Reading Scientific Papers 2 - the warm-up revision

Task 1: Read the passage below about DNA.

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.

Task 2: Vocabulary: Match the words on the left with their meanings on the right

Word	Definition
1 Cell	A an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus
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

Task 3: Pronoun referents:
8 What does those in paragraph 2 refer to?
9 What does the first its in  paragraph 3 refer to?
10 What does the second its in paragraph 3 refer to?

Task 4: Structure questions:
11 What is the subject of paragraph 2?
12 What is the topic sentence of paragraph 3?

Task 5: 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 6: 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. 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). (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. These allowable base components of nucleic acids can be arranged in the polymer 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 7: 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 8: 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".