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9.1: The Structure of DNA - Biology

9.1: The Structure of DNA - Biology


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In the 1950s, Francis Crick and James Watson worked together at the University of Cambridge, England, to determine the structure of DNA. Other scientists, such as Linus Pauling and Maurice Wilkins, were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. X-ray crystallography is a method for investigating molecular structure by observing the patterns formed by X-rays shot through a crystal of the substance. The patterns give important information about the structure of the molecule of interest. In Wilkins’ lab, researcher Rosalind Franklin was using X-ray crystallography to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule using Franklin's data (Figure 9.1.1). Watson and Crick also had key pieces of information available from other researchers such as Chargaff’s rules. Chargaff had shown that of the four kinds of monomers (nucleotides) present in a DNA molecule, two types were always present in equal amounts and the remaining two types were also always present in equal amounts. This meant they were always paired in some way. In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine for their work in determining the structure of DNA.

Now let’s consider the structure of the two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The building blocks of DNA are nucleotides, which are made up of three parts: a deoxyribose (5-carbon sugar), a phosphate group, and a nitrogenous base (Figure 9.1.2). There are four types of nitrogenous bases in DNA. Adenine (A) and guanine (G) are double-ringed purines, and cytosine (C) and thymine (T) are smaller, single-ringed pyrimidines. The nucleotide is named according to the nitrogenous base it contains.

Figure 9.1.2: (a) Each DNA nucleotide is made up of a sugar, a phosphate group, and a base. (b) Cytosine and thymine are pyrimidines. Guanine and adenine are purines.

The phosphate group of one nucleotide bonds covalently with the sugar molecule of the next nucleotide, and so on, forming a long polymer of nucleotide monomers. The sugar–phosphate groups line up in a “backbone” for each single strand of DNA, and the nucleotide bases stick out from this backbone. The carbon atoms of the five-carbon sugar are numbered clockwise from the oxygen as 1', 2', 3', 4', and 5' (1' is read as “one prime”). The phosphate group is attached to the 5' carbon of one nucleotide and the 3' carbon of the next nucleotide. In its natural state, each DNA molecule is actually composed of two single strands held together along their length with hydrogen bonds between the bases.

Watson and Crick proposed that the DNA is made up of two strands that are twisted around each other to form a right-handed helix, called a double helix. Base-pairing takes place between a purine and pyrimidine: namely, A pairs with T, and G pairs with C. In other words, adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. This is the basis for Chargaff’s rule; because of their complementarity, there is as much adenine as thymine in a DNA molecule and as much guanine as cytosine. Adenine and thymine are connected by two hydrogen bonds, and cytosine and guanine are connected by three hydrogen bonds. The two strands are anti-parallel in nature; that is, one strand will have the 3' carbon of the sugar in the “upward” position, whereas the other strand will have the 5' carbon in the upward position. The diameter of the DNA double helix is uniform throughout because a purine (two rings) always pairs with a pyrimidine (one ring) and their combined lengths are always equal. (Figure 9.1.3).

The Structure of RNA

There is a second nucleic acid in all cells called ribonucleic acid, or RNA. Like DNA, RNA is a polymer of nucleotides. Each of the nucleotides in RNA is made up of a nitrogenous base, a five-carbon sugar, and a phosphate group. In the case of RNA, the five-carbon sugar is ribose, not deoxyribose. Ribose has a hydroxyl group at the 2' carbon, unlike deoxyribose, which has only a hydrogen atom (Figure 9.1.4).

RNA nucleotides contain the nitrogenous bases adenine, cytosine, and guanine. However, they do not contain thymine, which is instead replaced by uracil, symbolized by a “U.” RNA exists as a single-stranded molecule rather than a double-stranded helix. Molecular biologists have named several kinds of RNA on the basis of their function. These include messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)—molecules that are involved in the production of proteins from the DNA code.

How DNA Is Arranged in the Cell

DNA is a working molecule; it must be replicated when a cell is ready to divide, and it must be “read” to produce the molecules, such as proteins, to carry out the functions of the cell. For this reason, the DNA is protected and packaged in very specific ways. In addition, DNA molecules can be very long. Stretched end-to-end, the DNA molecules in a single human cell would come to a length of about 2 meters. Thus, the DNA for a cell must be packaged in a very ordered way to fit and function within a structure (the cell) that is not visible to the naked eye. The chromosomes of prokaryotes are much simpler than those of eukaryotes in many of their features (Figure 9.1.5). Most prokaryotes contain a single, circular chromosome that is found in an area in the cytoplasm called the nucleoid.

The size of the genome in one of the most well-studied prokaryotes, Escherichia coli, is 4.6 million base pairs, which would extend a distance of about 1.6 mm if stretched out. So how does this fit inside a small bacterial cell? The DNA is twisted beyond the double helix in what is known as supercoiling. Some proteins are known to be involved in the supercoiling; other proteins and enzymes help in maintaining the supercoiled structure.

Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus (Figure 9.1.6). At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The DNA is wrapped tightly around the histone core. This nucleosome is linked to the next one by a short strand of DNA that is free of histones. This is also known as the “beads on a string” structure; the nucleosomes are the “beads” and the short lengths of DNA between them are the “string.” The nucleosomes, with their DNA coiled around them, stack compactly onto each other to form a 30-nm–wide fiber. This fiber is further coiled into a thicker and more compact structure. At the metaphase stage of mitosis, when the chromosomes are lined up in the center of the cell, the chromosomes are at their most compacted. They are approximately 700 nm in width, and are found in association with scaffold proteins.

In interphase, the phase of the cell cycle between mitoses at which the chromosomes are decondensed, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. There is a tightly packaged region that stains darkly, and a less dense region. The darkly staining regions usually contain genes that are not active, and are found in the regions of the centromere and telomeres. The lightly staining regions usually contain genes that are active, with DNA packaged around nucleosomes but not further compacted.

CONCEPT IN ACTION

Watch this animation of DNA packaging.

Summary

The model of the double-helix structure of DNA was proposed by Watson and Crick. The DNA molecule is a polymer of nucleotides. There are four nitrogenous bases in DNA, two purines (adenine and guanine) and two pyrimidines (cytosine and thymine). A DNA molecule is composed of two strands. Each strand is composed of nucleotides bonded together covalently between the phosphate group of one and the deoxyribose sugar of the next. From this backbone extend the bases. The bases of one strand bond to the bases of the second strand with hydrogen bonds. Adenine always bonds with thymine, and cytosine always bonds with guanine. The bonding causes the two strands to spiral around each other in a shape called a double helix. Ribonucleic acid (RNA) is a second nucleic acid found in cells. RNA is a single-stranded polymer of nucleotides. It also differs from DNA in that it contains the sugar ribose, rather than deoxyribose, and the nucleotide uracil rather than thymine. Various RNA molecules function in the process of forming proteins from the genetic code in DNA.

Prokaryotes contain a single, double-stranded circular chromosome. Eukaryotes contain double-stranded linear DNA molecules packaged into chromosomes. The DNA helix is wrapped around proteins to form nucleosomes. The protein coils are further coiled, and during mitosis and meiosis, the chromosomes become even more greatly coiled to facilitate their movement. Chromosomes have two distinct regions which can be distinguished by staining, reflecting different degrees of packaging and determined by whether the DNA in a region is being expressed (euchromatin) or not (heterochromatin).

Glossary

deoxyribose
a five-carbon sugar molecule with a hydrogen atom rather than a hydroxyl group in the 2' position; the sugar component of DNA nucleotides
double helix
the molecular shape of DNA in which two strands of nucleotides wind around each other in a spiral shape
nitrogenous base
a nitrogen-containing molecule that acts as a base; often referring to one of the purine or pyrimidine components of nucleic acids
phosphate group
a molecular group consisting of a central phosphorus atom bound to four oxygen atoms

Describe the structure of dna ? (6mrks) gcse edexcel 9-1

DNA structure. DNA is made up of molecules called nucleotides. Each nucleotide contains a phosphate group, a sugar group and a nitrogen base. The four types of nitrogen bases are adenine (A), thymine (T), guanine (G) and cytosine (C).

question: which statement best describes the different properties of metals?

answer: they are shiny and bend without breaking.

since metals have certain characteristics properties, they include the following: they are ductile, malleable, shiny, hard, lustrous, flexible and they are good conductor of heat and electricity. so therefore, metals are not dull and they are not non-flexible as listed. instead, they are shiny and flexible.


The structure of the checkpoint clamp 9-1-1 complex and clamp loader Rad24-RFC in Saccharomyces cerevisiae

The 9-1-1 complex is a circular heterotrimeric complex composed of Rad9-Hus1-Rad1. In response to DNA damage, the 9-1-1 complex will be loaded onto the DNA damage site by clamp loader Rad24-RFC to activate the cell cycle checkpoint. The C-terminal of Ddc1/Rad9 is critical for checkpoint activation. However, there is little structural information about the intact 9-1-1 complex and the interaction with Rad24-RFC. Here, we determined the structure of the intact 9-1-1 complex in S. cerevisiae by cryo-Electron Microscopy (cryo-EM) and identified the Ddc1 C-tail module for the first time. We found that the C-terminal of Ddc1 has structural flexibility and it plays a critical role for Mec1/Ddc2 activation in G1/G2 phase. At the same time, we got a glimpse of the structure of Rad24-RFC and captured the interaction between the 9-1-1 complex and Rad24-RFC. The structural information greatly helped us to understand the process of clamp-loading.

Keywords: 9-1-1 complex DNA damage response Ddc1 C-tail Mec1/Ddc2 Rad24-RFC.


DNA Structure (Genetics and Evolution) Revision Poster [AQA GCSE Biology Double and Triple 9-1]

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A revision poster covering DNA Structure in Paper 2 of AQA Biology for both Double and Triple students.

These handwritten posters have been constructed using the AQA specification, MyGCSEScience and revision textbooks to maximise the content on the posters. They cover the content required in 4.6.1.5 of the AQA Biology specification and are useful for revision purposes. They are very useful for supporting student’s revision through covering everything they need to know in the perfect amount of detail, and can be used in a variety of ways.

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Inheritance, Variation and Evolution (Paper 2) Revision Posters [AQA GCSE Biology Double and Triple 9-1]

This resource bundle contains all the revision posters covering Inheritance, Variation and Evolution in Paper 2 of AQA Biology for both Double and Triple students. Each resource: These handwritten posters have been constructed using the AQA specification, MyGCSEScience and revision textbooks to maximise the content on the posters. They cover the content required in 4.6 Inheritance, Variation and Evolution of the AQA Biology specification and are useful for revision purposes. They are very useful for supporting student's revision through covering everything they need to know in the perfect amount of detail, and can be used in a variety of ways.


DNA Structure (Biology Only) - New AQA Biology GCSE

Lesson for Inheritance, Variation and Evolution Chapter in new AQA Biology GCSE.

LO:
Describe the structure of DNA using diagrams.
Explain how the bases on the two strands link together.
HT: Describe in simple terms how a protein is synthesised.
HT: Explain the importance of the shape of a protein for enzyme action and function.
HT: Describe what a mutation is and how a mutation could affect the formation of a protein.
HT: Explain that most mutations have little effect but a few have more serious effects on the function of the protein.

It will take 2-3 lessons to cover this topic.

Please provide feedback so I can improve my lesson if required.

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How DNA Is Arranged in the Cell

DNA is a working molecule it must be replicated when a cell is ready to divide, and it must be “read” to produce the molecules, such as proteins, to carry out the functions of the cell. For this reason, the DNA is protected and packaged in very specific ways. In addition, DNA molecules can be very long. Stretched end-to-end, the DNA molecules in a single human cell would come to a length of about 2 meters. Thus, the DNA for a cell must be packaged in a very ordered way to fit and function within a structure (the cell) that is not visible to the naked eye. The chromosomes of prokaryotes are much simpler than those of eukaryotes in many of their features (Figure 9.6). Most prokaryotes contain a single, circular chromosome that is found in an area in the cytoplasm called the nucleoid.

Figure 9.6 A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called the nucleoid.

The size of the genome in one of the most well-studied prokaryotes, Escherichia coli, is 4.6 million base pairs, which would extend a distance of about 1.6 mm if stretched out. So how does this fit inside a small bacterial cell? The DNA is twisted beyond the double helix in what is known as supercoiling. Some proteins are known to be involved in the supercoiling other proteins and enzymes help in maintaining the supercoiled structure.

Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus. At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The DNA is wrapped tightly around the histone core. This nucleosome is linked to the next one by a short strand of DNA that is free of histones. This is also known as the “beads on a string” structure the nucleosomes are the “beads” and the short lengths of DNA between them are the “string.” The nucleosomes, with their DNA coiled around them, stack compactly onto each other to form a 30-nm–wide fiber. This fiber is further coiled into a thicker and more compact structure. At the metaphase stage of mitosis, when the chromosomes are lined up in the center of the cell, the chromosomes are at their most compacted. They are approximately 700 nm in width, and are found in association with scaffold proteins.

In interphase, the phase of the cell cycle between mitoses at which the chromosomes are decondensed, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. There is a tightly packaged region that stains darkly, and a less dense region. The darkly staining regions usually contain genes that are not active, and are found in the regions of the centromere and telomeres. The lightly staining regions usually contain genes that are active, with DNA packaged around nucleosomes but not further compacted.

Figure 9.7 These figures illustrate the compaction of the eukaryotic chromosome.


9.1: The Structure of DNA - Biology

Sc hool Biology Notes: How proteins are synthesised - role of DNA and RNA

The functions of DNA & RNA in Protein Synthesis

Doc Brown's school biology revision notes: GCSE biology, IGCSE biology, O level biology,

US grades 8, 9 and 10 school science courses or equivalent for

14-16 year old students of biology

This page will help you answer questions such as . What is a nucleotide? What is its structure? What is the structure of DNA? Why is it classed as a polymer? How does DNA code for amino acids and hence proteins? What is the function of DNA? How are proteins synthesised? What is RNA? What is the function of RNA? What is a triplet code? How can we extract DNA from cells? How do cells make proteins in the cytoplasm? What functions to proteins have in living organisms?

(a) How was the structure of DNA discovered?

DNA (deoxyribonucleic acid) was first isolated, from white blood cells, by the Swiss scientist Friedrich Miescher in 1869.

Before the crucial X-ray photograph of Rosalind Franklin, chemical analysis showed that four bases seem to occur in ratios of 1 : 1 for one pair and 1 : 1 for another pair.

What were the roles of the scientists Watson, Crick, Franklin and Wilkins?

In the 1950s, Rosalind Franklin working for Maurice Wilkins examined strands of DNA using a technique called X-ray diffraction analysis.

The sample under investigation, e.g. a DNA crystal strands, is bombarded with X-rays and the layers of atoms behave like a diffraction grating and scatter the X-rays in particular pattern that depends on the 3D arrangement of atoms in the molecule. The path of the scattered X-rays is recorded on a photographic plate.

Rosalind Franklin died tragically young from cancer, and never received the Nobel Prize she would have undoubtedly received, BUT, in one of the last things she wrote in her laboratory notebook, she speculated that DNA had a helix structure.

Later Frances Crick and James Watson gathered together this X-ray data (Crick had access to Rosalind Franklin's 'classic' X-ray photograph of crystallised DNA, characteristic of a helical structure) with other information .

e.g. the chemical analysis of DNA, particularly the ratios of the four bases (adenine, cytosine, guanine and thymine), the shape of the four base molecules .

and then built a model and deduced what we recognise today as the double helix structure of DNA - brilliant insight, more Nobel Prize winners along with Maurice Wilkins.

The important thing is that the experimental observations from chemical and structural analysis fitted the evidence based model.

Rosalind Franklin, Physicist and Biologist, tragically dying young from a combination of pneumonia and advanced cancer. All the other three scientists mentioned above received the ultimate accolade of a Nobel prize. Rosalind Franklin would also have received a Nobel prize, if she had not died so tragically young..

(b) The structure of nucleotides and DNA - deoxyribonucleic acid

Introduction to DNA and its function

DNA (deoxyribonucleic acid) is a large molecule essential for life and cell replication and is another example of a natural polymer.

Its structure was worked out in the 1950s, notably by the Nobel Prize winners Crick and Watson, though several other notable scientists made important contributions.

DNA, a natural polymer is made up of string of repeating units (the monomer) called nucleotides.

The DNA forms two linked strands coiled together in the shape of a double helix (more DNA structure later).

DNA molecules hold all of an organism's genetic material, that is all the chemical instructions for individual cells and complex organisms to grow and develop.

All the instructions that are needed for an organism to grow, develop and reproduce is encoded in the DNA.

The contents of your DNA directly determines what your inherited characteristics are.

The DNA is organised into long coiled up sections called chromosomes in the cell nucleus, and within the chromosomal DNA there are shorter sections called genes.

Each chromosome consists of many short sections of DNA called genes, one or more of which codes for one characteristic of an organism e.g. blood group, eye colour or hair colour.

The genes have the codes for making all the different proteins, many of which are enzymes and how to make large important molecules like haemoglobin.

Your total DNA, that is the full contents of your genes, is called the genome.

Chromosomes normally come in pairs and the both have the same type of genes in the same order along their very long length (in the molecular sense!).

Reminder- one chromosome from each parent makes up the pair, and human diploid cells have 46 chromosomes (23 pairs).

Apart from the nucleus, certain other parts of the cell can contain DNA e.g. mitochondria (sites of respiration).

Bacteria can contain free rings/strings of DNA called plasmids.

Plasmids are not part of a bacteria's chromosome, and do not help the functioning of the cell, but e.g. they contain genes that help them develop resistance against antibiotics, and so help in their survival.

DNA encodes genetic instructions for the development and functioning of living organisms and viruses.

e.g. every protein molecule needed by a living organism down to individual cell level is synthesised by other molecules reading the genetic DNA code and combining the right amino acids in the right order.

This means every different protein has its own specific number and precise order of amino acids.

After synthesis, the protein molecule (polymer chain of amino acids) folds into its own specific unique shape to perform its own unique function e.g. an enzyme to catalyse a specific biochemical reaction.

A section of DNA that codes for a particular protein is called a gene and it is the order of the bases in a gene that determines the order of amino acids in the protein, hence its structure and function.

The DNA not only codes for all the necessary proteins, it also determines what type a cell becomes e.g. blood cell, brain cell, muscle cell, skin cell etc.

Proteins are polymers of amino acids. DNA is a polymer of nucleotides.

So amino acids and nucleotides are monomers.

Every protein has a specific structure for a particular function including enzymes, and most be encoded in DNA.

The structure of nucleotides and the DNA molecule

Most DNA molecules consist of two polymer chains, made from four different monomers called nucleotides, connected together in the form of a double helix.

Unlike man-made poly(ethene), from the monomer ethene etc. DNA is a naturally occurring polymer - long molecular chains of joined up monomer (single) molecules.

The nucleotide is the small basic molecular unit - the monomer from which the polymer is formed.

Nucleotides form the building blocks of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). An individual nucleotide consists of three molecular bits combined together - the same phosphate group, a variable base (adenine, cytosine, guanine or thymine), and the same pentose sugar (pentose just means having a ring of 5 atoms). The phosphate group and base are attached to the sugar (see left diagram of a single nucleotide).

The DNA (and RNA) polymer chain is formed by a large number of phosphate-sugar linkages. The base is a sort 'branch' off the main chain, but this helps it to intermolecular bond with a base of another opposite strand of DNA.

The result is full DNA molecule consists of two 'molecular' strands coiled together to form a double helix, but how is this helix held together?

The two polymer strands of DNA are cross-linked by a series of complementary base pairs joined together by weak intermolecular bonds - cross links (base-pairing bonds shown here as on the diagram):

There are four bases in DNA holding the structure together and the same two bases are always paired together - known as complementary base pairing .

This is shown on the right diagram, holding the two strands of DNA together.

Adenine (A) with thymine (T) AT , and cytosine (C) with guanine (G) CG .

Whererepresents the weak (but crucial) intermolecular attractive bonding force between the pairs of bases. This weaker intermolecular bond is actually called a hydrogen bond, but you might not need to know any more detail at GCSE level.

These cross linking complementary base pair bonds hold the DNA molecules tightly together giving it the necessary stability to perform their genetic roles - but not to tightly, that they cannot be 'unzipped' - a necessary process in cell replication!

Here complementary means 'matching pairs'. A with T and C with G are the linked complimentary base pairs.

The double helix structure is shown in the diagram above on the right, illustrating how the DNA is held together by the cross-linking hydrogen bonds between the bases to hold together the double helix together.

A short section of DNA is illustrated in more detail below.

A more detailed diagram of a very short section of a double-helix DNA molecule showing the two different base pairings holding the two molecular strands together.

It is the order of the bases in the DNA strands of a gene that decides the order of amino acids in a protein.

(c) Details of protein synthesis

DNA code, bases, genes and the triplet code

As already mentioned, DNA polymer molecules contain the genetic codes that determine which proteins are synthesised.

These synthesised proteins control how all the cells in an organism function, in other words the DNA controls the production of all proteins - protein synthesis in the ribosomes, one of the sub-cellular structures in the cytoplasm of cells.

A short section of DNA that codes for a particular protein is known as a gene.

This means each gene codes for a particular set of amino acids that form a protein.

It is the order of the bases in the gene that determines the order of the amino acids in the protein.

Every gene has a different sequence of bases to code for all the proteins an organism requires.

Only 20 different amino acids are used to synthesise all the thousands of different proteins.

It is the genes of the DNA that tells the ribosomes in cells the correct order to assemble the amino acids to make a specific protein.

A ribosome, a tiny structure in the cytoplasm, is essentially a protein factory that makes everything from enzymes, keratin, muscle fibre cells, red blood cells etc. and all based on the DNA codes.

Every protein, a polymer chain of amino acids, has a unique structure based on a specific number of amino acids AND a specific sequence of amino acids.

Each protein also has a specific 3D shape, essential for it to carry out its particular function e.g. an enzyme or type of tissue.

The order of bases in a gene of the DNA determines the order of amino acids which will combine to form a specific the protein, which in turn, will perform a specific function in the living organism.

Every amino acid is coded for by a sequence of three bases in the gene, known as a triplet code (illustrated by diagram below for three 'fictitious' amino acids).

Every gene contains a different sequence of bases so it can code for a particular protein.

The order of bases on an organism's DNA is called the genetic code of the genome.

The genome is the whole of an organism's genetic material. See Introduction to the GENOME and gene expression - considering chromosomes, alleles, genotype, phenotype, variations

Examples of triplet base codes for amino acids

Example of three triplet codes based on the four bases: adenine A, thymine T, cytosine C, guanine G along the DNA molecule.

The triplet base codes are called codons .

Triplet code and amino acid: CCA is for proline, TCG is for serine and AGA for arginine

The amino acids are joined together to make the various proteins dependent on the order of the bases in the gene.

The diagram above shows how the triplet codes on DNA work.

A sequence of three bases (e.g. CCA) on a single strand of DNA codes for a particular amino acid. A sequence of three triplet codes will code for three amino acids in that particular sequence on that part of the gene.

Using letters to represent the sequence of bases on a strand of DNA is an example of a scientific model.

Reminder: The double helix structure of DNA is another spatial scientific model and this model must be tried and tested in the laboratory and all observations must back up any hypothesis to become a workable scientific model.

The cell chemistry allows the reading of the genetic triplet codes (sequence of bases) on the DNA code to eventually join these three amino acids together in the precise order dictated by the DNA code. In fact for any protein you are actually dealing with sequences of dozens-hundreds of triplet codes for a particular protein.

In the next section (after notes on non-coding DNA) we look at how we get from DNA triplet codes to the actual production of a protein and unfortunately its a bit more complicated than the above diagram suggests!

Notes on non-coding DNA

There are parts of the DNA strands that do NOT code for any amino acids, hence do NOT code for proteins.

However, some of these non-coding sections switch genes on and off, in other words, they control whether or not a gene is expressed to make a protein.

Therefore some of these non-coding regions of the DNA are involved in protein synthesis.

Before transcription can occur (involves reading the DNA code), the RNA polymerase (enzyme) has to bind to a non-coding section of DNA adjacent to the specific gene (coding for a specific protein).

If a mutation has occurred in this section of the DNA it can affect the ability of the RNA polymerase to bind to it - it might be harder or easier (or no effect).

The quantity and accuracy of how much mRNA is transcribed depends on how well this binding takes place - and therefore affects how well the protein is produced.

Therefore the production of the protein may be affected, and, depending on its function, that specific phenotype may also be affected.

This means that genetic variants in non-coding regions of DNA can affect the phenotypes exhibited by an organism, despite the fact that these non-coding sections of DNA done code for proteins themselves.

Example of a mutation in a triplet code

The original triplet code and amino acid sequence was: CCA for proline, TCG for serine and AGA for arginine.

If just one base has changed 'mutated', e.g. middle triplet from TCG to TGG, the 2nd amino acid is this sequence is changed.

The sequence is now: CCA for proline, TGG for threonine and AGA for arginine.

original sequence of triplet codes

The mutation causing the protein to have a slightly different structure can have consequences.

(i) It may not affect the function of the protein at all.

(ii) It may enhance the function of the protein.

(iii) BUT , it may adversely affect the function or activity of the protein e.g. the enzyme might not work as efficiently or maybe not at all due to a change in shape.

Effectively the gene is changed to a genetic variant of that gene, known as an allele, and can result in a different gene expression - a different phenotype.

These genetic changes in the DNA structure can involve substituting one base for another, deletion of a base or addition of a base. All of these change the triplet code sequence.

The formation of mRNA and t he actual synthesis of proteins in cytoplasmic ribosomes

DNA is found in a cell's nucleus and cannot move from it through the nucleus membrane because of the large size of its molecules.

Therefore there must be a means of getting the genetic information from the nucleus to the tiny structures, called ribosomes in the cytoplasm, in which the proteins are synthesised.

This is achieved using a molecule called messenger ribonucleic acid (mRNA, a type of RNA) i.e. how the cell gets the code from the nucleus to the ribosomes - the mRNA is a sort of 'messenger'.

mRNA is shorter than DNA and a single strand molecule, but still another polymer of nucleotides, but small enough to exit through the membrane of the nucleus.

The mRNA is the code used in the ribosomes to connect the amino acids together in the right order to assemble the protein molecule.

Note that there is an important difference between DNA and RNA.

In RNA the base thymine (T) is replaced by the base uracil ( U ), so the base pairings in RNA are C-G (as in DNA) but A-U in RNA (not A-T as in DNA).

As illustrated above, the DNA contains the gene's triple coding system for the amino acids to needed to be combined to form a specific protein - with specific molecular properties to perform a particular chemical function in an organism.

The process of TRANSCRIPTION - transferring the genetic code

The mRNA is made by copying the DNA base sequence of a gene - the process of transcription .

In the nucleus, using enzymes, the two strands of the DNA double helix unzip and become a template for the production of mRNA (messenger ribonucleic acid).

The enzyme RNA polymerase binds to the non-coding DNA in front of a gene sequence of bases.

The two DNA strands of the double helix unzip and the RNA polymerase moves along one of the strands of the DNA (see diagram on right).

Therefore the RNA polymerase uses the DNA coding of a gene as a template to make the mRNA.

Note: In the mRNA molecule, the base uracil (U) replaces the base thymine (T) in pairing up with adenine (A).

By pairing up the complementary bases on the DNA and RNA, the correct sequential nucleotides in the nucleus are brought together to form a complementary strand of mRNA, a step in the overall process called transcription taking place in the nucleus.

This means the mRNA is complimentary to the gene.

The smaller mRNA molecule can now migrate out of the cell nucleus into the cytoplasm and attach themselves to a ribosome (the actual protein 'factory'!).

The process of TRANSLATION - building the amino acid chain of the protein

In the cytoplasmic ribosomes, the mRNA now itself acts as a template of triplet codes for amino acids to be joined together in the correct sequence for a specific protein.

In order for this to happen, the amino acids in the cytoplasm are drawn into the ribosome complex and assembled in order to match the complementary triplet codes.

The correct amino acids are brought to the ribosomes by a carrier molecule called transfer ribonucleic acid (tRNA).

The amino acids are then joined together, by enzymes, in the correct order to make a particular protein in the ribosome.

The order of the amino acids connected together in the ribosome will match the order of the base triplets (called codons) on the mRNA molecule.

The complimentary triplet base sequence on the tRNA structure is called the anticodon.

This production of the protein, dictated by the complementary triplet codes on the mRNA, is called the translation stage, and this takes place in the cytoplasm.

So, the RNA and appropriate enzymes in the ribosome, join the amino acids together to form the protein - a polypeptide - meaning a polymer formed from the amino acid monomer units.

Immediately after its synthesis, the protein adopts its own unique 3D structure - its specific shape.

The above diagram shows translation in more detail, including the role of another type of RNA - transfer ribonucleic acid (tRNA) which brings the amino acids together onto the mRNA.

  • Points to consider when studying the translation diagram above
  • The joining together of the amino acids on the mRNA is done using transfer ribonucleic acid (tRNA).
  • These relatively short molecules of tRNA actually bring the amino acids together to match the mRNA triplet codes.
  • In other words the triplet codes of tRNA and mRNA are also complementary.
  • Note that In RNA (mRNA or tRNA) the base thymine (T) has been replaced by the base uracil (U), so complimentary base pairing is now U-A (not A-T), but C-G retained and its still all about matching complimentary base pairs.
  • The sequence of events is as follows:
  • The attachment of the mRNA to the ribosome
    • The mRNA has exited from the nucleus and docks into a ribosome
    • The triplet base codes for particular amino acids and their joining up sequence can now be read from the mRNA molecules.
    • After the mRNA joins onto a ribosome, molecules of transfer RNA (tRNA) bring the amino acid that matches the code on the mRNA, the complimentary base codes of the mRNA and tRNA ensure that all proteins are synthesised with their specific protein sequence, so all proteins are completely reproducible.
    • The tRNA is then 'empty' and free to collect another set of amino acids for the ribosome to join up.
    • The ribosome then acts as the catalytic site for linking the amino acids together to synthesise a specific protein.
    • This second process is called translation because the triplet base code sequence is read and translated into the amino acid sequence of a protein.
    • A sequence of amino acids joined together in a chain is called a polypeptide, a natural polymer or macromolecule.
    • All of these reaction are catalysed by enzymes.

    M ore on variants in non-coding DNA

    A mutation changes the base sequence in a DNA molecule in a gene.

    This produces a genetic variant that can lead to changes in an organisms phenotype - gene expression characteristics.

    Variants in non-coding sections of the DNA molecule can also affect the phenotype of an organism, despite the fact that the non-coding DNA does not code for proteins.

    This can happen because before transcription can take place, RNA polymerase needs to bind to a section of non-coding DNA in front of a gene sequence of bases.

    If a mutation occurs in the region of DNA, then it can affect the ability of RNA polymerase to bind to it - it might have no effect, promote binding or inhibit binding - there are always several possibilities in these sorts of situations - including driving evolution!

    Depending on how well RNA polymerase can bind to this non-coding section of DNA will affect how much mRNA is transcribed in the transcription process - therefore how much of the protein is synthesised.

    Therefore the structure and function of the protein is changed and the final phenotype of the organism can be affected.

    See also An introduction to genetic variation and the formation and consequence of mutations

    SUMMARY of protein synthesis

    So, to summarise, you start with DNA in the nucleus, then to complementary mRNA in the nucleus (transcription stage), mRNA moves into the cytoplasm and then the amino acids are joined together in the ribosomes via the complementary triplet codes (translation stage).

    The diagram 'sketch' below also 'attempts' to summarise what is actually a very complicated process!

    (d) How to extract DNA from plant cells - a simple experiment

    This section is illustrated by the extraction of DNA from strawberries.

    Humans have 23 pairs of chromosomes (46 in total). The modern common strawberry has 8 pairs of each of the 7 chromosomes (56 in total) and is a rich 'school/college experiment' source of DNA.

    1. You need an appropriate source e.g. split peas, strawberries, kiwi fruit, onions or bananas etc.

    However, it is reported that the 'white strands' of DNA from fruit, may actually contain pectin too!

    Any green leaves or stalk should be removed from the strawberry.

    You can use a plastic bag or beaker in the first steps, you then need a test tube and filter funnel and filter paper.

    2. The starting plant material is well mashed, but avoid creating air bubbles in the mash.

    Squishing!

    You can crush the strawberries in a plastic bag for a few minutes.

    3. The mash is scraped into a beaker containing a solution of detergent and salt (the DNA extraction liquid).

    You can add this mixture to the plastic bag or beaker of crushed strawberry.

    With a plastic bag, its easier to do further effective crushing if you add the detergent/salt solution to the bag.

    The detergent further helps to break down the cell membranes to release the DNA from the cell nuclei.

    The salt makes the DNA strands stick together.

    4. The resulting mixture is filtered into a test tube/2nd clean beaker. I used a hand held coffee filter paper!

    Filtering!

    In school/college you can use a normal filter funnel and filter paper, as in your chemistry lessons!

    This removes the froth and the bigger insoluble bits of the plant cells.

    Kitchen style!

    The filtrate was transferred from the 2nd clean beaker into a test tube (if not already in a test tube).

    5. Some ice-cooled alcohol is carefully added to the filtered mixture down the side of the test tube.

    Adding alcohol, mixture goes cloudy

    6. A band of white precipitated DNA strands should form - DNA is not soluble in cold alcohol.

    White coagulated mass of DNA

    7. You can then extract the DNA from this band with a glass rod.

    (e) A summary of DNA replication

    A more detailed diagram of the base sequence replication using the DNA template.

    1. The DNA double helix molecules splits in two, and the two strands then act as templates.

    2. Freely moving nucleotides can be matched up to form the weak bonds between the complimentary base pairs.

    3. Two identical strands of DNA produced, both identical in their original sequence of bases.

    The full DNA molecule consists of two 'molecular' strands coiled together to form a double helix.

    The two polymer strands of DNA are cross-linked by a series of complementary base pairs joined together by weak bonds - cross links

    There are four bases in DNA holding the structure together and the same two bases are always paired together - known as complementary base pairing.

    Complementary means 'matching pairs'. A with T and C with G links.

    i.e. adenine (A) with thymine (T) AT, and cytosine (C) with guanine (G) CG.

    These cross linking complementary base pair bonds hold the DNA strands tightly together giving it the necessary stability to perform their genetic roles.

    (f) Examples of the different functions of proteins

    As already mentioned, protein molecules adopt a very specific folded 3D shape in order to be able to carry out their specific function - so what are these functions?

    Every protein has its own unique shape to for its specific structure and function in an organism.

    These proteins may end up in muscle cells, brain cells, enzyme catalysts, haemoglobin molecules etc.

    BUT, note that proteins, particularly enzymes, are involved in building up non-protein molecules e.g. fats, cell walls, glycogen etc.

    (a) Enzymes are biological catalysts that control most chemical reactions in living organisms.

    Reminder: Enzymes have active sites of a specific shape that connect with substrate molecules, and this allows them to catalyse a specific chemical reaction in the biochemistry of living organisms.

    Enzymes are physiologically active proteins.

    The 'key and lock' mechanism of how an enzyme works - the correct 3D structure is crucial and that depends on the sequence and interconnection of the amino acids.

    The crucial 3D protein structure of an enzyme, and denaturing effect e.g. from a high temperature or wrong pH.

    (b) Many tissues are built of proteins e.g. collagen a strong structural protein (triple helix of polypeptides )that strengthens connective tissue like ligaments and cartilage of muscle systems of the joints.

    Elongated muscle cells made from the protein actin - forming the filaments in muscles.

    The strong fibres of our hair are made from the fibrous protein keratin.

    These particular tissues are partially built from structural proteins.

    (c) Carrier molecules like haemoglobin (conveys oxygen to cells) are also protein molecules.

    (d) Some antibodies are protein molecules.

    The shape of the protein must match the antigen of a pathogen e.g. of a virus.

    These particular antibodies are physiologically active proteins.

    See notes on Keeping healthy - defence against pathogens and infections

    (e) Many hormones are protein molecules e.g. insulin, the hormone released into the blood from the pancreas, controls blood sugar levels.

    The shape of the insulin molecule must match the shape of its receptor molecule.

    These particular hormones are physiologically active proteins.

    (Note there are many hormones which are NOT proteins e.g. some hormones involved in the menstrual cycle.)

    Sub-index of Genetics Notes - from DNA to GM and lots in between!


    DNA Forms: 7 Main Forms of DNA | Biochemistry

    The most common form of DNA which has right handed helix and proposed by Watson and Crick is called B-form of DNA or B-DNA. In addition, the DNA may be able to exist in other forms of double helical structure. These are A and C forms of double helix which vary from B- form in spacing between nucleotides and number of nucleotides per turn, rotation per base pair, vertical rise per base pair and helical diameter (Table 5.3).

    1. The B-Form of DNA (B-DNA):

    Structure of B-form of DNA has been proposed by Watson and Crick. It is present in every cell at a very high relative humidity (92%) and low concentration of ions. It has antiparallel double helix, rotating clockwise (right hand) and made up of sugar- phosphate back bone combined with base pairs or purine-pyrimidine.

    The base pairs are perpendicular to longitudinal axis of the helix. The base pairs tilt to helix by 6.3°. The B-form of DNA is metabolically stable and undergo changes to A, C or D forms depending on sequence of nucleotides and concentration of excess salts.

    2. The A-Form of DNA (A-DNA):

    The A-form of DNA is found at 75% relative humidity in the presence of Na+, K+ or Cs+ ions. It contains eleven base pairs as compared to ten base pairs of B-DNA which tilt from the axis of helix by 20.2°. Due to this displacement the depth of major groove increases and that of minor groove decreases. The A-form is metastable and quickly turns to the D-form.

    3. The C-Form DNA (C-DNA):

    The C-form of DNA is found at 66% relative humidity in the presence of lithium (Lit+) ions. As compared to A-and B-DNA, in C-DNA the number of base pairs per turn is less i.e. 28/3 or 9 1/3. The base pairs show pronounced negative tilt by 7.8°.

    4. The D-Form of DNA (D-DNA):

    The D-form of DNA is found rarely as extreme vanants. Total number of base pairs per turn of helix is eight. Therefore, it shows eight-fold symmetry. This form is also called poly (dA-dT) and poly (dG-dC) form. There is pronounced negative tilt of base pairs by 16.7° as compared to C form i.e. the base pairs are displaced backwardly with respect to the axis of DNA helix.

    5. The Z-Form of DNA (Z-DNA) or Left Handed DNA:

    In 1979, Rich and coworkers at MIT (U.S.A.) obtained Z-DNA by artificially synthesizing d (C-G) 3 molecules in the form of crystals. They proposed a left handed (synistral) double helix model with zig-zag sugar-phosphate back bone running in antiparallel direction.

    Therefore, this DNA has been termed as Z-DNA. The Z-DNA has been found in a large number of living organisms including mammals, protozoans and several plant species.

    There are several similarities with B-DNA in having:

    (ii) Two antiparallel strands, and

    (iii) Three hydrogen bonds between G-C pairing.

    In addition, the Z-DNA differs from the B-DNA in the following ways:

    (a) The Z-DNA has left handed helix, while the B-DNA has right handed helix.

    (b) The Z-DNA contains zig-zag sugar phosphate back bone as compared to regular back bone of the B-DNA.

    (c) The repeating unit in Z-DNA is a dinucleotide due to alternating orientation of sugar residues, whereas in B-DNA the repeating unit is a mononucleotide, and sugar molecules do not have the alternating orientation.

    (d) In the Z-DNA one complete turn contains 12 base pairs of six repeating dinucleotide, while in B-DNA one full turn consists of 10 base pairs i.e. the 10 repeating units.

    (e) Due to the presence of high number (12) of base pairs in one turn of Z-DNA, the angle of twist per repeating unit i.e. dinucleotide is 60° as compared to 36° of B-DNA molecule.

    (f) In Z-DNA the distance of twist making one turn of 360° is 45Å as against 34Å in B-DNA.

    (g) The Z-DNA has fewer diameters (18Å) as compared to the B-DNA (20Å diameter).

    6. Single Stranded (ss) DNA:

    Almost all the organisms contain double stranded DNA except a few viruses such as bacteriophage φ × 174 which consists of single stranded circular DNA. It becomes double stranded only at the time of replication.

    The differences of ssDNA from the dsDNA are as below:

    (a) The dsDNA absorbs wavelength 2600 Å of ultra violet light constantly from 0 to 80°C, thereafter rise sharply, whereas in ssDNA absorption of UV light increases steadily from 20° to 90°C.

    (b) The dsDNA resists the action of formaline due to closed reactive site, while the ss DNA does not resist it due to exposed reactive sites.

    (c) Base pair composition in dsDNA is equal i.e. A=T and G=C, in ssDNA the composition of A, T, G, C is in proportion of 1:1.33:0.98:0.75.

    (d) The dsDNA always remains in linear helical form, while the ssDNA remains in circular form however, it becomes double stranded only during replication (i.e. replicative form).

    7. Circular and Super Helical DNA:

    Almost in all the prokaryotes and a few viruses, the DNA is organised in the form of closed circle. The two ends of the double helix get covalently sealed to form a closed circle. Thus, a closed circle contains two unbroken complementary strands. Sometimes one or more nicks or breaks may be present on one or both strands, for example DNA of phage PM2 (Fig. 5.7 A).

    Besides some exceptions, the covalendy closed circles are twisted into super helix or super coils (Fig.5.7 B) and is associated with basic proteins but not with histones found complexed with all eukaryotic DNA.

    This histone like proteins appear to help the organization of bacterial DNA into a coiled chromatin structure with the result of nucleosome like structure, folding and super coiling of DNA, and association of DNA polymerase with nucleoids. Several histones like DNA binding proteins have been described in bacteria (Table 5.4).

    These nucleoid-associated proteins include HU proteins, IHF, protein H1, Fir A, H-NS and Fis. In archaeobacteria (e.g. Archaea) the chromosomal DNA exists in protein-associated form. Histone like proteins has been isolated from nucleoprotein complexes in Thermoplasma acidophilurn and Halobacterium salinanim.

    Thus, the protein associated DNA and nucleosome like structures are detected in a variety of bacteria. If the helix coils clockwise from the axis the coiling is termed as positive or right handed coiling. In contrast, if the path of coiling is anticlockwise, the coil is called left handed or negative coil.

    Table 5.4 : Histone-like proteins of E. coli

    The two ends of a linear DNA helix can be joined to form each strand continuously. However, if one of ends rotates at 360° with respect to the other to produce some unwinding of the double helix, the ends are joined resulting in formation of a twisted circle in opposite sense i.e. opposite to unwinding direction.

    Such twisted circle appears as 8 i.e. it has one node or crossing over point. If it is twisted at 720° before joining, the resulting super helix will contain two nodes (Fig. 5.7B).

    The enzyme topoisomerases alter the topological form i.e. super coiling of a circular DNA molecule. Type I topoisomerases (e.g. E.coli Top A) relax the negatively super coiled DNA by breaking one of the phosphodiester bonds in dsDNA allowing the 3′-OH end to swivel around the 5′-phosphoryl end, and then resealing the nicked phosphodiester backbone.

    Type II topoisomerases need energy to unwind the DNA molecules resulting in the introduction of super coils. One of type II isomerases, the DNA gyrase, is apparently responsible for the negatively super coiled state of the bacterial chromosome. Super coiling is essential for efficient replication and transcription of prokaryotic DNA.

    The bacterial chromosome is believed to contain about 50 negatively super coiled loops or domains. Each domain represents a separate topological unit, the boundaries of which may be defined by the sites on DNA that limit its rotation.


    AQA GCSE Grade 9-1 Biology Foundation Tier

    I will add the past paper links as soon as they become available from the examination board website

    AQA GCSE 9-1 Biology May June Summer foundation and higher Examination Papers 2018

    AQA GCSE 9-1 Biology 8461 8461/2F Biology Foundation Tier Paper 2 June 2018

    AQA GCSE 9-1 Biology 8461 8461/2H biology Higher Pier Paper 2 June 2018

    AQA GCSE 9-1 Biology May June Summer foundation and higher Examination Papers June 2019

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    AQA GCSE 9-1 Biology 8461 8461/2H higher biology Paper 2 June 2019

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    AQA GCSE 9-1 Biology May June Summer foundation and higher Examination Papers June-November 2020

    AQA GCSE 9-1 Biology 8461 8461/2F biology foundation Paper 2 June-November 2020

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    AQA GCSE 9-1 Biology May June Summer foundation and higher Examination Papers June 2021

    AQA GCSE 9-1 Biology 8461 8461/2F biology foundation Paper 2 June 2021

    AQA GCSE 9-1 Biology 8461 8461/2H biology higher Paper 2 June 2021

    ALL AQA GCSE (Grade 9-1) Level 1/Level 2 SCIENCES specifications and syllabus revision summary links


    Watch the video: Απλοειδή και Διπλοειδή Κύτταρα-Ομόλογα Χρωμοσώματα (July 2022).


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