The importance of DNA and RNA in heredity

1. The importance ofDNA and RNA in heredity

2. Central Dogma of Molecular Biology DNA is self-replicating. DNA is transcribed to produce mRNA. mRNA is translated to produce protein.

3. Revision – What are DNA and RNA DNA – deoxyribonucleic acid RNA – ribonucleic acid • Both are polynucleotide chains but they have different functions and structures. • Nucleotides are composed of a base, a phosphate group and a sugar.

4. Parts of a Nucleotide • Base • Nitrogen containing ring compounds • Two types – purine (two rings) or pyrimidine (one ring) • Purines – adenine and guanine • Pyrimidines – thymine, cytosine and uracil • Phosphate group • Used to form phosphodiester linkage between 5’ and 3’ carbons of adjacent nucleotides in order to form polynucleotide chains. • Sugar • Nucleotides contain a 5 carbon sugar • The sugar used in RNA is b-D-ribose • The sugar used in DNA is b-D-deoxyribose • There is one less oxygen on the sugar used for DNA hence the name deoxyribonucleic acid.

5. Subunits of a Nucleotide

6. Nomenclature (naming) of Nucleotides • Nucleoside refers to base + sugar • Nucleotide refers to base + sugar + phosphate

7. Key differences between DNA and RNA

8. Structure of DNA • Watson and Crick modelled the structure of DNA in 1953 based on observations of other scientists including Rosamond Franklin • Now accepted that DNA is a double-stranded helix (like a curved staircase) formed by cross-linking of two anti-parallel nucleotide strands with complementary nucleotide sequences.

9. Why complementary base pairs? • Chargraff’s chromatography data examining the base composition of DNA from several different organisms indicated that in all cases • Ratio A:T was 1 • Ratio C:G was 1 • Further work showed that adenine forms two hydrogen bonds with thymine while guanine forms three bonds with cytosine. • There are approximately 10 complementary base pairs per helical turn in the DNA helix. • A purine (double ring) is always paired with a pyrimidine (single ring) in order for the helix to fit together properly. • Uracil is only found in RNA – it is complementary to the DNA base adenine and replaces thymidine during the transcription process.

10. Four Types of RNA • Messenger RNA (mRNA) • Copied portion of coding DNA • Carries genetic information from the DNA out of the nucleus into the cytoplasm • Transfer RNA (tRNA) • Transports amino acids to the ribosome during protein synthesis • Ribosomal RNA (rRNA) • Structural component of ribosomes • snRNA (snRNA) • Involved in splicing of pre-mRNA message in the nucleus to remove introns

11. Nucleotide bases form the basis of the genetic code • The genetic codes consists of four nucleotides (A, C, G, T) and provides the instructions to make each of the 100,000+ proteins in the human body • The code is read from 5’ to 3’ end of a DNA sequence and is usually written from left to right • A group of three bases codes for one amino acid • DNA code is copied (transcribed) to produce mRNA, and the order of amino acids in proteins is determined by the sequence of the three letter codes in mRNA • The mRNA sequence reads the same as the 5’ to 3’ DNA sequence except for the substitution of U for T.

12. Why do we need both DNA and RNA? • DNA holds all the genetic information/instructions for the proteins produced in a cell so why do we need RNA. • It is BECAUSE DNA holds all the genetic information, this means it is EXTREMELY important. • If DNA is damaged in any way, the coding sequence can change and a MUTATION will arise that will potentially influence the particular protein and perhaps the whole cell or organism. • If DNA ventured into the cytoplasm to give instructions for protein synthesis it would be vulnerable to damage from chemicals, UV radiation and other mutagens. • RNA acts as a messenger. Damage to mRNA will not permanently affect function of the cell as the DNA template is undamaged.

13. Central Dogma of Molecular Biology DNA is self-replicating. DNA is transcribed to produce mRNA. mRNA is translated to produce protein.

14. DNA is self-replicating • In order for genetic information to be passed on to new cells, chromosomal DNA must be replicated prior to cell division. • Replication of DNA creates the sister chromatids found in chromosomes that are preparing to divide. • This process duplicates the whole chromosome, and the sister chromatids are then held together by a common centromere until they are separated in the process of cell division.

15. Steps in DNA Replication 1. Unwinding the DNA molecule 2. Making new DNA strands 3. Rewinding the DNA molecule • Different enzymes are involved in different stages of DNA replication, and although they are shown as separate entities in most diagrams, they will tend to cluster together forming a ‘replication complex’

16. Unwinding the DNA Molecule • Replication of DNA begins at a sequence of nucleotides called the origin of replication. • An enzyme called helicase unwinds the dsDNA helix and single-stranded binding proteins (SSBP) react with the ssDNA and stabilize it. • At the same time, DNA gyrase relieves the strain that unwinding causes on the molecule by cutting, winding and rejoining DNA strands. • Under an electron microscope the unwound section looks like a “bubble” and thus is known as the replication bubble.

17. Making New DNA Strands • DNA polymerase III is the major enzyme involved in DNA replication. • It adds nucleotides to the 3’ end of a pre-existing chain of nucleotides thus generating a new complementary strand of DNA, but it cannot initiate a nucleotide chain. • An RNA polymerase called primase is needed to start a new nucleotide chain. • Primase constructs an RNA primer (sequence of about 10 nucleotides complementary to the parent strand) which DNA polymerase III can then add nucleotides to. • The unwound DNA exposes two parental strands of DNA which are antiparallel. This means they are orientated in different directions and must be replicated by different mechanisms. • The leading strand elongates towards the replication fork (in the direction of unwinding) by the simple addition of nucleotides to is 3’ end by DNA polymerase III. • The lagging strand must elongate away from the replication fork. It is synthesized discontinuously as a series of short segments called Ozaki fragments. When DNA polymerase III reaches the RNA primer on the lagging strand, it is replaced by DNA polymerase I, which removes the RNA primer and replaces it with DNA. DNA ligase then attaches and forms phosphodiester bonds.

18. Rewinding the DNA Molecule • Since each new strand is complementary to its old template strand, two identical new copies of the DNA double helix are produced during replication. • In each new helix, one strand is the old template and the other is new synthesised, therefore replication is said to be semi-conservative. • The two DNA molecules rewind into the double-helices, then each double-helix is coiled around histone proteins and further wrapped up to form separate chromatids (still joined by a common centromere). • The two chromatids will become separated in the cell division process to form two separate chromosomes.

19. Overview of DNA replication

21. Central Dogma of Molecular Biology DNA is self-replicating. DNA is transcribed to produce mRNA. mRNA is translated to produce protein.

22. Transcription of DNA • Process of transcription begins when a section of DNA (a gene) unwinds and the bases separate exposing two single strands of DNA with unpaired bases. • One of these strands act as a template for the formation of an mRNA molecule (it is transcribed) • Individual nucleotides of RNA align with the exposed bases on the DNA template according to base pairing rules. Nucleotides are added to 3’ end of growing RNA molecule. • The formation of the mRNA molecule is catalysed by the enzyme RNA polymerase. • This molecule is actually referred to as pre-mRNA. It is complementary to the template strand but requires some post-transcriptional modification. • Post-transcriptional modification of pre-mRNA or nuclear mRNA involves the removal of introns (non-coding regions within genes) and stitching together of exons (coding regions of genes). This process is known as RNA splicing. • Following RNA splicing a chemical cap is added to the 5’ end of the molecule and a poly-A tail (string of A nucleotides) to the 3’ end. The 5’ cap enables efficient protein synthesis as it is part of the structure recognized by the small ribosomal subunit. The poly-A tail is also important for initiating translation. It also has a role in regulating the degradation of mRNA molecules in the cytoplasm.

23. Comparison of transcription in eukaryotes and prokaryotes

25. Central Dogma of Molecular Biology DNA is self-replicating. DNA is transcribed to produce mRNA. mRNA is translated to produce protein.

26. Translation of mRNA • mRNA exits the nucleus through nuclear pores and binds to ribosomes within the cytoplasm. • Translation of mRNA begins with the sequence AUG (start codon). • Transfer RNAs (tRNA) bring specific amino acids to the ribosome and these are added to the growing polypeptide chain by condensation polymerisation. New amino acids are added to the carboxyl (COOH) end of the polypeptide. • The tRNA drops away from the mRNA and acquires another specific amino acid from the pool in the cytoplasm. Each tRNA can only carry one type of amino acid. • Translation ends when the ribosome reaches a stop codon – the tRNA molecules corresponding to the stop codons UAG, UGA and UAA don’t carry a amino acid. • The mRNA is then released from the ribosome.

27. Structure of tRNA molecule • Once a tRNA gene is transcribed, the RNA that is produced folds to form the shape of a three-leafed clover. This is a functional tRNA molecule. • This tRNA is charged with the amino acid lysine at the amino acid attachment site. The anticodon UUU will bind to the complementary AAA sequence in the mRNA.

30. Gene Regulation • All the somatic cells in your body contain the same chromosomes and therefore the same DNA and same genes. • However, these cells are able to have different shapes and sizes and perform different functions and change throughout your lifespan. • These differences are possible because of different mechanisms that control the expression of individual genes. These mechanisms are collectively referred to as mechanisms for gene regulation.

31. How are genes regulated? • There are many steps involved in the expression of gene, therefore there are many different mechanisms for regulating expression: • The structure of genes varies • The rate of transcription can be regulated • Post-transcriptional modifications can influence which protein is produced • The rate of translation can be regulated • The activity of the protein product (enzyme) can be regulated

32. Role of different mechanisms in gene regulation • Gene structure • All genes contain an upstream promoter region. This consists of a binding site for RNA polymerase and other base sequences known as upstream promoter elements (UPEs). UPEs initiate transcription. Genes vary in the number and type of UPEs. A gene with only one UPE will be weakly expressed. A gene with many UPEs is actively transcribed. • Other DNA sequences known as enhancers increase the rate of transcription. • Genes which code for the production of essential proteins are often present as multiple copies. • Genes can be permanently inactivated in some cells by changes in the chromosome’s structure. • Transcription rate • DNA binding proteins called transcription factors, regulate the rate at which a gene is transcribed. These proteins bind with the upstream region of the gene and stimulate transcription. • Transcription factors may be activated by hormones.

33. Role of different mechanisms in gene regulation • Post-transcriptional modifications • Some pre-mRNAs can be modified in more than one way. Pre-mRNA may be spliced differently in different tissues, leading to different protein products. • Translation • Cells can regulate the amount of translation which occurs by controlling the life-span of mRNA; mRNA may be inactivated after only a short time being translated, or may survive longer in the cell and be translated many times. • Protein activity • Gene expression may be regulated by controlling the activity of the proteins produced in translation. For example, enzyme inhibitors may inactivate an enzyme until it is needed. • Some proteins may control the production of other proteins – e.g. repressor proteins can bind to promoter region of DNA and prevent transcription.

34. Other factors in gene regulation • It is important to realize that the environment of a cell can also influence the expression of genes. This includes factors such as: • Light • Temperature • Ions • Hormones

35. Lac Operon – an example of gene regulation in E. Coli • The bacterium Escherichia coli is capable of producing the enzyme b-galactosidase which splits lactose to produce glucose and galactose. • This enzyme is only produced when the bacteria encounters lactose. When lactose is not present, a protein binds to the promoter region of the b-galactosidase gene and prevents transcription (RNA polymerase cannot access the promoter). This protein is referred to as a repressor protein. • When lactose is present in the growth medium of the bacteria, it enters the cell and binds to the repressor protein causing it to be removed from the DNA and allowing transcription to occur. • The gene is ‘on’ or ‘off’ depending on the nutrients available to the cell.