BIO 2 - Information flow in Biology

Question 1

*What is the difference between genotype and phenotype?

Answer 1

Genetype: digital information stored in an organims genes (DNA)

Phenotype: the collection of an organisms characteristics i.e. the manifestation of the genotype. Shape, weight, height, smooths, wrinkled.

Question 2

*What does the central dogma expresses?

Answer 2

It expresses that the principal direction of genetic information flow in biology is from DNA to RNA to Protein.

Exceptions include copying of information from RNA to DNA is some rare cases (viruses), but never from protein to RNA or DNA

Question 3

What is the structure of DNA known as?

Answer 3

A double Helix, solved in 1953. H, O, N, C, P

Question 4

*How can 2 m of human DNA be squeezed into a nucleus of 5 um diameter?

Answer 4

DNA is a charged polymer (polyelectrolyte) and would normally adopt an expanded random coil structure. It is strongly compressed and organized in a highly condensed structure called chromatin.

Histone proteins: small positively charged proteins which DNA can bind to leading to DNA being more compact.

Question 5

What is the difference between Euchromatin and Hetereochromatin?

Answer 5

The structure DNA is condensed in is called chromatin.
Euchromatin: more lightly packed form of chromatin, in which the DNA is more easily accessible for transcription
Heterochromatin: more densely packed.

Question 6

What happens in DNA Replication?

Answer 6

DNA replication:
Initiation: Both strands are separated by helicases and other proteins.
Elongation: new complementary strands to each of the two strands are synthesized in opposite directions. One leading strand and one lagging strand.

Termination: separation, coiling and repacking the independent double-stranded molecules

Question 7

What is the first step of DNA replication?

Answer 7

The first step of DNA replication is initiation, during which helicases (enzyme) unwind the double helix structure of the DNA molecule at specific sites called origins of replication.

Question 8

What enzyme is responsible for unwinding the DNA strands during DNA replication?

Answer 8

Helicases are responsible for unwinding the DNA strands during DNA replication by breaking the hydrogen bonds between the complementary base pairs.

Question 9

What is the role of DNA polymerases in DNA replication?

Answer 9

DNA polymerases are enzymes that catalyze the synthesis of new DNA strands by adding complementary nucleotides to the template strand. They also proofread the newly synthesized DNA to ensure accuracy.

Question 10

Describe the difference between the leading and lagging strands during DNA replication

Answer 10

The leading strand is synthesized continuously in the 5’ to 3’ direction, while the lagging strand is synthesized discontinuously in the 5’ to 3’ direction away from the replication fork, resulting in the formation of Okazaki fragments.

Question 11

What is the function of RNA primers in DNA replication?

Answer 11

RNA primers are synthesized by primase and provide a starting point for DNA polymerases to begin synthesis. They are later removed and replaced with DNA nucleotides.

Question 12

Explain the process of termination in DNA replication

Answer 12

Termination involves the completion of DNA synthesis and the separation of the newly synthesized DNA molecules. This includes the removal of RNA primers, synthesis of DNA in place of the RNA primers, and ligation of the DNA fragments into continuous strands.

Question 13

How does DNA replication ensure the accuracy of the genetic information passed on to daughter cells?

Answer 13

DNA replication involves proofreading mechanisms carried out by DNA polymerases, which correct errors in base pairing. Additionally, mismatch repair mechanisms detect and repair errors that escape the proofreading process. These mechanisms collectively ensure the accuracy of the genetic information passed on to daughter cells.

Question 14

What does DNA replication requires?

Answer 14

Replication requires:
DNA template
4 deoxyribonucleotide triphosphates (dATP, dGTP, dCTP, dTTP) building blocks
DNA polymerase (enzyme complex)
a primase to generate an RNA primer that allows the DNA polymerase to initiate DNA synthesis

Question 15

What is Nanopore sequencing?

Answer 15

A DNA sequencing method, whereby long DNA strands are translocated through small pores and the change in ionic current when each base passes through the hole, is recorded and analysed to determine the nature of the nucleotide.

Question 16

What happens during transcription?

Answer 16

One of the two DNA strands of a double helix is copied into RNA. Both strands can in principle act as templates.

Question 17

What does transcription requires?

Answer 17

DNA template
4 ribonucleotide triphosphates (ATP, GTP, CTP, UTP) building blocks
RNA polymerase (enzyme)

Question 18

What are the 3 phases of transcription?

Answer 18

Transcription process has 3 phases:
Initiation, RNA polymerase starts RNA synthesis
Elongation, RNA chain lengthening
Termination, RNA polymerase stops RNA synthesis, dissociates from DNA

Question 19

What are the differences between the structure of DNA and RNA?

Answer 19

DNA and RNA are very similar except:

RNA: has OH group on the carbon atom number 2 in the ribose ring
DNA: Has not

Base pairs
RNA: Uracil
DNA: Thymine

Question 20

What are the differences between the properties of DNA and RNA?

Answer 20

DNA: long term information storage
RNA: Short term messaging to make sure a given protein is produced at a given point in time.

Their stabilities are very different due to intrinsic thermodynamic stability differences but also because enzymes that can degrade RNA are everywhere.

Question 21

What happens in translation?

Answer 21

RNA is translated to polypeptide or protein. The genetic information stored in RNA (originally from DNA) is converted into an amino acid sequence. This happens in the ribosome.

Question 22

Which 4 letters does the RNA alphabet contains?

Answer 22

A , C , G , U

Question 23

How can translation displays a significantly higher level of specificity than one would expect

Answer 23

Due to the introduction of a high energy intermediate. It leads to two points alonge the reaction where wrong building blocks can deteach which can gives us a higher specificity. It costs energy.

Question 24

*What is the principle of the PCR reaction and what is it used for?

Answer 24

The Polymerase chain reaction is used to demonstrate the presence of a particular DNA sequence in a given sample.

Its principle is based on the use of DNA polymerase which is an in vitro replication of specific DNA sequences. This method can generate tens of billions of copies of a particular DNA fragment (the sequence of interest, DNA of interest, or target DNA) from a DNA extract (DNA template).

applications including biomedical research and forensic science.

Question 25

*What are the overall ideas behind DNA sequencing by synthesis and nanopore DNA sequencing?

Answer 25

Nanopore sequencing: Long DNA strands are translocated through small pores and the change in ionic current when each base passes through the hole is recorded and analysed to determine the nature of the nucleotide.

Sequencing by synthesis: where a complementary strand is sequenced and the individual nucleotides are read off through different fluorescent colors

Question 26

*Does the entire genome of an organism consist only of genes, i.e. encodes proteins?

Answer 26

In humans, only 5% of the DNA of the genome actually encodes proteins. The rest serves either as regulatory sequences that specify the conditions under which a gene will be transcribed, as introns (sequences that are transcribed but not translated), or as spacer DNA of yet unknown function.

Question 27

*What are the requirements and sequential steps of DNA transcription into RNA?

Answer 27

Transcription requires:
DNA template
4 ribonucleotide triphosphates (ATP, GTP, CTP, UTP) building blocks
RNA polymerase (enzyme)

Transcription process has 3 phases:
Initiation, RNA polymerase starts RNA synthesis
Elongation, RNA chain lengthening
Termination, RNA polymerase stops RNA synthesis, dissociates from DNA

Question 28

*What is the chemical difference between DNA and RNA?

Answer 28

DNA and RNA are very similar, except for the absence of the OH group on the carbon atom number 2 in the ribose ring of DNA, and the substitution of thymine by uracil in RNA.

DNA is double-stranded, forming a double helix, while RNA is usually single-stranded. The sugar in DNA is deoxyribose, whereas RNA contains ribose.

Furthermore, DNA uses the bases adenine, THYMINE, cytosine, and guanine
while RNA uses adenine, URACIL, cytosine, and guanine.

Question 29

*What are the different roles of DNA and RNA in an organism?

Answer 29

DNA: Long term information storage
RNA: short term messaging to make sure a given protein is produced at a given point in time.

Question 30

What different types of RNA are there?

Answer 30

mRNA = messenger RNA, tRNA = transfer RNA, rRNA= ribosomal RNA, snRNA = small nuclear RNA

Question 31

What happens in translation? What is the ribosome?

Answer 31

Ribosomes: large RNA-protein complexes convert mRNA to proteins
The genetic code (determined by tRNA’s and aminoacyl-tRNA synthetases)

Question 32

*How many different amino acids are used to make proteins? How are they encoded by nucleotides in RNA?

Answer 32

The RNA alphabet is of 4 letters A, C, G, U referring to the four nucleotides in RNA.
They are in a sequence coding for specific amino acids.
In the ribosome this sequence is read. Start by the start codon in the sequence AUG. Every CODON consists of 3 RNA letters. These can be placed in 64 different combinations. All 61 referring to a specific amino acid the 3 remaining are stop CODONS.

Question 33

Start og stop codon

Answer 33

START: AUG
STOP: UAA, UAG, UGA

Question 34

Number og possible codons for each amino acid

Answer 34

Leucine: 6 codons
Cysteine: 2 codons
Serine: 6
Valine: 4
Stop codons: 3

Question 35

You need to be able to compare the combinatorial diversity of DNA/RNA and protein sequences of different lengths

Answer 35

Combinatorial diversity: total number of unique combinations possible within a given system.

DNA sequence of length 10 the diversity would be 4^10
RNA sequence of length 15 the diversity would be 4?15.

Question 36

*What is kinetic proof reading and why does it exist?

Answer 36

In cells, kinetic proofreading helps to reduce errors in processes like DNA replication and protein synthesis, ensuring that the final product—whether it’s a new DNA strand or a protein—is as accurate as possible.

enhance the accuracy of molecular processes such as DNA replication, transcription, and translation

Question 37

*What is an (open) reading frame? You need to be able to determine/estimate how many reading frames there are in a given piece of dsDNA or in a piece of DNA of given length (see exercises).

Answer 37

ORF: A stretch of DNA or RNA that potentially encodes a protein. It starts with a start codon and ends with a stop codon with a length that is a multiple of three nucleotides.

Question 38

*Why does gene expression need to be regulated?

Answer 38

Gene regulation is how a cell controls which genes, out of the many genes in its genome, are “turned on” (expressed). Thanks to gene regulation, each cell type in your body has a different set of active genes – despite the fact that almost all the cells of your body contain the exact same DNA. These different patterns of gene expression cause your various cell types to have different sets of proteins, making each cell type uniquely specialized to do its job.
For example, one of the jobs of the liver is to remove toxic substances like alcohol from the bloodstream. To do this, liver cells express genes encoding subunits (pieces) of an enzyme called alcohol dehydrogenase. This enzyme breaks alcohol down into a non-toxic molecule. The neurons in a person’s brain don’t remove toxins from the body, so they keep these genes unexpressed, or “turned off.” Similarly, the cells of the liver don’t send signals using neurotransmitters, so they keep neurotransmitter genes turned off

Question 39

*What is an operon? How does the lac operon work (schematically)?

Answer 39

An operon controls the expression of genes. The lac operon allow bacteria to use lactose as an energy source.

For bacteria to use lactose as energy source the bacteria must express the lac operon genes which encodes key enzymes for lactose uptake and metabolism.

When: Lactose is available and glucose is not available.

Question 40

What are epigenetic modifications?

Answer 40

Epigenetics: refers to changes in gene expression controlled by factors other than changes in DNA sequence.

covalent modifications of DNA bases (cytosine) by methylation and covalent modifications (acetylations, methylations) of histone proteins.

Question 41

What are advantages and disadvantages of DNA as a data storage medium?

Answer 41

It is slow to read and write, but very energy efficient, stable and represents a universal modality.

Question 42

What is CRISPR-Cas and what is it used for?

Answer 42

Scientists uses this technique to remove or replace genes. Inspired from bacteria that uses CRISPR as a tool to protect them from viruses hijacking them. Like a immunsystem. Very precise technique to take out some bad genes.

Question 43

DNA sequencing methods:

Answer 43

1. Chain termination methods
   2) Sequencing by synthesis
   3) Nanopore sequencing