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[h] IB DP Biology HL D1.2 Protein synthesis Flashcards
[q] D1.2.1—Transcription as the synthesis of RNA using a DNA template
[a] Students should understand the roles of RNA polymerase in this process.
[q] D1.2.2—Role of hydrogen bonding and complementary base pairing in transcription
[a] Include the pairing of adenine (A) on the DNA template strand with uracil (U) on the RNA strand.
[q] D1.2.3—Stability of DNA templates
[a] Single DNA strands can be used as a template for transcribing a base sequence, without the DNA base sequence changing.
In somatic cells that do not divide, such sequences must be conserved throughout the life of a cell.
[q] D1.2.4—Transcription as a process required for the expression of genes
[a] Limit to understanding that not all genes in a cell are expressed at any given time and that transcription, being the first stage of gene expression, is a key stage at which expression of a gene can be switched on and off.
[q] D1.2.5—Translation as the synthesis of polypeptides from mRNA
[a] The base sequence of mRNA is translated into the amino acid sequence of a polypeptide.
[q] D1.2.6—Roles of mRNA, ribosomes and tRNA in translation
[a] Roles of mRNA, ribosomes and tRNA in translation simultaneously to the large subunit.
[q] D1.2.7—Complementary base pairing between tRNA and mRNA
[a] Include the terms “codon” and “anticodon”.
[q] D1.2.8—Features of the genetic code
[a] Students should understand the reasons for a triplet code.
Students should use and understand the terms “degeneracy” and “universality”
[q] D1.2.9—Using the genetic code expressed as a table of mRNA codons
[a] Students should be able to deduce the sequence of amino acids coded by an mRNA strand.
[q] D1.2.10—Stepwise movement of the ribosome along mRNA and linkage of amino acids by peptide bonding to the growing polypeptide chain
[a] Focus on elongation of the polypeptide, rather than on initiation and termination.
[q] D1.2.11—Mutations that change protein structure
[a] Include an example of a point mutation affecting protein structure.
[q] D1.2.12—Directionality of transcription and translation
[a] Students should understand what is meant by 5′ to 3′ transcription and 5′ to 3′ translation.
[q] D1.2.13—Initiation of transcription at the promoter
[a] Consider transcription factors that bind to the promoter as an example.
However, students are not required to name the transcription factors.
[q] D1.2.14—Non-coding sequences in DNA do not code for polypeptides
[a] Limit examples to regulators of gene expression, introns, telomeres and genes for rRNAs and tRNAs in eukaryotes
[q] D1.2.15—Post-transcriptional modification in eukaryotic cells
[a] Include removal of introns and splicing together of exons to form mature mRNA and also the addition of 5′ caps and 3′ polyA tails to stabilize mRNA transcripts.
[q] D1.2.16—Alternative splicing of exons to produce variants of a protein from a single gene
[a] Students are only expected to understand that splicing together different combinations of exons allows one gene to code for different polypeptides. Specific examples are not required.
[q] D1.2.17—Initiation of translation
[a] Include attachment of the small ribosome subunit to the 5′ terminal of mRNA, movement to the start codon, the initiator tRNA and another tRNA, and attachment of the large subunit.
Students should understand the roles of the three binding sites for tRNA on the ribosome (A, P and E) during elongation.
[q] D1.2.18—Modification of polypeptides into their functional state
[a] Students should appreciate that many polypeptides must be modified before they can function.
The examples chosen should include the two-stage modification of pre-proinsulin to insulin.
[q] D1.2.19—Recycling of amino acids by proteasomes
[a] Limit to the understanding that sustaining a functional proteome requires constant protein breakdown and synthesis.
[q] What is protein synthesis?
[a] The process of making proteins by using the information present in the DNA
[q] What are the two stages of protein synthesis?
[a] 1. Transcription
2. Translation
[q] What is the role of the different types of RNA in protein synthesis?
[a] 1. mRNA carries the message from the DNA in the nucleus to the ribosomes in the cytoplasm.
2. tRNA carries amino acids from teh cytoplasm to the ribosomes.
3. rRNA combines with ribosomal proteins to construct cytoplasmic ribosomes.
[q] What is the structure of a gene?
[a] A gene is made up of 3 sections:
1. A non-coding promoter region where transcription begins
2. The coding gene section with intron non-coding regions
3. A non-coding terminator region where transcription ends
[q] What are 3 words used to describe the genetic code?
[a] 1. Degenerate: there may be more than one codon for each amino acid.
2. Universal: all organisms share the same genetic code (with some minor differences)
3. Non-overlapping: each triplet is read as discrete codons (in sections of 3)
[q] What is an example of a point mutation affecting protein structure?
[a] When guanine (G) in alanine is replaced by Adenine (A), it makes valine.
This causes the haemoglobin in red blood cells to form strands and give them a sickle shape, resulting in sickle cell anaemia.
[q] What is a non-coding region of DNA?
[a] A region which doesn’t code for proteins.
[q] What are examples of non-coding DNA?
[a] 1. Regulators of gene expression e.g. promoters, terminators etc.
2. Genes coding for rRNA or tRNA
3. Telomeres
4. Introns
[q] What is a telomere and its function?
[a] Telomeres are structural features at the ends of chromosomes made up of repetitive non-coding DNA sequences.
Its function is to protect the chromosome.
[q] What are the 2 functions of RNA polymerase in transcription?
[a] 1. RNA polymerase breaks the hydrogen bonds between the complementary bases, unzipping the DNA strand.
2. It then joins together the nucleotides of the mRNA strand with phosphodiester bonds.
[q] How many copies of the gene does the RNA polymerase make?
[a] It transcribes multiple mRNA strands from the same gene to make lots of the protein.
[q] What are the names of the 3 strands involved in transcription and what are they?
[a] 1. Template/nonsense strand- The strand which is read and used as a template to create the mRNA.
2. mRNA strand- The strand which is synthesised.
3. Sense strand- The strand which is not read but carries the ‘sense’ of the mRNA strand.
[q] What happens in transcription? (detailed)
[a] 1. Transcription factors, followed by RNA polymerase binds to the non-coding promoter region at the start of the gene.
2. It unzips the gene by breaking hydrogen bonds and joins the free RNA nucleotides together from the 5′ to the 3′ end, which have lined up according to complementary base pairing.
3. When it reaches the terminator region, the RNA polymerase falls away from the DNA, leaving a pre-mRNA strand.
[q] What is the structure of a pre-mRNA molecule in eukaryotes?
[a] A pre-mRNA molecule consists of introns (non-coding) and exons (coding).
[q] How is pre-mRNA modified?
[a] Before the pre-mRNA leaves the nucleus, it is modified.
It undergoes ‘splicing’ which is carried out by spliceosomes where the intron sections of the mRNA are cut out.
[q] What is the function of the 5′ cap and 3′ poly-A tail?
[a] They stabilise the mRNA molecule and prevent it from being broken down by enzymes in the cytoplasm.
[q] What is a spliceosome made of?
[a] An enzyme and RNA
[q] What is the advantage of splicing?
[a] The order of the exons can be mixed up, meaning that 1 gene can code for several different proteins.
[q] What happens after transcription and splicing?
[a] The mRNA leaves the nucleus through the nuclear pore and travels via the cytoplasm to the ribosome for translation.
[q] How many codons does the ribosome deal with at a time?
[a] 2 codons
[q] What are the different sites on a ribosome and what happens at each one?
[a] A- Holds the tRNA carrying the next amino acid to be added to the polypeptide chain
P- Holds the tRNA carrying the growing polypeptide chain
E- Discharges the tRNA that has lost its amino acid
[q] What direction does the ribosome move?
[a] From the 5′ to the 3′ end of the mRNA strand
[q] What is an initiation complex?
[a] This is when an initiator tRNA pairs with the mRNA start codon (AUG) and the ribosome attaches to the 5′ end of the mRNA.
[q] What happens after the initiation complex is formed?
[a] The large subunit of the ribosome is added and then the initiator tRNA is bound to the P site, leaving the A empty for the tRNA carrying a functional amino acid.
[q] What happens in translation? (detailed)
[a] 1. The mRNA strand binds to the smaller bottom ribosome subunit then the larger subunit of the ribosome attaches.
2. The initiation complex is formed after which tRNA molecules bring in the amino acids and line up next to the messenger RNA according to the rules of complementary base pairing.
3. The incoming tRNA anticodon binds to the A site of the ribosome.
A peptide bond forms between its amino acid and the adjacent one in the P site and the ribosome moves along, causing the tRNA in the E site to detach and the tRNA in the P site to move to the E site.
4. This repeats until the ribosome reaches a termination codon, it stops translation and the full polypeptide chain has now formed.
[q] What happens to the tRNA molecule after it leaves the E site of the ribosome?
[a] The tRNA will collect an amino acid complementary to its anticodons and return to the ribosome when its needed.
[q] What is a polysome?
[a] A structure made up of many ribosomes on one mRNA chain with different lengths of polypeptide chains.
They all translate the mRNA molecule at the same time for fast protein production.
[q] What must happen to many polypeptides before they can carry out their function?
[a] They must be modified
[q] What is an example of a protein which needs modification?
[a] Insulin
[q] How is insulin modified before it is secreted?
[a] 1. Insulin starts out as pre-proinsulin, produced in the beta cells of the pancreas.
2. A signal peptide (short peptide chain) directs it to the endoplasmic reticulum and is removed as it enters, producing proinsulin.
3. Proinsulin is exposed to enzymes that break peptide bonds which result in the removal of a section of peptides.
This is the final step in the production of the mature form of insulin.
[q] What is a proteome?
[a] The entire set of proteins that is/can be expressed by a cell.
[q] Why do proteins need to be replaced?
[a] – They are no longer useful/needed because they only provide a cellular function for a short time
– They become damaged
[q] What carries out the process of recycling of proteins?
[a] Proteases degrade proteins by breaking peptide bonds.
They are contained in lysosomes to protect cellular proteins.
[q] What do eukaryotic cells use to get rid of damaged or un-needed proteins?
[a] They mark proteins with a chemical called ubiquitin.
These proteins are then destroyed by organelles called proteasomes.
The marked protein enters at one end and amino acids exit at the other.
[q] What is the word equation for the degradation of proteins in eukaryotes?
[a] marked protein -> proteasome -> amino acids
[q] What happens to the free amino acids?
[a] They are reused by the cell during protein synthesis.
[q] D 1.2.1 Transcription as the synthesis of RNA using DNA template
[a] Transcription is the process by which DNA is copied (transcribed) to messenger RNA (mRNA).
– DNA is used as a template for the mRNA.
– Complementary base pairing between DNA and RNA.
– In transcription, only one small part of DNA is being copied.
RNA polymerase is an enzyme that is responsible for copying a DNA sequence into an RNA sequence; durimg transcription.
[q] D 1.2.2 Role of hydrogen bonding and complementary base pairing in transcription
[a] In transcription, complementary base pairing ensures that the piece of DNA is transcribed correctly into the mRNA.
Complementary base pairing is all about hydrogen bonds forming.
In transcription, base pairs (of complementary base pairing) are held together by hydrogen bonds; the pairs have the correct chemical structure to form hydrogen bonds, that hold them together.
Base pairs:
adenine – thymine (uracil is used in RNA)
cytosine – guanine
[q] D 1.2.3 Stability of DNA templates
[a] DNA is a very stable molecule.
– a lot of its stability is due to the complementary bae pairing of its two strands.
In somatic (non sex/reproductive) cells, the DNA sequence must be conserved throughout their cells, so that they continue to carry out their original function.
[q] D 1.2.4 Transcription as a process required for the expression of genes
[a] In order for the information inside genes to be expressed, proteins have to be made.
Expressing genes means making proteins.
The process of transcription is the first step for the expression of genes.
– trancription is the key stage where gene expression can be turned on/off;
determines whether a gene is goinig to be expression or not/ whether a gene is going to be transcribed or not (if a gene is not transcribed, a protein can not be made).
Not allowing transcription is the key way for differentiation.
– not all genes are expressed in all cells or at any given time
[q] D 1.2.5 Translation as the synthesis of polypeptides from mRNA
[a] Translation is the process of translating the sequence of messenger RNA (mRNA) to a sequence of amino acids (polypeptide – unbranched chain of amino acids joined by peptide bonds).
– mRNA is read and told what amino acids to link together.
[q] D 1.2.6 Role of mRNA, ribosomes, and tRNA in translation
[a] Role of mRNA in translation:
– molecule created during transcription.
– instructions.
– First thing that happens during translation, the mRNA binds to the small subunit of the ribosome.
Role of ribosomes in translation:
– site of translation.
– holds mRNA (to be read) and tRNA (so amino acids can link toegther).
– made of two different subunits (small and large), that are put together during the process of translation.
Role of tRNA in translation:
– carry the amino acids to the ribsome.
– 2 tRNAs can bind to the ribosome at the same time; ends up with 2 amino acids side-by-side (they link together by letting go of the tRNA)
– picks up more amino acids after being let go by amino acids; continuous process
[q] D 1.2.7 Complementary base pairing between tRNA and mRNA
[a] Complementary base pairing allows tRNA to know that it is binding to the correct mRNA.
A codon is a three-nucleotide or triplet sequence found on mRNA that codes for a certain amino acid during translation.
The anticodon is a three-nucleotide sequence found on tRNA that binds to the corresponding mRNA sequence.
[q] D 1.2.8 Features of the genetic code
[a] The genetic code is:
– degenerate: there is more than one codon for many of the amino acids.
– universal: the same in all living organisms.
[q] D 1.2.9 Using the genetic code expressed as a table of mRNA codons
[a] Each codon is three nucleotides.
Translation always begins with the codon AUG, amino acid methionine.
STOP codons are the end of the polypeptide chain because there are no amino acids or tRNA that correspond to them; stops the building of the chain.
[q] D 1.2.10 Stepwise movement of the ribosome along mRNA and linkage of amino acids by peptide bonding to the growing peptide chain
[a] Stepwise movement of the ribosome along mRNA and linkage of amino acids by peptide bonding to the growing peptide chain
1. The ribsomes moves along the mRNA reading its codons.
2. As the 2 tRNA binds to the ribosome, the amino acids attached to the tRNAs link together and make the polypepetide chain longer.
[q] D 1.2.11 Mutations that change protein structure
[a] Mutations can change the structure of a protein.
Example: GAG to GTG
– the change in nucleotide is a mutation.
– GAG mRNA = CUC
– GTG mRNA = CAC
– changing a single nucleotide, changed the amino acid that the codon coded for.
Mutations that do not have an observable effect on the amino acid sequence are called silent mutations.
– mutations can be silent because the genetic code is degenerate.
[q] D 1.2.12 Directionality of transcription and translation
[a] Directionality of transcription
– the RNA polymerase laids down the new strand of mRNA 5′ end to 3′ end
Directionality of translation
– the ribosome reads the mRNA from the 5′ end to the 3′ end.
[q] D 1.2.13 Initiation of transcription at the promoter
[a] Transcription begins at a region called the promoter.
Mechanisms involved in whether a gene is transcribed or not:
– transcription factors (RNA polymerase and other proteins).
– repressor sequences (allows proteins to bind that block the binding of RNA polymerase;
blocks the promoter sequence; above of the promoter sequences (where the RNA polymerase is going to bind))
– activator sequences (allows RNA polymerase to bind)
These are within the promoter region.
[q] D 1.2.14 Non-coding sequences in DNA that do not code for polypeptides
[a] Non-coding sequences in DNA that do not code for polypeptides
– Introns: a sequence within a gene that gets removed before translation.
– Telomeres: the region at the end of a piece of DNA.
– Genes for rRNA: the material that makes up the ribosome.
– Genes for tRNA: the material that makes tRNA.
– Regulatory sequences: repressor sequences, activator sequences, etc.
[q] D 1.2.15 Post-transcriptional modification in eukaryotic cells
[a] Post-transcriptional modification in eukaryotic cells (modifying mRNA after it is transcribed)
1. Introns are removed.
2. Exons are spliced together.
3. A cap is added to the 5′ end and a poly A tail (a bunch of nucleotides containing adenine) to the 3′ end.
[q] D 1.2.16 Alternative splicing of exons to produce variants of a protein from a single gene
[a] Due to post-transcriptional modification, multiple different proteins can be produced by a single gene (because one segment is not said to just be an intron or an exon).
By altering which segments are cut out as introns, the cell can make more than one proten from a single gene.
[q] D 1.2.17 Intitiation of Translation
[a] Intitiation of Translation
1. The ribosome binds to the 5′ end of the mRNA, and starts moving towards the 3′ end of the strand until it reaches the start codon (AUG).
Just the small subunit of the ribosome
2. When the ribosome gets to the start codon, the tRNA binds to the start codon.
The large subunit of the ribosome locks on
3. Another tRNA comes and binds to the next codon (because the ribosome has room for 2 tRNAs).
4. Once the 2 tRNAs are side-by-side, each holding onto an amino acid, the amino acids form a peptide (covalent) bond;
in order for the first amino acid to bind to the second amino acid (or for the amino acids to bind to each other in general), they have to let go of the tRNA.
5. The ribosome slides towards the 3′ end of the mRNA one codon which ejects the first tRNA and the second tRNA moves to where the first tRNA was.
6. Process is repeated until a STOP codon is reached; at this point, the polypeptide chain is released, the ribosome runs off the mRNA and falls apart, and translation is over.
[q] D 1.2.18 Modification of polypeptides into their functional state
[a] Modification of polypeptides into their functional state (after translation)
– Methonine is removed.
– Phosphorylation (the attachment of a phosphate group to a molecule or an ion) of an amino acid side chain.
– Addition of a carbohydrate to a side chain.
– Folding and stablizing with intermolecular interactions (ex: disulfide bridge); reinforcement
– Part of the chain is removed.
– Multiple polypeptide chains are combined.
– Non-polypeptide components are added.
These are all modifications that could happen between translation and protein’s functional state.
Not all of these modifications happen to every proteins.
[q] Preproinsulin to insulin
[a] Preproinsulin to insulin is example of a modification of polypeptides into their functional state
1. When it comes off of the ribosome, it is 110 amino acids long (preproinsulin)
2. Enters the endoplasmic reticulum (ER), where 24 amino acids are removed from the N’ terminal end (proinsulin)
3. Folded with 3 disulfide bridges into tertiary structure
4. Two peptide bonds are broken (in different location), releasing 33 amino acids and producing an A-chain and a B-chain
5. Two amino acids are removed from the C-terminal end of the B-chain; insulin molecule is achieved.
[q] D 1.2.19 Recycling of amino acids by proteasomes
[a] All the amino acids that were cut off or broken down using enzymes, can be picked up by the appropriate tRNAs and go be used in translation somewhere else.
[q] Linking Questions
[a] 1. How does the diversity of proteins produced contribute to the functioning of cells?
– carrier proteins, channel proteins, pumps, enzymes (structural)
2. What biological processes depend on hydrogen bonding?
– dna replication, protein synthesis (transcription, translation)
[x] Exit text
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