Week 1 revision.
Read the passage below about DNA and answer
the questions that follow.
Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the biological development of
a cellular form of life
or a virus. All known cellular life and some viruses
have DNAs. DNA is a long polymer of nucleotides (a polynucleotide) that encodes
the sequence of amino acid residues in proteins, using the genetic code: each amino acid is represented by
three consecutive nucleotides (a triplet code).
In eukaryotic cells, such as those of plants,
animals, fungi
and protists, most of the DNA is located in the cell nucleus, and each DNA molecule is usually packed
into a chromosome and shaped as a double helix.
By contrast, in simpler cells called prokaryotes, including the eubacteria and archaea, DNA is directly in the cytoplasm (not separated by a nuclear envelope) and is circular. The cellular
organelles known as chloroplasts and mitochondria also carry DNA. DNA is thought to
have originated approximately 3.5 to 4.6 billion years ago.
DNA is responsible for the genetic propagation of most inherited
traits. In humans, these
traits range from hair color to disease susceptibility.
The genetic information encoded by an organism's DNA is called its genome.
During cell division, DNA is replicated, and during reproduction is transmitted to offspring. The offspring's genome is a
combination of the genomes of its parents. Lineage studies can be
done because mitochondrial DNA only
comes from the mother, and the Y chromosome only comes from the father.
In humans, the mother's mitochondrial DNA together with 23 chromosomes from each parent combine to form
the genome of a zygote, the fertilized egg.
As a result, with certain exceptions such as red blood cells, most human cells contain 23
pairs of chromosomes, together with mitochondrial DNA inherited from the
mother.
|
Word |
Definition |
|
1 Cell |
A an organism
with a complex cell or cells,
in which the genetic material is organized into a membrane-bound
nucleusnuclei |
|
2
Polymer |
B a discrete structure of a cell
having specialized functions |
|
3 Nucleotide |
C the structural and functional unit of all living organisms,
and is sometimes called the "building block of life |
|
4 Eukaryote |
D a chemical compound that consists of a heterocyclic base, a sugar, and
one or more phosphate
groups |
|
5 Chromosome |
E a jelly-like material that fills cells. |
|
6 Cytoplasm |
F a large macromolecule into which DNA is normally packaged
in a cell. |
|
7
Organelle |
G a term used to describe molecules consisting of structural
units and a large number of repeating
units connected by covalent chemical bonds |
Pronoun referents:
8 What does those in line 1 of paragraph 2 refer to?
9 What does its in line 3 of paragraph 3 refer to?
10 What does its in line 5 of paragraph 3 refer to?
Main point questions:
11 What is the subject of paragraph 2?
12 What is the topic sentence of paragraph 3?
Comprehension questions:
13 What does this passage tell us some viruses and all forms of cellular life have in common?
14 When is DNA replicated?
15 How old is DNA?
16 Why is the number 23 significant in human DNA?
Task 1
Read the following
passage and make up
5 vocabulary
questions, 5 pronoun referent questions, 3 main point or topic sentence
questions and 5 comprehension questions. Remember to write down the answers on
a separate piece of paper. When you are finished the teacher will check your
questions/answers.
DNA Overview
DNA consists of a pair of molecules, organized as
strands running start-to-end and joined by hydrogen bonds along their lengths.[2] Each strand is a chain of chemical
"building blocks", called nucleotides, of which there are four types: adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T).[2] (Thymine should not be confused with thiamine, which is vitamin B1.) The
DNA of some organisms, most notably of the PBS1 phage,
have Uracil (U) instead of T.[3] These allowable base components of
nucleic acids can be arranged in thepolymer in any order, giving the molecules a
high degree of uniqueness.
DNA contains the genetic information, that is
inherited by the offspring of an organism. This information is determined by
the sequence of base pairs along its length. A
strand of DNA contains genes, areas that regulate genes, and areas that either have no
function, or a function yet unknown. Genes are the
units of heredity and can be loosely viewed as the organism's
"cookbook" or "blueprint". DNA is often referred to as the
molecule of heredity.
Each base on one strand forms a bond with just one kind of base on another
strand, called a "complementary" base: A bonds with T, and C bonds
with G. Therefore, the whole double-strand sequence can be described by the
sequence on one of the strands, chosen by convention.[2] Two nucleotides paired together are
called a base pair. On rare occasions, wrong pairing can
happen, when thymine goes into its enol
form or cytosine goes into its imino
form.
The double-stranded structure of DNA provides a simple mechanism for DNA replication: the two strands are separated,
and then each strand's complement is recreated by exposing the strand to a
mixture of the four bases. An enzyme makes the complement strand by
finding the correct base in the mixture and bonding it with the original
strand. In this way, the base on the old strand dictates which base appears on
the new strand, and the cell ends up with an extra copy of its DNA.
Other interesting points:
·
DNA is an acid because of the phosphate groups between
each deoxyribose. This is the primary reason why DNA has a negative charge.
·
The "polarity" of each pair is important: A+T
is not the same as T+A, and C+G is not the same as G+C (note that the term "polarity"
is never used in this context -- it's just a suggestive way to get the idea
across).
·
Mutations are the results
of the cells' attempts to repair chemical imperfections in this process, where
a base is accidentally skipped, inserted, or incorrectly copied, or the chain
is trimmed, or added to. Many mutations can be described as combinations of
these accidental "operations". Mutations can also occur after
chemical damage (through mutagens), light (UV damage), or through other more complicated
gene swapping events.
·
DNA molecules that act as enzymes
are known in laboratories, but none have been known to be found in life so far.
·
In addition to the traditionally viewed duplex form of
DNA, DNA can also acquire triplex and quadruplex forms. They have Hoogsteen base pairing
instead of the Watson-Crick base pairing found in duplex forms.
·
DNA differs chemically from ribonucleic acid (RNA) by having a sugar
2-deoxyribose instead of ribose in its backbone. In addition, in
most RNA, the nucleotides thymine (T) are replaced by uracil
(U).
Task 2
Read the following passage and make up
5 vocabulary questions, 5 pronoun referent questions, 3 main
point or topic sentence questions and 5 comprehension questions. Remember to
write down the answers on a separate piece of paper. When you are finished the
teacher will check your questions/answers.
Molecular
Structure
Although sometimes called "the molecule of heredity", DNA
macromolecules as people typically think of them are not single molecules.
Rather, they are pairs of molecules, which entwine like vines, in the shape of
a double helix. Each molecule
is a strand of DNA: a chemically linked chain of nucleotides, each of which consists of a sugar
(deoxyribose), a phosphate and one of five kinds of nucleobases ("bases"). Because DNA
strands are composed of these nucleotide subunits, they are polymers.
The diversity of the bases means that there are five kinds of nucleotides,
which are commonly referred to by the identity of their bases. These are adenine (A), thymine (T), uracil
(U), cytosine (C), and guanine (G). U is rarely found in DNA except as
a result of chemical degradation of C, but the DNA of some viruses, notably
PBS1 phage DNA, has U and not T. Similarly, RNA usually contains U in place of
T, but in certain RNAs such as transfer RNA, T is always found in some
positions. Thus, the major difference between DNA and RNA is the sugar,
2-deoxyribose in DNA and ribose in RNA.
In a DNA double helix, two polynucleotide strands can associate through the
hydrophobic effect and pi stacking. Which strands associate depends on
complementary pairing. Each base forms hydrogen bonds readily to only one other base,
A to T forming two hydrogen bonds, and C to G forming three hydrogen bonds. The
GC content and length of each DNA molcule dictates the strength of the
association; the more complementary bases exist, the stronger and
longer-lasting the association, characterised by the temperature required to
break the hydrogen bond, its melting temperature (also
called Tm value)).
A cell's machinery separates the DNA double helix, and uses each DNA strand
as a template for synthesizing a new strand which is nearly identical to the
previous strand. Errors that occur in the synthesis are called mutations. This process of replication is
mimiced in vitro by a process called Polymerase chain
reaction (PCR).
Because pairing causes the nucleotide bases to face the helical axis, the
sugar and phosphate groups of the nucleotides run along the outside; the two
chains they form are sometimes called the "backbones" of the helix.
In fact, it is chemical bonds between the phosphates and the sugars that link
one nucleotide to the next in the DNA strand.
Task 3
Read the following passage and make up
5 vocabulary questions, 5 pronoun referent questions, 3 main
point or topic sentence questions and 5 comprehension questions. Remember to
write down the answers on a separate piece of paper. When you are finished the
teacher will check your questions/answers.
Nucleotide Sequence
Within a gene, the sequence of nucleotides along a DNA strand defines a
messenger RNA sequence which then defines a protein, that an organism is liable to manufacture or "express" at one or several points in its
life using the information of the sequence. The relationship between the
nucleotide sequence and the amino-acid sequence of the
protein is determined by simple cellular rules of translation,
known collectively as the genetic code. The genetic
code consists of three-letter 'words' (termed a codon) formed from a sequence
of three nucleotides (e.g. ACT, CAG, TTT). These codons can then be translated
with messenger RNA and then transfer RNA, with a codon corresponding to a
particular amino acid. There are 64 possible codons (4 bases in 3 places 43) that encode 20 amino
acids. Most amino acids, therefore, have more than one possible codon. There
are also three 'stop' or 'nonsense' codons signifying the end of the coding
region, namely the UAA, UGA and UAG codons.
In many species, only a small fraction of the total
sequence of the <genome appears to encode protein. For example,
only about 1.5% of the human genome consists of
protein-coding exons. The function of the rest is a matter of
speculation. It is known that certain nucleotide sequences specify affinity for
DNA binding proteins,
which play a wide variety of vital roles, in particular through control of
replication and transcription. These sequences are frequently called regulatory sequences, and
researchers assume that so far they have identified only a tiny fraction of the
total that exist. "Junk DNA" represents
sequences that do not yet appear to contain genes or to have a function. The
reasons for the presence of so much non-coding DNA in eukaryotic genomes and the extraordinary
differences in genome size ("C-value") among species represent a long-standing
puzzle in DNA research known as the "C-value enigma".
Some DNA sequences play structural roles in chromosomes. Telomeres and centromeres typically contain few (if any)
protein-coding genes, but are important for the function and stability of
chromosomes. Some genes code for "RNA genes" (see tRNA
and rRNA). Some RNA genes code for transcripts that
function as regulatory RNAs (see siRNA) that influence the function of other RNA
molecules. The intron-exon structure of some genes (such as immunoglobin and
protocadeherin genes) is important for allowing alternative splicing of
pre-mRNA which allows several different proteins to be made from the same gene.
Indeed, the 34,000 human genes encode some 100,000 proteins. Some non-coding
DNA represents pseudogenes, which have been
hypothesized to serve as raw genetic material for the creation of new genes
through the process of gene duplication and divergence. Some
non-coding DNA provided hot-spots for duplication of short DNA regions; such
sequence duplication has been the major form of genetic change in the human
lineage (see evidence from the Chimpanzee Genome
Project). Exons interspersed with introns allows for "exon
shuffling" and the creation of modified genes that might have new adaptive
functions. Large amounts of non-coding DNA is probably adaptive in that it
provides chromosomal regions where recombination between
homologous portions of chromosomes can take place without disrupting the
function of genes. Some biologists such as Stuart Kauffman have speculated that non-coding
DNA may modify the rate of evolution of a species.
Sequence also determines a DNA segment's susceptibility to cleavage by restriction enzymes, the
quintessential tools of genetic engineering. The
position of cleavage sites throughout an individual's genome determines one
kind of an individual's "DNA fingerprint".