sl and HL transcription

Question 1

Transcription as the synthesis of RNA using a DNA template
- Students should understand the roles of RNA polymerase in this process.

Answer 1

Transcription is the synthesis of RNA, using DNA as a template. It takes place in the nucleus. The cell`s machinery copies the gene sequence into messenger RNA (mRNA), which is single stranded.

Question 2

Translation as the synthesis of polypeptides from mRNA
- The base sequence of mRNA is translated into the amino acid sequence of a polypeptide.

Answer 2

Translation is the synthesis of a polypeptide or protein from the base sequence of the mRNA. Three nucleotide bases of the mRNA code for one amino acid. The sequence of amino acids determines the shape of the polypeptide and therefore the protein

Question 3

Transcription as the synthesis of RNA using a DNA template
- Function of genes within DNA
- Function of proteins
- Francis Crick: CENTRAL DOGMA

Answer 3

• The sequence of bases in a gene does not give any observable characteristics in an organism. The function of most genes is to specify the sequence of amino acids in a particular polypeptide.
• It is proteins that often directly or indirectly determine the observable characteristics of an individual.
• Francis Crick coined the phrase “central dogma” to describe the two-step process by which he believed genes were expressed and proteins built.
• Genetic information is first transcribed from DNA to RNA, and then translated from RNA to protein.

Question 4

Transcription as the synthesis of RNA using a DNA template
- Students should understand the roles of RNA polymerase in this process. (6)

Answer 4

• binds to a site of DNA at the start of the gene that is being transcribed
• unwinds DNA double helix and separates it into the template and coding strand
• moves along template strand
• adds COMPLIMENTARY RNA nucleotides to template strand (U instead of T)
• links together RNA nucleotides with covalent sugar-phosphate bonds forming a continuous strand of DNA
• DETACHES ASSEMBLED RNA STRAND FROM TEMPLATE STRAND, allowing the DNA double helix to reform

Question 5

Directionality of transcription and translation
- Students should understand what is meant by 5’ to 3’ transcription and 5’ to 3’ translation.

Answer 5

• A single strand of DNA or RNA has directionality. This means that the two ends of the strand are different – because of its antiparalellarity
• This directionality and the specificity of enzymes determines the direction in which transcription and translation occur.

Question 6

Directionality of transcription and translation!!!

Answer 6

Transcription
- Carried out by enzymes (RNA polymerases) which synthesize RNA in a 5’ to 3’ direction
- DNA is read off in 3’ to 5’ direction
- The 5’ end of the next free RNA nucleotide is attached to a free –OH group at the 3’ end of an already synthesized RNA molecule.

Translation
- The ribosome moves along the codons on the mRNA molecule towards its 3’ end.
- Translation is therefore also always in 5’ to 3’ direction.

Question 7

3 stages of portion synthesis

Answer 7

1. initiation
2. elongation
3. termination

Question 8

Initiation of transcription at the promoter
- Consider transcription factors that bind to the promoter as an example. However, students are not required to name other types.

Answer 8

• Transcription starts by recognizing a short specific sequence of 100 – 1000 base pairs on the DNA, called the promoter.
• The promoter INITIATES gene transcription
• RNA polymerase attaches to the promoter on the DNA together with a variety of transcription proteins. This initiates transcription.
• The promoter interacts with transcription factors. These are proteins such as repressors, activators and other (general) transcription factors, which initiate and regulate the transcription of genes and which bind to specific DNA sites (enhancer, silencers,…) near the promotor. RNA Polymerase is not a transcription factor!

Question 9

More on transcription factors

Answer 9

• Activator proteins bind to pieces of DNA called enhancers. Their binding causes the DNA to bend, bringing them near a gene promoter, even though they may be thousands of base pairs away. A repressor would bind to a silencer region, slowing down transcription.
• Other transcription factor proteins join the activator proteins, forming a protein complex which binds to the gene promoter. This protein complex makes it easier for RNA polymerase to attach to the promoter and start transcribing a gene.

Question 10

NOTE: Activators and repressor transcription proteins (regulatory proteins) communicate with the general transcription factors and link in a tight complex to the TATA box in the core promoter region. This allows the RNA polymerase to attach to the core promoter

Question 11

Elongation

Answer 11

• The RNA polymerase proceeds down one strand moving in the 5’-3’ direction adding each new nucleotide to the 3’-OH group of the previous nucleotide.
• DNA reforms behind it and RNA peels off.

Question 12

NOTE: By transcribing the antisense strand, the base sequence of the mRNA will be the same as the coding DNA-except U replaces T.

Question 13

Role of hydrogen bonding & complementary base pairing in transcription
- Include the pairing of adenine (A) on the DNA template strand with uracil (U) on the RNA strand.

Answer 13

the pairing of bases happens through H-bonding.

ensures the genetic code in DNA is accurately transcribed into an mRNA molecule.

Question 14

Termination

Answer 14

• RNA polymerase reaches the terminator and the RNA polymerase stops.
• Once transcription is terminated, the mRNA molecule separates from the RNA polymerase. The polymerase dissociates from the DNA molecule and is available to bind to another promoter region.
• The mRNA in prokaryotes can be used right away unlike eukaryotic mRNA which requires further modification .

Question 15

Transcription as the synthesis of RNA Summary (7 STEPS)

Answer 15

1. RNA polymerase binds to site of DNA at the start of a gene
2. RNA polymerase travels along gene and unwinds DNA double helix
3. Template strand - DNA strand being read off / Coding strand - DNA strand that is identical to base sequence of mRNA strand (except for U instead of T)
4. RNA polymerase adds COMPLIMENTARY RNA nucleotides to the template strand
5. Matching bases are linked together w/ H-bonds and nucleotides are linked together with covalent bonds
6. RNA polymerase separated from the DNA molecule, which then reforms into a double helix

Question 16

Stability of DNA templates
- Single DNA strands are 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.

Answer 16

• The fact that DNA is stable and doesn’t change its code easily is important for the conservation of the original code. The stability is ensured by the sugar-phosphate backbone and hydrogen bonds between nucleotides.
• For some somatic (body) cells which don’t divide to replace itself – e.g nerve cells – this means the code must stay unchanged throughout a lifetime. (still need proteins)
• The stability of DNA may become compromised by free radicals, chemicals, cigarette smoke or exposure to UV or nuclear radiation. This damage can lead to a (harmful or beneficial) mutation. Cells have repair mechanism in place to help fixing the problem, but they are not always successful.

Question 17

Transcription as a process required for the expression of genes
- 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.

Answer 17

• Gene expression is the process by which information carried by a gene is turned into an observable effect on an organism. This occurs by transcription and translation.
• The DNA sequence itself does not determine the observable characteristics, only the specific sequence which is transcribed does.
• Genes can be ”switched on” and “switched off”. The expression pattern of a cell depends on the information from both inside and outside the cell.

Question 18

EXAMPLE - LIVER AND NEURONS

Question 19

Non-coding sequences in DNA do not code for polypeptides (background)
- Limit examples to regulators of gene expression, introns, telomeres and genes for rRNAs and tRNAs in eukaryotes.

Answer 19

• Most nuclear DNA does not code for proteins at all (ca. 98%). Only ca. 1.5-3% of the genome is protein coding DNA - these are shorter sections of bases of DNA that have a unique sequence. Each sequence provides the code to make a specific protein.

Question 20

Non-coding sequences in DNA do not code for polypeptides
- Introns

Answer 20

Introns - non-coding nucleotide sequences found in eukaryotes, which interrupt the coding sequences (exons) of eukaryotic genes.

They are found in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place following transcription (post-transcriptional modification). Here, the introns are removed and the remaining exons joined together.

Question 21

Non-coding sequences in DNA do not code for polypeptides
- Example) Telomeres

Answer 21

• Telomers are the short repeating sequences of DNA at the terminal parts at the end of chromosomes.
• Every time the cell divides and copies its DNA, the very end of the telomere cannot be copied, and the total telomere length is shortened.
• Telomeres protect the organism’s genes from being lost with each cycle of DNA replication. The progressive shortening of telomeres is associated with ageing, age-related diseases and mortality.

Question 22

Non-coding sequences in DNA do not code for polypeptides
- function of tRNA molecules

Answer 22

• The function of tRNA molecules is to carry corresponding amino acids to the growing polypeptide on a ribosome. rRNA makes up ribosomes.
• Genes in the tRNA gene family provide instructions for making molecules called transfer RNAs (tRNAs).

Question 23

Post-transcriptional modification in eukaryotic cells
- 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.

Answer 23

• Following transcription, the mRNA product experiences some changes to prepare for translation.
• Prokaryotes have a different cell organization compared to eukaryotes, which have the nuclear membrane separating the DNA from the cytoplasm.
• The separation into compartments allows for post-transcriptional modification before the mature mRNA transcript leaves the nucleus.

Question 24

3 main types of post-transcriptional modification:

MPS

Answer 24

1. Methyl guanosine capping
2. Poly AAA Tails
3. Splicing

Question 25

methylguanosine capping

Answer 25

• vital in the creation of stable and mature messenger RNA able to undergo translation during protein synthesis. Mitochondrial and chloroplast mRNA are not capped
• A methylated guanosine nucleotide (7-methylguanosine) is added on to the 5’ end of the mRNA.

Question 26

purpose of methylguanosine capping (RPP)

Answer 26

Regulation of nuclear transport

Prevention of degradation by nucleases

Promotion of translation.

Question 27

polyadenation (poly AAA tail)

Answer 27

• The poly A-tail is a long chain of adenine nucleotides (ca. 100 - 250 residues) which are added to the mRNA after transcription. The adenine nucleotides are added to the 3’ end of the mRNA molecule by the enzyme poly A polymerase. This process is called polyadenation.
• The poly A tail makes the RNA more stable, prevents degradation by enzymatic nucleases. It also encourages further modification of the mRNA

Question 28

splicing
- note: exons expressed by translation into an amino acid

Answer 28

• RNA transcribed from genes coding for polypeptides contains alternating exons and introns. The introns are removed and digested into single nucleotides and the remaining exons are spliced together. The mature mRNA can now be translated.

Question 29

Alternative splicing of exons to produce variants of a protein from a single gene
- Use alternative splicing of transcripts of the troponin T gene in foetal and adult heart muscle as an example.

Answer 29

• This is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within, or excluded from, the final, processed messenger RNA (mRNA) produced from that gene.
• Alternative splicing can result in many different mRNA transcripts from the same gene
• Tropomyosin gene has 11 exons, but nowhere are they all used at the same time. Alternative splicing allows the body to fine tune a single gene and its gene product to meet the unique needs of each cell in different types of tissue. (controls interaction of acting and myosin during muscle contractions)