GENETICS: Library Report
Genetics
Library Report:
1. Research the following concepts and indicate your
references.
A.
Discuss
what are bacteriophage
B.
Identify
and explain the DNA and RNA structure
C.
Explain
the importance of DNA and RNA as genetic materials
D.
Discuss
the concept of double helix
E.
Differentiate
the process of transcription and translation
A. Discuss about bacteriophage
·
Bacteriophage, a virus that infects bacterial cells; commonly
called a phage.
o
Term bacteria from greek word phagein (to devour)
o
Composed
of proteins that encapsulate a DNA or RNA genome, and may have relatively
simple or elaborate structures.
o
A
second pivotal was reported by Alfred Hershey and Martha Chase in 1952.
§ They studied cells
of the intestinal bacterium Escherichia
coli after infection by the virus T2.
§ A virus that attacks
bacterial cells is called a bacteriophage often shortened to phage.
(bacteria-eater)
§ Composed of head
(contains phage DNA), collar, tail and tail fibers.
B. Identify and explain the DNA and RNA structure
·
Chromosomes and DNA
o
Before
a cell divides, the chromosomes in its nucleus are doubled-stranded. Each
strand is called a chromatid.
o
A
chromatid is made up of tremendously long deoxyribonucleic
acid (DNA) molecules tightly coiled
around a mass of proteins called histones.
o
The
basic unit of a chromosome is called a nucleosome.
·
The structure of DNA
o
The
structure of DNA was confirmed in 1953 by Francis C. Crick (British) and James
D. Watson(American) who were working at Cavendish Laboratory in Cambridge
University, UK. They presented that each DNA molecule is a double-helix, made
up of complementary polynucleotide strands, that can ‘unzip’ to make copies of
itself.
§ DNA duplicates
itself and controls hereditary traits and undergoes mutation
o
Prior
to this event, Maurice F. Wilkins and Rosalind Elsie Franklin (both British)
had been doing X-ray diffraction studies of DNA at King’s College in London.
Their results had influenced the way Crick and Watson viewed the DNA molecule.
o
In
1962, Crick, Watson and Wilkins were awarded the Nobel Prize in Medicine for
their work on the structures of DNA. Since, the prize could not be awarded
posthumously, Franklin was not included as recipient because she had died of
cancer in 1958.
(Rabago,
Ph.D. et.al. (2003).Functional biology modular approach. Davao City: Vibal
Publishing House, Inc.)
·
Four Bases of DNA
o
Adenine (A)
o
Guanine (G)
o
Thymine (T)
o
Cytosine (C)
§ At any position on
the paired strands of a DNA molecule, if one strand has an A, then the partner
strand has a T; and if one strand a G, then the partner strand has a C.
§ Nothing restricts
the sequence of bases in a single strand, so any sequence could be present
along one strand.
·
DNA and the concept
of a Gene
o
DNA
is a genetic material; that is it is here where the gene is located.
o
A
gene is a portion of a DNA molecule that is responsible for transmission of a
trait from parents to offspring.
·
RNA STRUCTURE
o
There is another type of nucleic acid called ribonucleic acid (RNA) that plays an
equally important role in heredity.
o
For RNA, nucleosides are formed similarly to DNA. RNA exist as a single strand. Hairpin
is a common secondary/tertiay structure. It requires complementarity betweem
part of the strand. the figure on the left is a schematic representation of the
haipin structure.
o
Although DNA and RNA are
both nucleic acids (polymers of nucleotides), they differ in three main ways:
1.
The sugar in RNA is
ribose, not deoxyribose as it is in DNA.
2.
In RNA, the nucleotide
Thymine is replaced by the nucleotide Uracil.
3.
RNA is a single strand
and does not form a double helix as DNA does.
o
A ribozyme is an RNA
molecule that functions as an enzyme.
·
The Central Dogma of
Molecular Genetics
o
In
1958, Crick first proposed the idea that the sequence involved in the expression
of hereditary characteristics is from DNA to RNA to protein.
C. Explain the importance of DNA and RNA as genetic
materials
Nucleic
acids contain information regarding the amino acid sequence that results in
protein of functional importance.
- DNA
- Deoxy ribo Nucleic Acid
act as cellular library that contains necessary information for building
cells and tissues of an organism.
- RNA
– Ribo Nucleic Acid
has pivotal role in protein synthesis.
Structure
of DNA and RNA composed of multiple chemical units (polymer) of single chemical
units (monomers) called Nucleotides.
Length:
- DNA : composed of several hundred million nucleotides.
- RNA : composed of hundreds to thousands of nucleotides.
DNA and
RNA consist of four types of nucleotides which is linked through phosphoester
bond to a five carbon sugar molecule (pentose) that in turn linked to a base.
(Retrieved on Feb. 11, 2014 from http://www.understandbiology.com/2013/06/DNA-and-RNA.html)
RNA has a variety of different functions in the cell. Three of
these are listed below.
·
Messenger RNA (mRNA)
o Messenger RNA contains
genetic information. It is a copy of a portion of the DNA.
o It carries genetic
information from the gene (DNA) out of the nucleus, into the cytoplasm of the
cell where it is translated to produce protein.
·
Ribosomal RNA (rRNA)
o This type of RNA is a
structural component of the ribosomes. It does not contain a genetic message.
·
Transfer RNA (tRNA)
o Transfer RNA functions to
transport amino acids to the ribosomes during protein synthesis.
·
Small nuclear RNA (snRNA)
o These strands of RNA are
complexed with protein producing small nuclear ribonucleoproteins (snRNP). One
function, described later in this chapter, is the modification of the RNA transcript.
(Retrieved on Feb. 11, 2014 from http://faculty.clintoncc.suny.edu/faculty/michael.gregory/files/bio%20101/bio%20101%20lectures/Gene%20Expression/gene%20expression.htm)
D. Discuss the concept of double helix
·
Double Helix, is
a description of the molecular shape of a double-stranded DNA molecule.
o
In 1953, Francis Crick and James Watson first described the
molecular structure of DNA, which they called a "double helix," in
the journalNature. For this breakthrough discovery, Watson, Crick, and
their colleague Maurice Wilkins won a Nobel Prize in Physiology, or Medicine,
in 1962. However, a crucial contribution that enabled this discovery was made
by Rosalind Franklin, who was not acknowledged at that time. After her death,
Crick said that her contribution had been critical.
o
Describes the appearance of double stranded DNA, which is
composed of two linear strands that run opposite to each other, or anti
parallel, and twist together.
o
Each DNA strand within the double helix is a long, linear
molecule made of smaller units called nucleotides that form a chain.
o
The chemical backbones of the double helix are made up of sugar
and phosphate molecules that are connected by chemical bonds, known as sugar-phosphate
backbones.
o
The two helical strands are connected through interactions
between pairs of nucleotides, also called base pairs.
o Two
types of base pairing occur:
§ nucleotide
A pairs with T
§ nucleotide
C pairs with G
(Retrieved on Feb. 11, 2014 from http://www.nature.com/scitable/definition/double-helix-277)
E. Differentiate the process of transcription and
translation
·
Transcription is the synthesis of RNA from a DNA template.
·
Only one strand of DNA is copied.
·
A single gene may be transcribed
thousands of times.
·
After transcription, the DNA strands
rejoin.
·
Some of the RNA produced by
transcription is not used for protein synthesis. These RNA molecules have other
functions in the cell.
·
Transcription is the process by which DNA is copied (transcribed) to
mRNA, which carries the information needed for protein synthesis. Transcription
takes place in two broad steps. First, pre-messenger RNA is formed, with the
involvement of RNA polymerase enzymes. The process relies on Watson-Crick base
pairing, and the resultant single strand of RNA is the reverse-complement of
the original DNA sequence. The pre-messenger RNA is then "edited" to
produce the desired mRNA molecule in a process called RNA
splicing.
Retrieved on Feb. 11, 2014 from http://www.atdbio.com/content/14/Transcription-Translation-and-Replication)
·
The enzyme RNA polymerase is
responsible for creating RNA by copying the template strand of DNA.
·
Before transcription can begin in
eukaryotes, proteins called transcription factors must
bind to a region of the DNA called the promoter. The
promoter identifies the start of a gene, which strand is to be copied, and the
direction that it is to be copied.
·
RNA polymerase binds to the
transcription factors and the promoter.
·
In bacteria, RNA polymerase binds
directly to the promoter without the assistance of transcription factors.
·
RNA polymerase unwinds the DNA.
·
RNA polymerase arranges nucleotides
that are complimentary to the DNA strand being copied. RNA contains uracil
instead of thymine.
·
The direction of synthesis is 5' to
3'.
·
A gene can be transcribed many times
by multiple RNA polymerase molecules all transcribing at the same time. One RNA
polymerase molecule follows another as transcription proceeds.
·
In bacteria and in eukaryotes,
transcription ends after a specific code is transcribed. In bacteria,
a termination sequence in the DNA indicates where
transcription will stop. In eukaryotes, transcription stops shortly after a
sequence of bases called the polyadenylation signal.
·
The strand of RNA that is initially
produced by transcription is called a primary transcript.
·
Some primary transcripts are never
translated into protein. These RNA molecules have other functions in the cell.
·
In eukaryotic cells, primary
transcripts that are to be translated into protein are modified. These
transcripts are called precursor mRNA (or pre-mRNA).
·
A modified guanine nucleotide
"cap" is added to the 5’ end and a poly-A tail (50 to 250 adenines)
is added to the 3’end of the molecule. These modifications are thought to 1)
enhance the movement of mRNA through the nuclear pores into the cytoplasm, 2)
prevent the destruction of mRNA by hydrolytic enzymes, and 3) help ribosomes
attach during translation.
·
The 5' end and the 3' end each
contain nucleotides that are not translated into protein. These two regions are
called the 5' UTR (untranslated region) and the 3' UTR.
·
Eukaryotic genes contain regions
that are not translated into proteins. These regions of DNA are called introns (intervening
sequences) and must be removed from mRNA by a process called RNA splicing.
Their function is not well understood.
·
The remaining portions of DNA that
are translated into protein are called exons (expressed).
After intron-derived regions are removed from mRNA, the remaining fragments-
derived from exons- are spliced together to form a mature mRNA
transcript.
·
The process of RNA splicing is
carried out by complexes of proteins and small RNA molecules called
spliceosomes. The RNA component of spliceosomes is called small nuclear RNA or
snRNA. The snRNA is joined together with protein to form small nuclear
ribonuclearprotein (snRNP). Small ribonuclearproteins and other proteins
together form spliceosomes.
·
Some introns have catalytic (enzyme)
capabilities and they are able to catalyze their own removal from the primary
transcript.
·
Transcription and mRNA processing
occur in the nucleus.
·
Alternative
RNA Splicing
·
A single gene is capable of
producing more than one different polypeptide by removing different introns
from the primary RNA transcript.
·
For example, humans have an
estimated 20,000 genes. These genes produce as many as 100,000 different
proteins due to alternative RNA splicing.
TRANSLATION
·
The
mRNA formed in transcription is transported out of the nucleus, into the
cytoplasm, to the ribosome (the cell's protein synthesis factory). Here, it
directs protein synthesis. Messenger RNA is not directly involved in protein
synthesis − transfer RNA (tRNA) is required for this. The process by which mRNA
directs protein synthesis with the assistance of tRNA is called translation.
·
The
ribosome is a very large complex of RNA and protein molecules. Each three-base
stretch of mRNA (triplet) is known as a codon, and one
codon contains the information for a specific amino acid. As the mRNA passes
through the ribosome, each codon interacts with the anticodon of a specific transfer RNA (tRNA)
molecule by Watson-Crick base pairing.
·
This
tRNA molecule carries an amino acid at its 3′-terminus, which is incorporated
into the growing protein chain. The tRNA is then expelled from the ribosome.
(Retrieved
on Feb. 11, 2014 from http://www.atdbio.com/content/14/Transcription-Translation-and-Replication)
·
Translation is the process of translating the
sequence of a messenger RNA (mRNA) molecule to a sequence of amino acids during
protein synthesis. The genetic code describes the relationship between the
sequence of base pairs in a gene and the corresponding amino acid sequence that
it encodes. In the cell cytoplasm, the ribosome reads the sequence of the mRNA
in groups of three bases to assemble the protein.
Translation Processes
·
Initiation: When a
small subunit of a ribosome charged with a tRNA+the amino acid methionine
encounters an mRNA, it attaches and starts to scan for a start signal. When it
finds the start sequence AUG, the codon (triplet) for the amino acid
methionine, the large subunit joins the small one to form a complete ribosome
and the protein synthesis is initiated.
·
Elongation: A new
tRNA+amino acid enters the ribosome, at the next codon downstream of the AUG
codon. If its anticodon matches the mRNA codon it basepairs and the ribosome
can link the two aminoacids together.(If a tRNA with the wrong anticodon and
therefore the wrong amino acid enters the ribosome, it can not basepair with
the mRNA and is rejected.) The ribosome then moves one triplet forward and a
new tRNA+amino acid can enter the ribosome and the procedure is repeated.
·
Termination: When the ribosome reaches one of three stop codons,
for example UGA, there are no corresponding tRNAs to that sequence. Instead
termination proteins bind to the ribosome and stimulate the release of the
polypeptide chain (the protein), and the ribosome dissociates from the mRNA.
When the ribosome is released from the mRNA, its large and small subunit
dissociate. The small subunit can now be loaded with a new tRNA+methionine and
start translation once again. Some cells need large quantities of a particular
protein. To meet this requirement they make many mRNA copies of the
corresponding gene and have many ribosomes working on each mRNA. After
translation the protein will usually undergo some further modifications before
it becomes fully active.
(Retrieved on Feb. 11, 2014 from http://www.nobelprize.org/educational/medicine/dna/b/translation/translation_process.html)
Terminologies
·
A codon is a trinucleotide sequence of DNA or
RNA that corresponds to a specific amino acid. The genetic code describes the
relationship between the sequence of DNA bases (A, C, G, and T) in a gene and
the corresponding protein sequence that it encodes. The cell reads the sequence
of the gene in groups of three bases. There are 64 different codons: 61 specify
amino acids while the remaining three are used as stop signals.
·
Base
pairs are
the building blocks of the DNA double
helix, and contribute to the folded structure of both DNA and RNA. Dictated
by specific hydrogen bonding
patterns, Watson-Crick base pairs (guanine-cytosine and adenine-thymine)
allow the DNA helix to maintain a regular helical structure that is independent
of itsnucleotide sequence. The complementary nature of this based-paired structure
provides a backup copy of all genetic information encoded within double-stranded DNA.
The regular structure and data redundancy provided by the DNA double helix make
DNA well suited to the storage of genetic information, while base-pairing
between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA, and RNA polymerase transcribes DNA into RNA. Many
DNA-binding proteins can recognize specific base pairing patterns that identify
particular regulatory regions of genes.
·
Intramolecular
base pairs can
occur within single-stranded nucleic acids. This is particularly important in
RNA molecules (e.g., transfer RNA),
where Watson-Crick base pairs (G-C and A-U) permit the formation of short
double-stranded helices, and a wide variety of non-Watson-Crick interactions
(e.g., G-U or A-A) allow RNAs to fold into a vast range of specific
three-dimensional structures.
In addition, base-pairing between transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for themolecular
recognition events
that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence ofproteins.
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