TU Lecture 1 introduction + Quiz

Question 1

DNA Replication

Answer 1

Topoisomerase relaxes the supercoiled DNA and allows DNA-Helicase to unwind the DNA. The rest of the process is strand dependent. For the leading strand DNA polymerase III can bind directly and add nucleotides from the ‘5 prime end to the ‘3 prime end. For the lagging strand the primerase creates a small primer which DNA Pol III can use to replicate part of the sequence, when the Pol III cannot continue replication due to the binding of a primer it detaches leaving a small gap. Polymerase I fills this gap with the required nucleotide and DNA ligase is used to ligate it together.
DNA synthesis occurs in the 5’ to 3’ direction

Question 2

DNA is packed in the nucleus

Answer 2

DNA Double Helix → Basic structure.
Nucleosome → DNA wraps around histone proteins.
Chromatin Fiber → Nucleosomes compact into a thicker fiber.
Looped Domains → Chromatin fiber forms loops attached to a protein scaffold.
Chromosome → Highly condensed structure during cell division.

Question 3

differences between Prokaryotic and Eukaryotic transcription and translation

Answer 3

1. Cellular Compartmentalization: Eukaryotes have transcription in the nucleus and translation in the cytoplasm, while in prokaryotes, both processes occur in the cytoplasm.
2. mRNA Processing: Eukaryotic mRNA undergoes extensive processing (capping, splicing, polyadenylation) before translation, while prokaryotic mRNA does not.
3. Translation Initiation: Prokaryotic initiation involves the Shine-Dalgarno sequence and formylmethionine, while eukaryotic initiation involves the 5’ cap and methionine.

Question 4

DNA is translated and transcribed to proteins in Prokaryotes

Answer 4

Itranscription and translation are coupled, in the cytoplasm.
Transcription:
RNA polymerase binds to the promoter region of the DNA, guided by sigma factors. synthesizes mRNA
Transcription ends at a terminator sequence, releasing the mRNA.

Translation starts immediately as ribosomes bind to the mRNA’s Shine-Dalgarno sequence, near the start codon (AUG).
The initiator tRNA, pairs with the start codon.
Ribosomes then move along the mRNA, reading codons and adding corresponding amino acids to the growing polypeptide chain. Translation ends at a stop codon

Question 5

Within what size range are genomes usually?

Answer 5

Prokaryote 0.5-10 Mb
* Bacteria 0.5 to 10 megabases (Mb). Most are 1-5 Mb
* Archaea: Similar to bacteria, usually ranging from 0.5 to 5 Mb.
Eukaryotes
* Yeast: 12 to 20 Mb (e.g., Saccharomyces cerevisiae has about 12 Mb).
* Plants: Varies widely; small genomes can be around 100 Mb, while larger genomes can exceed 10 Gb.
* Animals: Typically range from 10 Mb to over 1 Gb. For example, the human genome is about 3.2 Gb.

Question 6

Why is small subunit rRNA a good phylogenetic marker?

Answer 6

Because it has orthologues in all known organisms and is of a suitable leng

Question 7

You have the single-stranded oligonucleotide GATCCATAGTTCGGTGTACAGA. You want to make it double-stranded with DNA polymerase and a short primer of 5 nucleotides long. The sequence of that primer should be

Answer 7

complementary so CTAGG and from 3’ - 5’ as the olionucelotide is from 5-3

Question 8

Acetylation of lysines in histones is usually associated with

Answer 8

gene expression
Mechanism: Acetylation involves the addition of an acetyl group (–COCH₃) to the lysine residues on histone proteins.
Effect on Chromatin Structure: This modification neutralizes the positive charge of lysines, reducing the affinity of histones for the negatively charged DNA. This leads to a more relaxed or open chromatin structure.
Gene Expression: The open chromatin state allows for greater accessibility of transcription factors and RNA polymerase to the DNA, promoting transcription and therefore gene expression.