BIO2 - Information flow in biology Flashcards
What are genotype and phenotype of an organism?
The genotype of an organism is the specific set of alleles within the organism’s genome. The phenotype of an organism is how the genotype is expressed.
i.e. a person receives two genes /alleles that codes for the phenotype eye color. On from their mother, and one from their father. These alleles could code for blue and brown. Since blue is a recessive allele, the expressed phenotype would be brown eye color.
What is the principal direction of information flow in the central dogma of molecular biology?
From DNA to RNA to Protein.
What is the role/significance of the DNA double strand structure?
The double stranded structure of DNA has a few great effects. First and foremost, the double stranded structure, and the base-pairing principle, ensures that DNA can be reassembled correctly upon duplication.
By what mechanism is the DNA compacted such that it fits into the nucleus?
The DNA in our genome is tightly packaged around proteins called histones.
What is the principle of the PCR reaction and what is it used for?
PCR is a mechanism for duplicating specific sequences of DNA. You add a double-stranded piece of DNA to your solution, along with free nucleotides, a primer and a protein called DNA-polymerase.
The solution is then heated until the hydrogen bonds that form between the two strands of the DNA are broken. The primer can then attach itself to the single strands of DNA (assuming that it matches), and DNA-polymerase begins adding nucleotides to the strand of DNA. Hence, after one cycle, we will have doubled the amount of DNA in the solution.
After n of such cycles, we should have 2^n strands in the solution
What are the overall ideas behind DNA sequencing by synthesis and nanopore
DNA sequencing?
Sequencing by synthesis is a way to sequence shorter strands of DNA. A plate is coated with short strands that fit with the end and beginnning of the single stranded DNA that you want to sequence.
This strand can then be amplified by the same principles as DNA duplication. Letting polymerase create a double strand between an end piece and a beginning piece, then cleaving. Resulting in to complimentary strands being bound to either an end piece or a beginning piece. Then the process is repeated, until all pieces are “filled”. Then either the lead og lagging strand is washed away, and sequencing can begin by adding flourescent nucleotides. Once these nucleotides are attached, they omit a small light signal (different from each nucleotide). By analysing this signal, the strands can be sequenced.
Nanopore sequencing is the sequencing of a single DNA strand, by passing it through a membrane channel/protein that reacts to the different nucleotides, by omitting a different electrical current. This current can be measured and used to identify the sequence of the strand.
What is the chemical difference between DNA and RNA?
First of all, the nucleotide Thymin (T) is replaced with Uracil (U) in RNA. Furthermore, the deoxyribose is the sugar in DNA, whereas the sugar in RNA is “just” ribose
What are the different roles of DNA and RNA in an organism?
DNA is used for long-term storage of genetic information, whereas RNA is used for short-term messaging.
What happens in translation? What is the ribosome?
In translation, a mRNA strand is converted to the final protein by the ribosomes. Ribosomes are enzymes that attach to mRNA and create a polypeptide amino-acid strand by reading the nucleotide sequence.
How many different amino acids are used to make proteins? How are they encoded by nucleotides in RNA?
20 amino acids make up the proteins found in the human body. They are encoded in pairs of three by the nucleotides.
What is kinetic proof reading and why does it exist?
Kinetic proofreading is a way of lowering the error rate of adding amino acids. It works by adding an intermediate step where the activation energy of a given amino acid is tested. This makes it less likely for a wrong amino acid to be added to the poly-peptide strand.
Why does gene expression need to be regulated?
The body is a fine-tuned machine, where it is important that proteins are only present in certain amounts. Therefore, gene expression needs to be regulated. Diabetes is an example of gene regulation gone wrong.
What is an operon? How does the lac operon work (schematically)?
An operon is a region within the bacterial genome, where gene expression is controlled. The lac operon works via a suppressor (and a dimer). The operon contains several short segments: a promoter region, an operator region, and the gene sequences that are regulated. When lactose is not present in the bacteria, the suppressor is bound to the operator region, ensuring that the genes are not transcribed. When lactose is present, the suppressor is inactive, and hence the genes can be expressed.
Furthermore, when lactose is present and glucose is not (or present in low concentrations) the bacteria reacts by attaching a dimer to the promoter region, that ensures positive regution (i.e. more of the lactose metabolizing compounds are produed)
What are epigenetic modifications?
Epigenetic modifications are changes in gene expression that is not related to a change in the DNA sequence.
What are advantages and disadvantages of DNA as a data storage medium?
Currently DNA is quite expensive to use as a storage medium, but this will likely change. That does not however mean, that DNA is always to be preferred. DNA is good for long term storage, as is very stable, and represents a universal medium. On the flip side, DNA is quite slow to read, which is why other mediums might be preferred for short term storge.
