chapter 2
2-12 What is the basic building block of DNA?
The nucleotide.
2-13 The three major components of a nucleotide are:
- sugar (deoxyribose)
- phosphate (link sugars to form uprights of the DNA ladder)
- nitrogen base (pair to form rungs of the DNA ladder).
2-17 What chemical bonds holds the base pairs together?
Hydrogen bonds hold the bases together. Two hydrogen bonds hold adenine and thymine together and three hydrogen bonds hold guanine and cytosine together.
2-18 How are the DNA hydrogen bonds broken?
Heating to about 90°C causes hydrogen bonds to break and the bases to separate. In heating, the sugar- phosphate bonds are unaffected. Thus, if DNA is heated, two long chains of nucleotides will result. If allowed to cool, hydrogen bonds will reform between complementary bases and the chains will rejoin.
2-19 How do RNA and DNA differ?
RNA is a single chain of nucleotides whereas DNA is composed of two chains running in opposite directions and held together by hydrogen bonds. At the nucleotide level, they differ in the pentose sugar present. DNA has deoxyribose whereas RNA has ribose. They also vary in that a DNA nucleotide may contain thymine. This is replaced in RNA with uracil.
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2-20 In simple terms, explain how DNA codes for proteins.
The order of bases in DNA determines the order that amino acids are assembled at the ribosomes.
2-21 Describe the relationship between DNA, genes and chromosomes.
A chromosome is a long molecule of DNA. Chromosomes can be divided into sub-units called genes. Each gene is a section of DNA that codes for the production of a particular protein or form of RNA. Genes are made of DNA and a series of linked genes forms a chromosome.
2-22 What are triplets, codons and anticodons?
The DNA code is a three-letter (or base) code. Three bases code for a particular amino acid. A sequence of three bases in DNA coding for one amino acid is called a triplet. In messenger RNA, a sequence of three bases coding for one amino acid is called a codon. In transfer RNA, a sequence of three bases coding for one amino acid is called an anticodon. The codon is the complement of the triplet and the anticodon is the complement of the codon.
2-23 In terms of nucleotides and triplets, what is a gene?
A gene is a piece of double-stranded DNA that codes information for a particular function. Most genes code for the production of a protein. Genes vary in length, from thousands to millions of nucleotides. The order of nucleotides and thus, the order of bases, determines the type of protein formed. Three bases or a triplet code for a particular amino acid. If a gene is three thousand bases long, it can be described as consisting of one thousand triplets. (Note: Not all triplets in eukaryotic genes code for amino acids. Non- coding sections or introns are edited out during transcription.)
2-24 What information is encoded by a gene?
A gene codes for the production of a protein and forms of RNA. All proteins consist of building blocks called amino acids. Individual triplets code for particular amino acids. Therefore, a gene is a plan to construct a sequence of amino acids that form a protein.
2-26 Introns and exons are parts of eukaryotic gene sequences. Which parts seem to have the more important function?
Exons are the coding part of genes and seem to have the most importance. The role of introns is less clear, but they may have a role in controlling the decoding process. During the production of a finished piece of mRNA, the introns are edited out.
2-28 Are all codons needed? How many amino acids are there?
There are twenty different amino acids used to synthesise proteins. Sixty-four codons are more than sufficient to specify the amino acids. In a number of cases, several different codons specify the same amino acid.
2-29 Do all codons code for amino acids?
Not all codons specify amino acids. Four codons act as punctuation – there is one start and three different stop codons.
2-32 Name two types of functions of genes. Explain whether all genes are responsible for the production of a protein.
Genes can have one of two major functions. ‘Structural genes’ are directly responsible for a protein that is part of an organism’s structure or has a function. The products of ‘regulator genes’ control the action of other genes by determining whether a gene is active or not. In this way, the rate of production of particular materials can be controlled.
2-34 How do eukaryotic and prokaryotic genes differ?
- Prokaryote, one promoter may initiate the transcription of a number of polypeptide coding regions (genes). No introns present.
- Eukaryote, one promoter for each polypeptide coding region (gene). Introns present.
2-35 Explain how the trp operon switches genes on and off in prokaryotes.
When tryptophan is present in high concentration, it binds to a repressor protein coded for by a regulatory gene. The resulting molecule binds to the operator of the trpE, trpD, trpC, trpB and trpA genes. This stops RNA polymerase binding with the promoter and therefore the genes are not transcribed, and tryptophan is not synthesised. When tryptophan is present in low concentrations the repressor cannot bind to the operator, RNA can bind to the promoter and the genes coding for tryptophan synthesis are expressed resulting in the synthesis of tryptophan.
2-39 What type of reaction links amino acids together?
Condensation and peptide bonds.
2-40 How is denaturing caused and what types of bonds are broken?
Denaturing may be caused by high temperatures. High temperatures break hydrogen bonds and van der Waals forces, destroying the quaternary and tertiary structure. Denaturing can be caused by extremes of pH, which break ionic bonds again destroying quaternary and tertiary structure. Denaturing may also be caused by solvents such as alcohol, by solutes such as urea and by detergents.
2-43 Where is DNA found in prokaryotic and eukaryotic cells?
In prokaryotic cells, DNA is found in the cytosol. In eukaryotic cells, DNA is found in the nucleus, mitochondria and chloroplasts.
2-46 The genetic code is universal. What does this mean and why is this important in genetic engineering?
The genetic code is universal. This means that the same DNA triplet/tRNA anticodon/mRNA codon codes for the same amino acid in all living organisms. This is important in genetic engineering in that DNA can be inserted into other species and still express the same protein.
2-50 What is the function of CRISPR-Cas9 in bacteria?
CRISPR-Cas9 is used by bacteria to edit DNA of infecting viruses.
2-52 What are the potential applications of CRISPR-Cas9 technology?
CRISPR-Cas 9 technology could be used to correct mutations that result in disease, add new genes or switch faulty genes off.
2-53 Explain the steps in the polymerase chain reaction (PCR) and give examples of its use.
The polymerase chain reaction (PCR) is used to make copies of DNA.
Steps involved in PCR:
- DNA is denatured by heating to around 95°C.
- The sample is cooled to approximately 50°C. Primers – synthetic single strand pieces of DNA (usually) that are complementary to the DNA sequence either side of the target sequence are added and anneal to the exposed DNA strands.
- DNA nucleotides are added.
- The sample is heated to approximately 72°C. Taq polymerase is added (heat tolerant enzyme from Taq bacteria). This joins nucleotides together starting at the primer and continuing until the end of the template DNA.
- The cycle is repeated many times resulting in a mixture of DNA strands, including many copies of the desired sequence of DNA.
Used for forensic tests when small tissue samples may remain. It is also used in prenatal diagnosis to produce enough DNA to analyse for genetic abnormalities.
2-54 Give two reasons for performing gel electrophoresis on DNA.
Gel electrophoresis is used to sort out pieces of DNA into different lengths. The results allow the use of DNA fingerprinting for forensics or paternity testing, examine DNA for evolutionary relationships, and testing for different genetic diseases.
2-55 Use three words to summarise the steps in each PCR cycle.
Three words that summarise the PCR cycle are: denature, anneal and extend.
2-56 Why is Taq polymerase, the restriction enzyme, often used in PCR?
Taq polymerase has been isolated bacteria that live in hot springs. Therefore, it is not denatured by high temperatures and therefore does not have to be added during the PCR process.
2-58 What two features of DNA allow it to be sorted using gel electrophoresis?
DNA is negatively charged, and the sample must contain DNA of different lengths.
2-59 What are short tandem repeats (STRs)?
STRs are non-coding chromosomal regions of repeated 2–6 base pairs. The number of repeats varies between individuals.
2-63 What is a recombinant plasmid?
A recombinant plasmid is a plasmid that has been genetically engineered to contain DNA from another organism.
2-64 What role do recombinant plasmids play in DNA manipulation?
Recombinant plasmids are used as a vector to transport (transform) DNA into other bacterial cells.
2-69 What is the difference between transformation and transfection?
Transformation is when foreign DNA is incorporated into a prokaryotic cell whereas transfection is when foreign DNA is incorporated into a eukaryotic cell.
2-70 List the ways foreign DNA can be inserted into a cell.
Ways foreign DNA can be inserted into host cells:
- liposomes
- plasmid vectors
- viral vectors
- pronuclear injection
- ballistic DNA injection.
chapter 3
3-3 What is the difference between anabolic and catabolic reactions?
Anabolic reactions are those involving the building or synthesis of molecules whereas catabolic reactions are breakdown reactions.
3-4 What is the difference between exergonic and endergonic reactions? Give an example of each type.
Exergonic reactions (breaking things) release energy, e.g. respiration. Endergonic reactions (making or doing things) require an input of energy for them to proceed, e.g. any synthesis reaction such as protein synthesis.
3-5 Define the term ‘enzyme’.
An enzyme is an organic catalyst. They are proteins that alter the rate of reactions – usually to speed them up to a biologically useful rate. Many reactions occur naturally but at extremely slow rates. Enzymes only alter the rate (amount produced in a given time) of reaction. They do not alter the final amount of product produced.
3-7 Use the terms ‘substrate’, ‘enzyme’ and ‘product’ to explain the role of enzymes in living organisms.
Substrates are the materials that are to be processed. The processing could be a breakdown reaction (e.g.: digestion) or a synthesis reaction (e.g.: making proteins). The materials present at the end of the reaction are the products. Enzymes allow the formation of product from substrate in a time that allows the efficient operation of an organism. Many of the reactions catalysed by the enzyme would otherwise occur too slowly.
3-10 What is an enzyme’s active site and how is it formed?
Enzymes are proteins. The folding of the protein into its tertiary structure provides a site that matches with specific substrates. This site is called the active site.
3-11 Enzymes can be denatured. How is this done and what are the consequences?
Enzymes are proteins so they can be denatured by:
• high temperatures (break H bonds and van der Waals forces, destroying the quaternary and tertiary structure)
• extremes of pH (break ionic bonds, destroying the quaternary and tertiary structure).
3-12 Explain the difference between competitive and non-competitive enzyme inhibitors.
Competitive inhibitors have a similar shape to the specific substrate on which an enzyme acts. They compete with the enzyme for the active site, reducing the amount of enzyme available to catalyse the reaction.
Non-competitive inhibitors do not bind to the active site. Instead, they bind to another area of the enzyme (allosteric site). This results in a change in the shape of the active site which decreases the amount of enzyme available to catalyse the reaction.
3-13 What are coenzymes and what do they do?
Coenzymes are small, non-protein molecules that temporarily bind to enzymes increasing the enzyme’s ability to bind to the substrate. Coenzymes are also carrier molecules – they may carry electrons, protons, specific atoms or groups of atoms such as phosphate and energy.