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macromolecules TOPIC 1 Chapter 1: Organisation L arge molecules, called macromolecules, are important in the biological world. Life’s main macromolecules are examples from the following main groups: Nucleic acids, Proteins, Polysaccharides and Lipids. Living cells make a vast number of these different molecules, there are millions of different types of protein in nature alone. Each macromolecule generally consists of smaller organic building blocks called monomers that are joined into chains to form polymers. M1 The chemical unit of genetic information in most organisms is DNA M1.1 Model the structure of DNA as a double helix made up of a sequence of complementary bases joined by weak bonds. The bases are attached to a sugar phosphate backbone Deoxyribonucleic Acid DNA) is a remarkable chemical found in virtually all forms of life. Since its isolation in 1869 by a Swiss chemist, Friedrich Miescher, DNA has been shown to be of fundamental importance in all living cells. Miescher identified a molecule that was acidic and contained the element phosphorus. As it was found primarily in the nuclei of cells it was named a nucleic acid. DNA may be found as a simple loop (as in some bacteria) that nonetheless contains all the information needed by the cell to reproduce identical offspring. Human DNA, on the other hand, has some 25,000 genes in it and, if stretched out, its length would be about 2 metres for each cell. Key Point • DNA is the chemical found in all cells that controls virtually everything that happens in cells It was in the early 1940s that the structure of DNA began to be unravelled. The two scientists credited with discovering the molecular structure of the molecule were a young American, James Watson, and a British scientist, Francis Crick. Their first task involved studying all of the data that was available to help piece together the 3D structure of the molecule. One technique that was particularly useful in deducing the double helical structure of DNA was X-ray diffraction as shown in Figure 101. Beams of X-rays diffracted from DNA crystal Source of X-rays Sample of DNA Figure 101 X-ray diffraction technique Photographic Film Figure 102 X-ray photograph Figure 102 shows a copy of the X-ray diffraction photograph of DNA obtained by Rosalind Franklin in London in 1952. It was this photograph that enabled Watson and Crick to formulate their model of the double helical structure of DNA which they announced in 1953. They were later awarded a Nobel Prize in 1962 for this discovery. 2 BIOLOGY: Key Ideas – THIRD EDITION MACROMOLECULES DNA was known to be composed of a long sugar phosphate backbone with organic bases attached to a sugar, as shown in Figure 103. Sugar Phosphate Base Sugar Phosphate Sugar Phosphate Base Base Sugar Phosphate Base Nucleotide Figure 103 The repeating nucleotide sequence in the molecule of DNA The repeating unit shaded in the box is the basic building unit of the DNA molecule called a nucleotide. In DNA there are four different bases: Adenine (A), Cytosine (C), Guanine (G) and Thymine (T). The sugar is ‘deoxyribose’ and gives rise to the name deoxyribo-nucleic acid which is abbreviated DNA. The phosphate of one nucleotide is attached to the sugar of the next nucleotide in a line that results in a backbone of alternating phosphates and sugars from which the bases project. Each base can form weak hydrogen bonds with an appropriate partner. Adenine only bonds with Thymine and Guanine only bonds with Cytosine i.e. A—T and G—C. The arrangement of atoms in the bases is such that A can link with T with two hydrogen bonds and G can link with C with three hydrogen bonds. Evidence for this complementary bonding is supported by the fact that each species has identical amounts of Adenine and Thymine bases in their DNA, and also identical amounts of Guanine and Cytosine. The sequence of bases varies from one molecule of DNA to another. A molecule of DNA varies in its length, often depending on the particular species in which it is found. In humans, a molecule of DNA may be up to 9 cm in length and consists of millions of nucleotide pairs. The DNA molecule has two complementary strands as shown in Figure 104. The actual double helical shape, as suggested by the X-ray diffraction and modelled by Watson and Crick, is illustrated in Figure 105. A T G C G G T A T C G T A C G C C A T A G C Figure 104 Base pairing in DNA One obvious advantage of this model was that its structure suggested the basic mechanism of DNA replication, a process in which DNA makes extra copies of itself. The hydrogen bonds that link the bases can easily be broken and re-formed, which is essential in both DNA replication and the process of protein synthesis. The sugar, phosphate and base represent the building blocks of DNA which is one nucleotide unit. Bases A T Deoxyribose sugar Phosphate Weak hydrogen bonds between bases Figure 105 Bonds are formed between DNA bases Essentials Text Book 3 macromolecules TOPIC 1 The sugar and phosphate groups form two spiral, parallel chains much like a rope ladder and the paired complementary bases form the rungs. See Figure 106. A T C G A T Key Points G A DNA: • determines our genetic make-up C C • is the chemical that enables cells to reproduce or make other copies of themselves T G G • is the chemical that makes us who we are • directs the synthesis of proteins (protein synthesis) C A T C G A DNA is made up of two strands to form a double helix structure (see Figure 104, 106). T A Each strand is made up of repeating nucleotide units called Nucleotides. T G A C T Figure 106 The DNA double helix Key Points One nucleotide is made up of • a sugar (deoxyribose) molecule • a base (A, T, C, G) molecule • a phosphate molecule (see Figure 105) Complementary bases link to each other to hold the double helix together. • A—T • G—C M2 The structural unit of information in the cell is the chromosome M2.1 Know that a chromosome is made up of many genes Chromosomes are thread-like structures that contain DNA and are found in the nucleus of eukaryotic cells. These chromosomes are not visible unless the cell is dividing, because they are too long and entangled to be easily identified. When stained and viewed through microscopes, the mass of chromosomes appears as a material called chromatin. Figure 108 shows a typical set of human male chromosomes. Such a set is known as the human karyotype. Parents pass on to their offspring coded information in the form of hereditary units called genes. Genes are made up of DNA, which as we have seen is a large molecule composed of a series of repeating units called nucleotides. It is the coded sequence of the four bases A, T, G and C that determines the actual type and nature of the genes. Most genes program cells to synthesize specific proteins and it is these that produce the organism’s inherited traits. Chromosomes, the structures that contain genes, may contain hundreds or thousands of genes. 4 BIOLOGY: Key Ideas – THIRD EDITION MACROMOLECULES DNA Chromosome Nucleus Cells Molecular code Structures made up of DNA that carry many genes The organelle that contains chromosomes The basic unit of structure and function. Contains the nucleus Genes A T G C G G T A T C G T A C G C C A T A G C Specific sequences of DNA that code for partcular proteins Figure 107 Cells, chromosomes, genes and DNA A gene’s specific location along the length of the chromosome is termed the gene’s locus. In Figure 107, the gene is represented as a sequence of lettered bases in a segment of DNA. The DNA consists of 2 strands, one strand containing the gene that codes for a polypeptide sequence, the other strand being complementary to this. The DNA is represented as a double helix molecule that is bound to proteins to form structures called chromosomes. Each chromosome, containing up to thousands of genes, is found in the nucleus of a cell. Tissue (somatic) cells in humans each have 46 such chromosomes. They are normally numbered from largest to smallest and in Figure 108 the small chromosomes lower right are called the sex chromosomes and referred to as X Figure 108 A set of male human and Y in a human male. chromosomes Key Points • Chromosomes are rod shaped structures found in cells; they are not visible in non dividing cells. • Chromosomes are made up of chromatin which is a complex of DNA and protein molecules. • Each chromosome contains one very long DNA molecule which averages around 1.5 108 nucleotide pairs. • Human cells contain 46 chromosomes (23 pairs). Cells in males have an odd matching pair of chromosomes; the sex chromosomes X and Y. Focus Questions 1. Draw a short section of three nucleotide pairs to illustrate the structure of DNA. Label- phosphate, sugar, base and nucleotide. 2. Explain the role of complementary base pairing in the double helix structure of DNA. 3. State the difference between chromatin and chromosomes. 4. Explain the difference between DNA, genes and chromosomes. Essentials Text Book 5 macromolecules TOPIC 1 M2.2 Explain that each chromosome has genes specific for that chromosome making it identifiable A gene is a section on a chromosome that codes for a protein or part of a protein molecule. Genes provide the code for an organism’s structural and functional characteristics. Thomas Morgan, a scientist working at Columbia University, first associated a specific gene with a particular chromosome. He worked with the fruit fly Drosophila melanogaster and traced a gene that was linked to the sex chromosome. Humans have approximately 25,000 genes in what is called the human genome. In 1990 the international effort directed at mapping the entire human genome began. Scientists set themselves the goal to work out the location of the genes located on the 46 chromosomes, working out the actual sequence of DNA bases in the entire human genome. It is estimated that there are about 3 billion DNA bases in a human. In order to sequence the human genome, maps of the chromosomes needed to be constructed. In the largest cooperative project in the history of the biological sciences, workers from USA, France, Britain, Canada, Japan, Australia and other countries participated in the Human Genome Project,. The main aim of this project is to map genes to chromosomes and sequence the human genome. At the Women’s and Children’s Hospital in Adelaide, researchers sequenced the DNA on chromosome 16. Biologists and researchers continue to be provided with vast amounts of information that will hold the key to understanding the structure, organisation and function of the DNA in chromosomes. Knowledge about DNA can potentially reveal such factors as the likelihood that people may suffer from certain conditions, or new ways to diagnose, treat or prevent diseases. There are several thousand human diseases with inheritance that is controlled by single genes that have been mapped to a specific location on the chromosomes. Each chromosome has specific gene positions or loci. The table beneath provides some information about some common genetic diseases. Figure 109 shows the loci of two genes on chromosome 19 in humans. Gene The chromosome number on which the gene is located ABO 9 HBB 11 BRCAI 17 Involved with the early onset of breast cancer PKUI 12 Involved with the disease of phenylketonuria Function or purpose of the gene Controls the production of protein markers on the red blood cells. ABO blood type Involved in determining the production of polypeptide chains in hameoglobin Gene associated with very high cholesterol Gene associated with a frequent form of muscular dystrophy Figure 109 Two human gene loci 6 BIOLOGY: Key Ideas – THIRD EDITION MACROMOLECULES Key Points • A gene is an inherited instruction or code made up of DNA. The code is the sequence and order of the DNA bases A, T, C, G. • Genes control the production of important chemicals in cells and as such they control the structure and function of cells. • It is thought there are about 25,000 genes required to code for a human being. • The position of a gene on a chromosome is called its locus (plural loci). • Each chromosome will contain from hundreds to several thousand genes. • Each chromosome has specific genes that are linked to that chromosome (see Figure 109b) M3 The functional unit of information on the chromosome is the gene M3.1 Know that a gene consists of a unique sequence of bases that codes for a polypeptide or an RNA molecule Genes are made up of DNA and located at specific points on particular chromosomes. From a functional point of view a gene is a DNA sequence that codes for a specific protein or polypeptide chain. Early work in this area in the 1930s by George Beadle and Edward Tatum working with bread mould led them to formulating the one gene – one enzyme hypothesis. They deduced that mutant forms of mould that were unable to synthesize particular molecules in metabolic pathways suffered from mutations on their DNA that interfered with their ability to make a necessary protein enzyme. It was soon discovered ,that there were other proteins e.g. keratin (a structural protein) and insulin (a hormone) that were also coded for by genes. Many proteins are constructed from two or more different polypeptide chains and each chain can be specified by its own gene. Nevertheless the hypothesis can be generally restated as ‘one gene – one polypeptide’. Even this is not fully correct, as some genes code for structural RNA molecules such as ‘ribosomal RNA’ and ‘transfer RNA’ molecules rather than polypeptide chains. There are three main types of RNA; ribosomal RNA, transfer RNA and messenger RNA. Ribosomal RNA counts for about 80% of cellular RNA and is mainly associated with protein to form the ribosomes, the sites of protein synthesis. Transfer RNA molecules are specific carriers of amino acids in the process of protein synthesis whilst mRNA is transcribed from the DNA to carry the gene message out to the ribosomes for translation into an amino acid sequence. In the sections that follow we will examine how genes are decoded and then used to synthesize polypeptides. We already know that in DNA there are four types of bases A, T, G and C. Genes are usually hundreds or thousands of nucleotides long and each gene has a specific sequence of bases. The DNA language is therefore a language of bases. A polypeptide sequence is comprised of amino acid building blocks, thus the language of proteins is an amino acid language. Focus Questions 1. The bonds between base pairs in DNA are weak hydrogen bonds. Of what significance might this be for the processes of protein synthesis and DNA copying? 2. Explain why genes are called the units of hereditary. 3. What does it mean to say that a gene is linked to a chromosome? Essentials Text Book 7 macromolecules TOPIC 1 M3.2 Describe how three bases, called a codon in mRNA, code for one amino acid Amino acids are organic molecules that can be regarded as the monomers or building blocks of protein molecules. Cells build up their proteins from 20 different kinds of amino acids. To understand the coding system, scientists needed to explain how the 4 bases in DNA could specify the 20 amino acids in proteins. If only one base was used as the code, then 4 bases could code for 4 amino acids. If two bases were the code, then there are 16 (42) possible amino acids, still not enough. Triplets of bases are the smallest units necessary to code for all 20 amino acids. Experiments have indeed supported the fact that information flow is based on a triplet code. Most amino acids have more than one triplet code. These triplets of three nucleotide sequences are termed codons. They are found on special messenger RNA (mRNA) molecules that transfer the DNA code from the nucleus of a cell to the cytoplasm during the process of protein synthesis. As codons are triplets of bases, the number of nucleotides that make up the genetic message must be three times the number of amino acids specified in the protein. Figure 110 (a) shows the 64 possible combinations of three bases (i.e. 43). The codons are taken from mRNA molecules. Stop codons are ones that terminate the polypeptide sequence when it is being decoded. The table below, Figure 110 (a) shows the names of the amino acids, together with the common abbreviations used in Figure 110 (b). UUU UUC UUA UUG phe phe leu leu UCU UCC UCA UCG ser ser ser ser UAU UAC UAA UAG tyr tyr stop stop UGU UGC UGA UGG cys cys stop trp CUU CUC CUA CUG leu leu leu leu CCU CCC CCA CCG pro pro pro pro CAU CAC CAA CAG his his gln gln CGU CGC CGA CGG arg arg arg arg AUU AUC AUA AUG ile ile ile start/met ACU ACC ACA ACG thr thr thr thr AAU AAC AAA AAG asn asn lys lys AGU AGC AGA AGG ser ser arg arg GUU GUC GUA GUG val val val val GCU GCC GCA GCG ala ala ala ala GAU GAC GAA GAG asp asp glu glu GGU GGC GGA GGG gly gly gly gly Figure 110 (a) The mRNA codons for all amino acids and signals ala = alanine gly = glycine pro = proline arg = arginine his = histidine ser = serine asn = asparagine ile = isoleucine thr = threonine asp = aspartic acid leu = leucine trp = tryptophan cys = cysteine lys = lysine try = tyrosine gln = glutamine met = methionine val = valine glu = glutamic acid phe = phenylalanine Figure 110 (b) Common abbreviations for the amino acids 8 BIOLOGY: Key Ideas – THIRD EDITION MACROMOLECULES Key Points • DNA directs the synthesis of proteins (gene expression). • Gene sequences provide the code (A, T, C, G) for making specific polypeptides. • The gene sequence on the DNA molecule acts as a template to make a complementary mRNA molecule. • Only one strand of the DNA is used to provide the code to make the mRNA and hence the polypeptide, this is called the template strand. • The term codon describes a three base mRNA sequence that codes for one amino acid. • The term codon is also used for a DNA bases triplet on the non-template strand. M4 The flow of information from DNA to protein is unidirectional in most organisms. i.e. from DNA RNA Protein M4.1 Describe and illustrate the processes of transcription and translation, including the roles of mRNA, tRNA and ribosomes There are two processes involved in the production of proteins in cells – transcription and translation. To understand the flow of information from DNA to protein we need to understand a little about four types of molecules that are involved in the processes. Below is a brief description of each molecule involved in the process of protein synthesis. a. DNA The structure of the DNA molecule has been explained under M1.1, in particular; • It is a double helical molecule that consists of two complementary strands. • It has four bases: adenine, guanine, cytosine and thymine. • One strand of the DNA acts as a template for the production of a molecule of mRNA. • A gene represents a length of DNA that contains the information for the synthesis of a polypeptide chain. b. Messenger RNA (mRNA ) In eukaryotes this molecule originates in the nucleus and later will migrate to the ribosomes in the cytoplasm in preparation for the process of protein synthesis. • It is a single-stranded molecule that is transcribed from a DNA coding strand. • It consists of a sequence of mRNA nucleotides, usually numbering several thousand. These are similar to DNA nucleotides with two specific differences. • Thymine is replaced with the base Uracil. The deoxyribose sugar is replaced by a ribose sugar. The bases in mRNA are Adenine, Guanine, Cytosine and Uracil. • When mRNA is transcribed from a molecule of DNA, Adenine (DNA) bonds to Uracil (mRNA) and Thymine (DNA) bonds to Adenine (mRNA), Guanine (DNA) bonds to Cytosine (mRNA) and Cytosine (DNA) bonds to Guanine (mRNA). Essentials Text Book 9 macromolecules TOPIC 1 As seen in M3.2, three bases on the mRNA called a codon, code for one amino acid. In this hypothetical, short segment of mRNA there are four codons. See Figure 111. Reading from left to right on the sequence, the codon AUU would code for the amino acid asparagine, UUU would code for phenylalanine and so on. The Figure 110 in M3.2 can be used to work out which amino acid is coded for by a particular codon. mRNA codons Amino acid sequence A A U asparagine U U U phenylalanine G C C C alanine C C Bases proline A three base sequence represents a codon Figure 111 A section of mRNA with the bases and codons Key Points The process of protein synthesis can be said to occur in two stages: • Transcription: DNA → mRNA • Translation: mRNA → polypeptide or protein The following base pairing rules apply for complementary binding: Transcription DNA mRNA A – U T – A G – C C – G Translation mRNA tRNA A – U U – A G – C C – G • It takes a 600 nucleotide sequence on mRNA to code for 200 amino acids in a polypeptide molecule. • The anticodon on tRNA binds in a complementary fashion to the codon on the mRNA. • A cell keeps its cytoplasm stocked with amino acids either made by the cell or obtained from the diet. c. Transfer RNA (tRNA) • Transfer RNA molecules, similar to mRNA, are actually transcribed from the DNA. • A tRNA molecule is a single RNA strand that is only about 80 nucleotides long and has a cloverleaf shape. • The function of a tRNA molecule is to place amino acids that will be linked into the polypeptide molecule specified by a particular sequence of bases on the mRNA. • Each type of tRNA molecule will carry only one of the 20 amino acids. • Some amino acids can be carried by more than one tRNA molecule. • A specific amino acid becomes attached to one end of the tRNA molecule. 10 BIOLOGY: Key Ideas – THIRD EDITION