SL IB Biology Protein Synthesis PDF

Head to www.savemyexams.com for more awesome resources SL IB Biology Your notes Protein Synthesis Contents Transcription in Protein Synthesis Translation in Protein Synthesis The Genetic Code Protein...

Head to www.savemyexams.com for more awesome resources SL IB Biology Your notes Protein Synthesis Contents Transcription in Protein Synthesis Translation in Protein Synthesis The Genetic Code Protein Structure & Mutations Page 1 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Transcription in Protein Synthesis Your notes Synthesis of RNA This process of protein synthesis occurs in two stages: Transcription – DNA is transcribed and an mRNA molecule is produced mRNA is a single stranded RNA molecule that transfers the information in DNA from the nucleus into the cytoplasm mRNA production requires the enzyme RNA polymerase Translation – mRNA (messenger RNA) is translated and an amino acid sequence is produced The process of transcription This stage of protein synthesis occurs in the nucleus of the cell Part of a DNA molecule unwinds (the hydrogen bonds between the complementary base pairs break) This exposes the gene to be transcribed (the gene from which a particular polypeptide will be produced) A complementary copy of the code from the gene is made by building a single-stranded nucleic acid molecule known as mRNA (messenger RNA) Free RNA nucleotides pair up (via hydrogen bonds) with their complementary (now exposed) bases on one strand (the template strand) of the ‘unzipped’ DNA molecule The sugar-phosphate groups of these RNA nucleotides are then bonded together by the enzyme RNA polymerase to form the sugar-phosphate backbone of the mRNA molecule When the gene has been transcribed (when the mRNA molecule is complete), the hydrogen bonds between the mRNA and DNA strands break and the double-stranded DNA molecule re-forms The mRNA molecule then leaves the nucleus via a pore in the nuclear envelope This is where the term messenger comes from - the mRNA is despatched, carrying a message, to another part of the cell DNA can't make this journey; it's too big to fit through the pores in the nuclear envelope Transcription in the nucleus diagram Page 2 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Your notes DNA is transcribed and an mRNA molecule is produced Examiner Tip Be careful – DNA polymerase is the enzyme involved in DNA replication; RNA polymerase is the enzyme involved in transcription – don’t get these confused. Page 3 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Hydrogen bonding & Complementary Base Pairing In the transcription stage of protein synthesis, free RNA nucleotides pair up with the exposed bases on Your notes the DNA molecule but only with those bases on one strand of the DNA molecule The RNA will have a complementary base sequence to the DNA strand and will bind to the DNA using hydrogen bonds The adenine of the DNA is complementary to uracil on the new RNA strand, because a thymine RNA nucleotide does not exist Complementary base pairing between the DNA and the RNA transcript table DNA template strand code TAC GGA AGA CTT GGG RNA transcript AUG CCU UCU GAA CCC The strand of the DNA molecule that carries the genetic code is called the coding strand The opposite DNA strand is called the template strand To get an RNA transcript of the coding strand, the template strand is the one that is transcribed to form the mRNA molecule This mRNA molecule will later be translated into an amino acid chain DNA coding and template strand during transcription diagram Page 4 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources The template strand of the DNA molecule is the one that is transcribed Your notes DNA Templates DNA is a very stable molecule due to the hydrogen bonding between the DNA bases of the two strands and the strong phosphodiester bonds between adjacent nucleotides in each strand This means that the genetic code is not prone to spontaneously breaking or changing This feature allows single DNA strands to act as reliable templates for transcription over several generations of cell replication In certain types of somatic cells that do not divide during their lifetimes, such as neurones and some types of muscle cells, the genetic sequence is conserved due to this stability and does not degrade over time Transcription & Gene Expression There are approximately 20,000 protein-coding genes in the human genome Not every protein is needed in every cell For example, the insulin protein is not needed in cardiac muscles of the heart As a result, our specialised cells have a way of switching certain genes off or on to match the requirements of the cell. This is called gene expression Genes that are expressed are 'switched on' and undergo the process of transcription and translation Genes that are not expressed are 'switched off' or silenced, and do not go through the process of transcription and/or translation There are various different mechanisms in the cell involved in controlling gene expression Transcription is the first stage of gene expression and so this is a key stage at which gene expression can be switched on or off Page 5 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Translation in Protein Synthesis Your notes Synthesis of Polypeptides Translation involves taking the genetic code from the mRNA and synthesising a polypeptide A polypeptide is a sequence of amino acids covalently bonded together The order of the amino acids is based on the information stored in the genetic code of the mRNA This stage of protein synthesis occurs in the cytoplasm of the cell The mRNA template comes from the process of transcription, and so translation always takes place following these events After transcription the mRNA moves out of the nuclear pore and diffuses into the cytoplasm towards the ribosome for translation Examiner Tip Make sure you learn both stages of protein synthesis fully. Don’t forget WHERE these reactions take place – transcription occurs in the nucleus but translation occurs in the cytoplasm! Page 6 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Roles of RNA & Ribosomes in Translation After leaving the nucleus, the mRNA molecule attaches to a ribosome Your notes A ribosome is a complex structure that is made of a large and small subunit Ribosomes are themselves made of proteins and RNA (called ribosomal RNA or rRNA) There are binding sites on the subunits for the various other molecules involved in translation The mRNA binds to the small subunit Two tRNA molecules are able to bind to the large subunit simultaneously mRNA in the ribosome diagram A ribosome is built of large and small subunits, ribosomal RNA and an area on the surface that catalyses the formation of peptide bonds in a newly-synthesised protein Translation depends on complementary base pairing between codons on mRNA and anticodons on tRNA In the cytoplasm, there are free molecules of tRNA (transfer RNA) The tRNA molecules bind with their specific amino acids (also in the cytoplasm) and bring them to the mRNA molecule on the ribosome The triplet of bases (anticodon) on each tRNA molecule pairs with a complementary triplet (codon) on the mRNA molecule tRNA and mRNA before translation diagram Page 7 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Your notes The translation stage of protein synthesis – tRNA molecules bind with their specific amino acids Page 8 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Codons & Anticodons Codons of three bases on mRNA correspond to one amino acid in a polypeptide Your notes A triplet is a sequence of three DNA bases that codes for a specific amino acid A codon is a sequence of three mRNA bases that codes for a specific amino acid A codon is transcribed from the triplet and is complementary to it An anticodon is a sequence of three transfer RNA (tRNA) bases that are complementary to a codon The transfer RNA carries the appropriate amino acid to the ribosome The amino acid can then be condensed onto the growing polypeptide chain Certain codons carry the command to stop translation when the polypeptide chain is complete. These are called stop codons Structure of tRNA diagram The anticodon is positioned at the bottom of the tRNA molecule and consists of three exposed RNA bases mRNA and tRNA binding diagram Page 9 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Your notes Complementary base pairing occurs between the mRNA and the corresponding tRNA molecule, resulting in the correct sequence of amino acids being synthesised into the polypeptide Analogy: Think of transcription and translation as being like converting between languages Each language has its alphabet, just as nucleic acids and proteins have their monomers Transcription is like converting text from English to French The same characters are used, but there are slight differences French uses the same alphabet as English but employs occasionally accented characters like â, é, or ç DNA and RNA employ largely the same monomers but with slight differences in the two pentose sugars and U replacing T. Translation is like converting text from a Western language to a language that uses a different alphabet, like Japanese A completely different set of characters is used The sequence of characters is unrecognisable from the original If we could see them, a chain of amino acids would look nothing like a chain of nucleotides Page 10 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Transcription and Translation Can be Likened to the Conversion Between Languages Table Your notes Examiner Tip Remember that complementary base pairing in RNA means that: Adenine (A) will pair up with Uracil (U) Cytosine (C) will pair up with Guanine (G) So if an mRNA codon has a sequence of CAG, then its complementary tRNA anticodon will have a sequence of GUC. Page 11 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources The Genetic Code Your notes Features of the Genetic Code The sequence of DNA nucleotide bases found within a gene is determined by a triplet (three-letter) code Each sequence of three bases (i.e. each triplet of bases) in a gene codes for one amino acid These triplets code for different amino acids – there are 20 different amino acids that cells use to make up different proteins For example: CAG codes for the amino acid valine TTC codes for the amino acid lysine GAC codes for the amino acid leucine CCG codes for the amino acid glycine Some of these triplets of bases code for start (TAC – methionine) and stop signals These start and stop signals tell the cell where individual genes start and stop As a result, the cell reads the DNA correctly and produces the correct sequences of amino acids (and therefore the correct protein molecules) that it requires to function properly The genetic code is non-overlapping Each base is only read once in which codon it is part of There are four bases, so there are 64 different codons (triplets) possible (43 = 64), yet there are only 20 amino acids that commonly occur in biological proteins This is why the code is said to be degenerate: multiple codons can code for the same amino acids The degenerate nature of the genetic code can limit the effect of mutations The genetic code is also universal, meaning that almost every organism uses the same code (there are a few rare and minor exceptions) The same triplet codes code for the same amino acids in all living things (meaning that genetic information is transferable between species) The universal nature of the genetic code is why genetic engineering (the transfer of genes from one species to another) is possible Page 12 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Deducing Amino Acid Sequences By observing the genetic code in the mRNA it is possible to determine the sequence of amino acids Your notes that are coded for in the polypeptide mRNA codons and amino acids table Page 13 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Worked example Your notes Use the rules of base-pairing and the mRNA Codons and Amino Acids Table (above) to deduce the amino acid sequence coded for by the following DNA coding strand sequence TTC GAG CAT TAC GCC Answer: Step 1: Work out the template sequence using A-T and C-G base pairing rules AAG CTC GTA ATG CGG Step 2: Work out the mRNA codons, complementary to the template strand UUC GAG CAU UAC GCC Step 3: Use the mRNA Codons and Amino Acids Table (above) to work out the first amino acid First base in codon = U, second base = U, third base = C So we're looking in the top-left box of the table; this amino acid is Phe Step 4: Repeat for the remaining 4 codons GAG = Glu CAU = His UAC = Tyr GCC = Ala The final sequence of amino acids is Phe-Glu-His-Tyr-Ala Page 14 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Elongation of the Polypeptide Chain During translation two tRNA molecules fit onto the ribosome at any one time, bringing the amino acid Your notes they are each carrying side by side The ribosome will move along the mRNA molecule, one codon at a time A peptide bond is then formed (by condensation) between the two amino acids The formation of a peptide bond between amino acids is an anabolic reaction It requires energy, in the form of ATP The ATP needed for translation is provided by the mitochondria within the cell This process continues until a ‘stop’ codon on the mRNA molecule is reached – this acts as a signal for translation to stop and at this point the amino acid chain coded for by the mRNA molecule is complete This amino acid chain is then released from the ribosome and forms the final polypeptide The process of translation diagram Page 15 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Your notes Page 16 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Your notes The translation stage of protein synthesis – an amino acid chain is formed Page 17 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Protein Structure & Mutations Your notes Protein Structure & Mutations A gene mutation is a change in the sequence of bases in a DNA molecule; this may result in a new allele Mutations occur all the time and occur randomly Mutations are copying errors that take place when DNA is replicated during S phase of interphase As the DNA base sequence determines the sequence of amino acids that make up a polypeptide, mutations in a gene can sometimes lead to a change in the polypeptide for which the gene codes Most mutations are harmful or neutral (have no effect) but some can be beneficial Inheritance of mutations: Mutations present in normal body cells are not inherited; they are eliminated once the affected cells die Mutations within gametes are inherited by offspring, so can lead to heritable genetic conditions Point mutations are mutations where one base in the DNA sequence is altered; this can result in a changed amino acid at this location Example of a point mutation: sickle cell disease A small change to a gene can have serious consequences for an organism Sickle cell disease is a genetic disorder caused by a single point mutation within the gene that codes for the alpha-globin polypeptide in haemoglobin (Hb) Most humans have the allele HbA The mutation results in a new allele HbS The sickle cell mutation Within the haemoglobin gene a point mutation changes the DNA triplet GAG to GTG on the coding strand The resulting DNA triplet (CAC) on the template strand is transcribed into the mRNA codon GUG, instead of GAG During translation the amino acid valine (Val) replaces the original amino acid glutamic acid (Glu) This occurs at the sixth position of the polypeptide Sickle cell anaemia point mutation diagram Page 18 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Your notes A base substitution on the DNA molecule results in a change in the amino acid at position 6 of the haemoglobin polypeptide, altering the overall structure and function of the protein The effects The protein haemoglobin S is produced instead of haemoglobin A; this causes a distortion in the shape of red blood cells, resulting in a sickle shape Sickle-shaped red blood cells: Have a limited oxygen-carrying capacity Block the capillaries and limit the flow of normal red blood cells People with sickle cell anaemia suffer from acute pain, fatigue and anaemia There is a correlation between the global distribution of sickle cell disease and malaria In areas with increased malaria cases there is an increased frequency of sickle cell alleles; this is thought to be due to increased resistance to the malaria parasite in individuals with the HbS allele Sickled cells diagram Page 19 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers  Head to www.savemyexams.com for more awesome resources Your notes Sickled cells can block the flow of blood through the capillaries, restricting oxygen supply to the tissues You will cover more on mutations later in the course; see this link Page 20 of 20 © 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers