translated (the A-site) as a ternary complex containing the aminoacyl-tRNA, guanosine triphosphate (GTP), and an elongation factor. As in the case of aminoacylation, the initial selection of the aminoacyl-tRNA on the ribosome would give approximately a 100-fold preference for the correct versus a nearly correct codon–anticodon interaction.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Set of three consecutive nucleotides in a transfer RNA molecule that recognizes, through base-pairing, the three-nucleotide codon on a messenger RNA molecule; this interaction helps to deliver the correct amino acid to a growing polypeptide chain.
Three nucleotides termed the anticodon, located at the center of one loop, can form base pairs with the three complementary nucleotides forming a codon in mRNA. As discussed later, specific aminoacyl-tRNA synthetases recognize the surface structure of each tRNA for a specific amino acid and covalently attach the proper amino acid to the unlooped amino acid acceptor stem.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Group of three consecutive nucleotides that specifies a particular amino acid or that starts or stops protein synthesis; applies to the nucleotides in an mRNA or in a coding sequence of DNA.
The actual genetic code used by cells is a triplet code, with every three nucleotides being “read” from a specified starting point in the mRNA. Each triplet is called a codon. Of the 64 possible codons in the genetic code, 61 specify individual amino acids and three are stop codons
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Segment of a eukaryotic gene that is transcribed into RNA and dictates the amino acid sequence of part of a protein.
Exons are the functional regions of genes that code for proteins and introns are the noncoding sequences.
The genome represents all chromosomal genetic data including coding and non-coding (intron) regions, approximately 3 billion DNA letters. Exons represent only 1.5% of the genome but result in around 85% of monogenic diseases.
From: Clinical and Translational Perspectives on WILSON DISEASE, 2019

General transcription factors
Proteins that assemble on the promoters of many eukaryotic genes near the start site of transcription and load the RNA polymerase in the correct position.
General transcription factors are proteins that help to position Pol II correctly on the promoter, the region of a gene where transcription is initiated, pull aside the two strands of DNA and then move Pol II into the elongation mode.
The general transcription factors comprise at least six distinct species: TFII A, B, D, E, F, and H (see Fig. 7.1b).
TFIID (300–750 kDa) is a multiprotein complex composed of a TATA (box)-binding protein (TBP) and up to 13 TBP-associated factors (TAFs).

From: Molecules to Networks (Third Edition), 2014

enzyme required for the movement of IS elements from one site in the chromosome to another

Not only carry the genes they need for their environment but also carry other genes
detected as mobile genetic elements that confer drug resistance (R plasmids ?)
consist of recognizable IS elements flanking a gene that encodes drug resistance(not always)

Mechanism of transposition in prokaryotes
Replicative method

Conservative method

Replicative Method
a new copy of the transposable element is generated in the transposition event

One copy appears at the new site and one copy remains at the old site
Tn 3

conservative method
The DNA of the element is not replicated and the element is lost from the site of the original chromosome
Also called “cut and paste” mechanism
Reaction is initiated by the element encoded transposase
Tn 10

Insertion into a new location
In one of the first steps of insertion, the transposase makes a staggered cut(5bp) in the target site DNA
Transposable element then inserts between staggered ends
Host DNA repair machinery fills in the gap opposite each strand overhang (how ?)

Class 1 retrotransposons:
Transpose through RNA intermediates
Encode a reverse transcriptase that produces double-stranded DNA copy (from an RNA intermediate)that is capable of integrating at a new position in the genome.

Class 2 DNA transposons
Encode a transposase that cuts the transposon from the chromosome and catalyze the reinsertion at other chromosomal locations
P elements (first DNA transposons to be molecularly characterized).

Ty elements in yeast are similar to retroviruses because
A) both Ty elements and retroviruses utilize an RNA transposition intermediate.
B) both Ty elements and retroviruses utilize reverse transcriptase.
C) introns are usually found in retroviruses and Ty elements.
D) all of the above
E) both a and b
E) both a and b

P elements
discovered as a result of studying hybrid dysgenesis—a phenomenon that occurs when females from laboratory strains of Drosophila melanogaster are mated with males derived from natural populations.

In such crosses, the laboratory stocks are said to possess an M cytotype (cell type), and the natural stocks are said to possess a P cytotype.

a large percentage of the dysgenically induced mutations
are unstable; they revert to wild type or to other mutant alleles at very high frequencies.

DNA transposons have been modified and used by scientists in two important ways:
(1)to make mutants that can be identified molecularly by having a transposon tag

(2) as vectors that can introduce foreign genes into the chromosome.

c-value paradox
The lack of correlation between genome size and biological complexity of an organism

What is responsible for the additional DNA in the larger genomes ?
repetitive DNA
Genome size is usually corresponds to the amount of transposable-element sequences rather than to gene content

LINE (Long Interspersed Elements)
move like a retrotransposon with the help of an element encoded reverse transcriptase
Autonomous, e.g. L1 elements

SINE (Short Interspersed Elements)
Do not encode their own reverse transcriptase
Nonautonomous, e.g. Alu

How do plants and animals survive and thrive with so many insertions in genes and so much mobile DNA in the genome ?
Transposable elements can insert into both introns and exons (subject to negative selection)

Only the insertion into introns will remain in the population (less likely to cause deleterious mutation)

Vast majority can no longer move (inactive)

A few elements remain active, and their movement into genes can cause disease
e.g; Three separate insertions of LINEs have disrupted the factor VIII gene, causing hemophilia A. At least 11 Alu insertions into human genes have been shown to cause several diseases, including hemophilia B (in the factor IX gene), neurofibromatosis (in the NF1 gene), and breast cancer (in the BRCA2 gene).

safe havens
Successful transposable elements insert into so-called safe havens in the genome

For the grasses, safe haven: insert into other retrotransposons

Heterochromatin or centromeres (few genes but lots of repetitive DNA)

Ty3 is targeted to specific safe havens
Ty3 inserts exclusively near but not in tRNA genes ( do not interfere with the production of tRNAs)
Ty3 proteins recognize and bind to subunits of the RNA polymerase complex that have assembled at RNA promoters

R1 and R2 elements of arthropods insert into safe havens
R1 and R2 are LINEs: Insert only into genes that produce ribosomal RNA (rRNA)

Tc 1
(DNA transposon) 32 in the worm gene, transposes in somatic but not germ-line cells

piRNAs in animals
In the germ lines of several animal species including Drosophila and mammals, active transposons are repressed through the action of piRNAs (Piwi-interacting RNAs).

Like siRNAs, piRNAs are short single-stranded RNAs (26-30 nt in mammals) that interact with a protein complex

Once associated, piRNAs guide piwi-Argonaute (a protein complex) to degrade complementary mRNAs
does not originate from double stranded mRNA pathway, located in loci called pi-clusters that serve as traps to catch active transposons

Initiator tRNA
Special tRNA that initiates the translation of an mRNA in a ribosome. It always carries the amino acid methionine.
The initiator tRNA is thought to bind directly to the P site of the small ribosomal subunit and to play a critical role in recognizing the start codon in the mRNA. Although the initiation factors clearly help mediate these events, the structure of the tRNA itself also plays a key role.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Noncoding sequence within a eukaryotic gene that is transcribed into an RNA molecule but is then excised by RNA splicing to produce an mRNA.
Introns and exons are nucleotide sequences within a gene. Introns are removed by RNA splicing as RNA matures, meaning that they are not expressed in the final messenger RNA (mRNA) product, while exons go on to be covalently bonded to one another in order to create mature mRNA.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Messenger RNA (mRNA)
RNA molecule that specifies the amino acid sequence of a protein.
mRNA is synthesized in the nucleus using the nucleotide sequence of DNA as a template.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

DNA sequence that initiates gene transcription; includes sequences recognized by RNA polymerase.
Promoter sequences are DNA sequences that define where transcription of a gene by RNA polymerase begins. Promoter sequences are typically located directly upstream or at the 5′ end of the transcription initiation site.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Enzyme that degrades proteins by hydrolyzing peptide bonds.
Proteases were the first enzymes to be commercialised, partly on account of the history of availability of the first commercial enzymes and partly on account of need, since proteins are ubiquitous in nature and can be found in a wide variety of consumer stains, for example, variety of food stains as milk, egg and soya, blood, grass and human body fluids, and hence are a natural fit for household detergents.
From: Handbook for Cleaning/Decontamination of Surfaces, 2007

Large protein machine that degrades proteins that are damaged, misfolded, or no longer needed by the cell; its target proteins are marked for destruction primarily by the attachment of a short chain of ubiquitin.
The proteasome is a multi-subunit assembly of proteases that selectively degrades proteins, including transcription factors that regulate the cell cycle.
From: Clinical Cardio-Oncology, 2016

Reading frame
One of the three possible ways in which a set of successive nucleotide triplets can be translated into protein, depending on which nucleotide serves as the starting point.
The initiator AUG codon defines the reading frame of a mRNA. Translation proceeds from this start in steps of three nucleotides (one codon). The frequent occurrence of termination codons out of frame prevents translation in the wrong frame for other than short stretches.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Ribosomal RNA (rRNA)
RNA molecule that forms the structural and catalytic core of the ribosome.
Messenger RNA (mRNA) molecules carry the coding sequences for protein synthesis and are called transcripts; ribosomal RNA (rRNA) molecules form the core of a cell’s ribosomes (the structures in which protein synthesis takes place); and transfer RNA (tRNA) molecules carry amino acids to the ribosomes during protein synthesis.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Large macromolecular complex, composed of ribosomal RNAs and ribosomal proteins, that translates messenger RNA into protein.
Ribosomes are the structures where polypeptides (proteins) are built. They are made up of protein and RNA (ribosomal RNA, or rRNA). Each ribosome has two subunits, a large one and a small one, which come together around an mRNA—kind of like the two halves of a hamburger bun coming together around the patty.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

An RNA molecule with catalytic activity.
A ribozyme is a ribonucleic acid (RNA) enzyme that catalyzes a chemical reaction. The ribozyme catalyses specific reactions in a similar way to that of protein enzymes. Also called catalytic RNA, ribozymes are found in the ribosome where they join amino acids together to form protein chains.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Why can’t retrotransposons move from one cell to another like retroviruses?
a. They do not encode the env protein.
b. They are nonautonomous elements.
c. They require reverse transcriptase.
d. Answer choices a and b are true.
a. They do not encode the env protein. Retroviruses encode the env protein that surrounds the virus. This protein allows the virus to leave the host cell and infect another cell. Without the env protein, the virus is unable to leave the cell. Retrotranspososns do not encode the env protein and hence are unable to move from one cell to another.

Unlike retrotransposons, DNA transposons
a. have terminal inverted repeats.
b. generate a target site duplication upon insertion.
c. transpose via an RNA intermediate.
d. are not found in prokaryotes.
a. have terminal inverted repeats. DNA transposons are found in both eukaryotes and prokaryotes and have terminal inverted repeats.

The major difference between retrotransposons and retroviruses is that a. retrotransposons encode reverse transcriptase.
b. retroviruses move from one site in the genome to another.
c. retroviruses encode the env gene, which allows them to move from one cell to another.
d. None of the above is correct
c. retroviruses encode the env gene, which allows them to move from one cell to another. Retroviruses and retrotransposons both encode gag and pol genes. The pol gene encodes the reverse transcriptase responsible for converting RNA into DNA. However, the env gene is only found in retroviruses, and env protein encoded by this gene allows viruses to move from one cell to another.

Which of the following is true of reverse transcriptase?
a. It is required for the movement of DNA transposons.
b. It catalyzes the synthesis of DNA from RNA.
c. It is required for the transposition of retrotransposons. d. Answer choices b and c are correct.
d. Answer choices b and c are correct. Reverse transcriptase is encoded by the pol gene, which is found in both retroviruses and retrotransposons. It catalyzes the synthesis of DNA from RNA and is required to convert the viral RNA genome into DNA and also for the transposition of retrotransposons.

hich transposable element is used to introduce foreign DNA into the fruit fly Drosophila melanogaster?
a. Ac element
b. P element
c. Alu element
d. composite transposons
b. P element

What is the major reason why the maize genome is much larger than the rice genome?
a. Maize has more genes than rice.
b. Rice has more genes than maize.
c. Maize has more DNA transposons than rice.
d. Maize has more retrotransposons than rice.
d. Maize has more retrotransposons than rice. Genome size of organisms usually corresponds to the number of transposable element sequences rather than to gene content. Rice and maize are evolutionary relatives with a common ancestor. The genome size of maize is much larger simply because, over the years, maize has accumulated more retrotransposons.

Why are transposable elements found much more often in introns than in exons?
a. Transposable elements prefer to insert into introns.
b. Transposable elements prefer to insert into exons.
c. Transposable elements insert into both exons and introns but selection removes exon insertions.
d. None of the above is true.
c. Transposable elements insert into both exons and introns but selection removes exon insertions. Transposable elements can get inserted into both exons and introns; however, the insertions into exons can cause deleterious effects to the host organism and hence are subject to negative selection. Insertions into introns would not cause deleterious mutations and would remain in the population. Introns are an example of a safe heaven, meaning that insertion of transposable elements into these regions would not cause deleterious damage to the host organism.

Approximately what percent of the human genome is derived from transposable elements?
a. 10 percent
b. 25 percent
c. 50 percent
d. 75 percent
c. 50 percent. Human genome sequence revealed that around 50 percent of the human
genome is derived from transposable elements.

Why do plants and animals thrive with so many transposable elements in their genomes?
a. Most of the transposable elements are inactive due to mutation.
b. Active transposable elements are silenced by the host.
c. Most transposable elements are inserted in safe havens.
d. All of the above are true.
d. All of the above are true. This is mainly due to three reasons. Most transposable elements have accumulated mutations over time and are inactive. As a result, they prevent the production of functional transposase and reverse transcriptase and are unable to move any longer. Active transposable elements are silenced by the host regulatory mechanisms such as RNAi pathway in plants and C. elegans and piRNA pathway in animals. Finally, most transposable elements are inserted in safe havens, such as introns, and do not have a deleterious effect on the host.

RNA polymerase
Enzyme that catalyzes the synthesis of an RNA molecule from a DNA template using nucleoside triphosphate precursors.
RNA polymerase links ribonucleotides together in a 5′ to 3′ direction. The polymerase induces the 3′ hydroxyl group of the nucleotide at the 3′ end of the growing RNA chain which attacks (nucleophilic) the a phosphorous of the incoming ribonucleotide. A diphosphate is released and the 5′ carbon of the incoming nucleotide is linked through a phosphodiester bond to the 3′ carbon of the preceding nucleotide.
Reference: http://www2.csudh.edu/nsturm/CHEMXL153/RNASynthesisProcessing.htm

RNA processing
Broad term for the modifications that a precursor mRNA undergoes as it matures into an mRNA. It typically includes 5′ capping, RNA splicing, and 3′ polyadenylation.
RNA processing includes the addition of a methylated guanine residue to the 5’ end (called the cap), removing segments (introns) of the RNA internally by a process called RNA splicing, and adding 100–200 adenine nucleotides to the 3’ end (a process called polyadenylation).
From: Surgical Research, 2001

RNA splicing
Process in which intron sequences are excised from RNA molecules in the nucleus during the formation of a mature messenger RNA.
RNA splicing is a process that removes the intervening, non-coding sequences of genes (introns) from pre-mRNA and joins the protein-coding sequences (exons) together in order to enable translation of mRNA into a protein.
From: Handbook of Clinical Neurology, 2014

Small nuclear RNA (snRNA)
RNA molecule of around 200 nucleotides that participates in RNA splicing.
Small nuclear RNA (snRNA) is one of the small RNA with an average size of 150 nt. Eukaryotic genomes code for a variety of non-coding RNAs and snRNA is a class of highly abundant RNA, localized in the nucleus with important functions in intron splicing and other RNA processing (Maniatis and Reed, 1987).
Reference: https://www.sciencedirect.com/topics/neuroscience/small-nuclear-rna

Large assembly of RNA and protein molecules that splices introns out of pre-mRNA in the nucleus of eukaryotic cells.
Spliceosome is a large RNPC which, as the name itself indicates, is involved in splicing (i.e., ligating) the coding regions (called exons) of a precursor messenger RNA (pre-mRNA) with the concomitant excision of intervening noncoding regions (termed introns) (Berget, Moore, & Sharp, 1977; Brody & Abelson, 1985; Chow, Gelinas, Broker, & Roberts, 1977; Grabowski, Seiler, & Sharp, 1985).
From: Advances in Protein Chemistry and Structural Biology, 2017

Process in which RNA polymerase uses one strand of DNA as a template to synthesize a complementary RNA sequence.
Gene transcription is the process by which genes are copied into different types of RNAs, such as messenger RNA (mRNA) leading to the synthesis of proteins through translation, or noncoding RNA such as micro RNA (mRNA), transfer RNA (tRNA), or ribosomal RNA (rRNA) (Bolsover et al., 1997).
From: Encyclopedia of Bioinformatics and Computational Biology, 2019

Transfer RNA (tRNA)
Small RNA molecule that serves as an adaptor that “reads” a codon in mRNA and adds the correct amino acid to the growing polypeptide chain.
A specific amino acid is enzymatically attached at one end to a transfer RNA in the cytoplasm. Each type of transfer RNA molecule can be attached to only one type of amino acid, so each cell needs many types of transfer RNA. The other end of the transfer RNA molecule contains a three-nucleotide sequence called the anticodon.
Reference: https://www.sciencedirect.com/topics/neuroscience/transfer-rna

Process by which the sequence of nucleotides in a messenger RNA molecule directs the incorporation of amino acids into protein.
The nucleotide sequence of a gene, through the medium of mRNA, is translated into the amino acid sequence of a protein by rules that are known as the genetic code. Each group of three consecutive nucleotides in RNA is called a codon, and each codon specifies either one amino acid or a stop to the translation process.
Reference: https://www.ncbi.nlm.nih.gov/books/NBK26829/

Translation initiation factor
Protein that promotes the proper association of ribosomes with mRNA and is required for the initiation of protein synthesis.
Translation initiation is a key step for regulating the synthesis of several proteins. In bacteria, translation initiation involves the interaction of the mRNA with the ribosomal small subunit. Additionally, translation initiation factors 1, 2, and 3, and the initiator tRNA, also assemble on the ribosomal small subunit and are essential for efficiently recruiting an mRNA for protein biosynthesis.
Reference: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/translation-initiation

A protein that binds to a specific regulatory region of DNA to permit transcription of an adjacent gene.
The transcription activator protein (TAP) converts the closed RNAP-promoter complex into an open complex through simple stabilizing protein-protein interactions with RNAP.
Reference: https://science.sciencemag.org/content/352/6291/1330

Combinatorial control
Describes the way in which groups of transcription regulators work together to regulate the expression of a single gene.
Unlike prokaryotes that often use single proteins for transcriptional regulation of a gene, eukaryotic gene expression regulation involves the coordination of multiple proteins and is therefore combinatorial. This mechanism effectively integrates many different signaling pathways to provide a more complex network to meet the higher regulatory demand of a higher organism.
Reference: Combinatorial control of gene expression. Attila Reményi1,2,4, Hans R Schöler1,3 & Matthias Wilmanns2

Process by which a cell undergoes a progressive, coordinated change to a more specialized cell type, brought about by large-scale changes in gene expression.
Cell differentiation occurs during multiple stages of development. During cell differentiation, the cell size and shape changes dramatically, as does its ability to respond to signaling molecules. Signaling molecules are molecules that bring messages to cells that help the cell know which activities and processes to perform.
Reference: https://study.com/academy/lesson/what-is-cell-differentiation-process-importance-examples.html

DNA methylation
The enzymatic addition of methyl groups to cytosine bases in DNA; this covalent modification generally turns off genes by attracting proteins that block gene expression.
DNA methylation refers to the addition of a methyl (CH3) group to the DNA strand itself, often to the fifth carbon atom of a cytosine ring. This conversion of cytosine bases to 5-methylcytosine is catalysed by DNA methyltransferases (DNMTs). These modified cytosine residues usually lie next to a guanine base (CpG methylation) and the result is two methylated cytosines positioned diagonally to each other on opposite strands of DNA.
Reference: https://www.news-medical.net/life-sciences/What-is-DNA-Methylation.aspx

Micro RNA (miRNA)
Small noncoding RNA that controls gene expression by base-pairing with a specific mRNA to regulate its stability and its translation.
miRNAs (microRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. They generally bind to the 3′-UTR (untranslated region) of their target mRNAs and repress protein production by destabilizing the mRNA and translational silencing.
Reference: Molecular Biology. Academic Cell Update Edition. Book • 2nd Edition • 2013

Positive feedback loop
An important form of regulation in which the end product of a reaction or pathway stimulates continued activity; controls a variety of biological processes, including enzyme activity, cell signaling, and gene expression.
Unlike negative feedback loops, positive feedback loops amplify the starting signal. Positive feedback loops are usually found in processes that need to be pushed to completion, not when the status quo needs to be maintained.
Reference: https://www.khanacademy.org/science/ap-biology/cell-communication-and-cell-cycle/feedback/a/homeostasis?modal=1

Post-transcriptional control
Regulation of gene expression that occurs after transcription of the gene has begun; examples include RNA splicing and RNA interference.
Post-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein.
Reference: https://courses.lumenlearning.com/wm-biology1/chapter/reading-post-translational-control-of-gene-expression/

Regulatory DNA sequence
DNA sequence to which a transcription regulator binds to determine when, where, and in what quantities a gene is to be transcribed into RNA.
The regulatory sequence elements fall into two broad categories based on their distances from the promoter. Promoter proximal elements are located within a few hundred base pairs upstream of the transcription start site. Enhancer sequences can be located from tens to hundreds of kilobases from the start of transcription.
Reference: Gene Expression*
In Cell Biology (Third Edition), 2017

A protein that binds to a specific regulatory region of DNA to prevent transcription of an adjacent gene.
Repressors are defined as individuals who tend to use avoidance, suppression, repression, and denial of potential threats and conflicts.
From: Biomedical Psychiatric Therapeutics, 1984

Noncoding mRNA elements that directly control gene expression in response to changes in cellular conditions.

Riboswitches are segments of noncoding mRNA, ranging from 35 to 200 nucleotides, which change their conformation upon binding to metabolites, coenzymes, small molecules, or ions, to regulate gene expression. Riboswitches function as aptamers that serve as specific receptors for a given ligand, binding it when its concentration in the medium reaches a certain level.
Reference: Regulation of Gene Expression
Antonio Blanco, Gustavo Blanco, in Medical Biochemistry, 2017

RNA interference (RNAi)
Cellular mechanism activated by double-stranded RNA molecules that results in the destruction of RNAs containing a similar nucleotide sequence. It is widely exploited as an experimental tool for preventing the expression of selected genes (gene silencing).
RNAi plays an important role not only in regulating genes but also in mediating cellular defense against infection by RNA viruses, including influenza viruses and rhabdoviruses, a group that contains the causative agent of rabies.
Reference: https://www.britannica.com/science/RNA-interference

Small interfering RNA (siRNA)
Short length of RNA produced from double-stranded RNA during the process of RNA interference. It base-pairs with identical sequences in other RNAs, leading to the inactivation or destruction of the target RNA.
It is a conserved biological mechanism controlling normal gene expression. The silencing mechanism occurs at the levels of transcription, post-transcription and translation. RNAi can also cause augmentation of gene expression due to direct effects on the translation (Ebbesen et al., 2008).
Reference: https://www.sciencedirect.com/science/article/pii/S1319562X12000629

Transcription regulator
Protein that binds specifically to a regulatory DNA sequence and is involved in controlling whether a gene is switched on or off.
Transcription regulation plays an essential role in the development, complexity, and homeostasis of all organisms, as transcription is the first step in the universal pipeline of biological information flow from genome to proteome.
From: Leveraging Biomedical and Healthcare Data, 2019

SCID: Severe Combined Immunodeficiency Disease
Caused by a mutation in the gene encoding the blood enzyme adenosine deaminase (ADA)
As a result of the loss of this enzyme, precursor cells that give rise to one of the cell types of the immune system are missing
Unable to fight infection
Treatment: Stem cells can be removed from bone marrow and the wild type copy of the ADA gene is introduced using a retrovirus vector.
Transformed cells can then be infused back into the patients.

Caveat: Insertion of the viral vector can inactivate important genes and some of the treated patients have developed leukemia

Briefly describe the experiment that demonstrates that the transposition of the Ty1 element in yeast takes place through an RNA intermediate.
Boeke, Fink, and their co-workers demonstrated that transposition of the Ty element in yeast involved an RNA intermediate. They constructed a plasmid using a Ty element that had a promoter that could be activated by galactose, and an intron inserted into its coding region. First, the frequency of transposition was greatly increased by the addition of galactose, indicating that an increase in transcription (and production of RNA) was correlated to rates of transposition. More importantly, after transposition they found that the newly transposed Ty DNA lacked the intron sequence. Because intron splicing occurs only during RNA processing, there must have been an RNA intermediate in the transposition event.

Explain how the properties of P elements in Drosophila make gene-transfer experiments possible in this organism.
P elements are transposable elements found in Drosophila. Under certain conditions, they are highly mobile and can be used to generate new mutations by random insertion and gene knockout. As such, they are a valuable tool to tag and then clone any number of genes. P elements can also be manipulated and used to insert almost any DNA (or gene) into the Drosophila genome. P-element- mediated gene transfer requires inserting the DNA of interest between the inverted repeats necessary for P-element transposition. This recombinant DNA, along with helper intact P-element DNA (to supply the transposase), are then co-injected into very early embryos. The progeny of these embryos are then screened for those that contain the randomly inserted DNA of interest.

What are safe havens? Are there any places in the much more compact bacterial genomes that might be a safe haven for insertion elements?
Some transposable elements have evolved strategies to insert into safe havens—regions of the genome where they will do minimal harm. Safe havens include duplicate genes (such as tRNA or rRNA genes) and other transposable elements. Safe havens in bacterial genomes might be very specific sequences between genes or the repeated rRNA genes.

Transposase protein can
a. bind to DNA.
b. catalyze the excision of a transposable element from a donor site.
c. catalyze the insertion of a transposable element into a target site.
d. All of the above are correct.
d. All of the above are correct. Transposase protein is encoded by the transposase gene in DNA transposons. It is responsible for the mobilization of the transposase gene from DNA. During transposition, first it binds to DNA and catalyzes the excision of the transposase gene from the chromosome, then it catalyzes its reinsertion at other chromosomal locations/target site.

Which of the following are safe havens for transposable element insertions?
a. introns
b. exons
c. other transposable elements
d. Answer choices a and c are correct.
d. Both answer choices a and c are correct. In order to prevent harm to their host, evolutionarily successful transposable elements have inserted into safe havens such as introns, telomeric regions, and other transposable elements.

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