Basic, lecture 1 Flashcards
Genetic locus
Location of the gene at the chromosomes
Central dogma
Information cannot be transferred from protein to protein or protein to nucleic acid but can be transferred between nucleic acids and from nucleic acid to protein
Microarray
Test for upregulated and downregulated genes, by using labelled complementary mRNA. Depending on the colour of the weel it can be seen which gene is up or downregulated. The method is used to quantitative the expression of all genes in the cell.
Blotting
Is used for detection of specific genes. DNA is cleaved and run on a gel to seperate based on size. The DNA is transfered to a membrane/filter, the filter is exposed to radio-labelled DNA/probes, that binds to the gene/fragment of interst.
X-ray is used to visualize the fragment.
Northern blotting uses RNA - Southern uses DNA.
Western uses proteins.
RT-PCR (reverse transcription PCR)
Paring PCR with a reverse transcription step using either random-primer or a PCR-primer to convert RNA templates to cDNA and then use regular PCR. Allows detection of RNAs by PCR.
Conjugation
A process in which two prokaryotic cells come in contact and transfer genetic material. In bacteria, DNA (typically in the form of plasmids) is transferred from a donor to a recipient cell.
Histones
Conserved DNA-binding proteins that form the basic subunit of chromatin in eukaryotes. H2A, H2B, H3, and H4 form an octameric core around which DNA coils to form a nucleosome.
Linker histones are external to the nucleosome.
qPCR
Paring PCR with a reverse transcription step using either random-primer or a PCR-primer to convert RNA templates to cDNA and then use regular PCR. Continuous monitoring of product formation. Uses dNTPs
Complementation test
A test that determines whether two mutations are alleles of the same gene. It is accomplished by crossing two different recessive mutations that have the same phenotype and determining whether the wild-type phenotype can be produced. If so, the mutations are said to complement each other and are probably not mutations in the same gene.
Transposition
The movement of a transposon to a new site in the genome.
Transposon
A DNA sequence able to insert itself (or a copy of itself) at a new location in the genome without having any sequence relationship with the target locus. Can sometimes create or reverse mutations and alter the cell’s genetic identity and genome size.
In vitro complementation
A functional assay used to identify components of a process. The reaction is reconstructed using extracts from a mutant cell. Fractions from wild-type cells are then tested for restoration of activity.
Nucleosome
The basic structural subuint of chromatin, consisting of approximately 200 bp of DNA ad an octamer of histone proteins.
Primer
A short sequence (typically of RNA) that is paired with one strand of DNA and that provides a free 3′–OH end at which a DNA polymerase can start the synthesis of a DNA chain - i.e. used for initiating replication.
Promoter
A region of DNA where RNA polymerase binds to initiate transcription. Controls the rate at which a gene is transcribed. Eukaryotic cells typically have a promoter each, whereas several prokaryotes share a promoter.
Genetic recombination
The exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. Also called “crossing over” - the homologous chromosome pairs will come together and can cross-over to exchange small parts of the chromosomes, giving the progeny cell chromatids that differ from those found in either parent.
Chromatid
Either of the two threadlike strands formed when a chromosome duplicates during the early stages of cell division. The two strands are held together at the centromere and separate into daugther chromosomes during anaphase.
Open reading frame (ORF)
A sequence of DNA consisting of triplets that can be translated into amino acids starting with an initiation codon (usually AUG) and ending with a termination codon (UAA, UAG, UGA).
Nuclease
Opposite polymerases. Enzyme that can break a phosphodiester bond in a nucleotide chain. Endonucleases cleave internal bonds, wheras exonucleases must begin at the end of a DNA chain.
Mitosis
Is a part of the cell cycle when replicated chromosomes are separated into two new nuclei. Cell division gives rise to genetically identical cells in which the number of chromosomes is maintained. S-phase of the interphase
mRNA
At transcription, DNA is transcribed to mRNA which will then move from the nucleus to the cytoplasm where it is translated to protein by ribosomes. Is thus an intermediate that represents one strand of a gene coding for polypeptide.
tRNA
The intermediate in protein synthesis that interprets the genetic code. Each tRNA molecule can be linked to an amino acid. It has an anticodon sequence that is complementary to a triplet codon representing the amino acid. Thus, the tRNA recognises which amino acid to add as the next in a growing polypeptide chain.
Telomere
Repetitive regions at the very ends of chromosomes, act as caps that protect the internal regions of the chromosomes. As DNA at the very end of the chromosome cannot be fully copied in each round of replication, they prevent the loss of genes at the chromosomes.
Topoisomerase
Works at the region ahead of the replication fork to prevent supercoiling.
Okazaki fragment
When replication occurs the lagging strand cannot be separated at once, therefore, is Okazaki fragments made.
The leading strand can be extended from one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments.
DNA polymerase III
Extends the primers, adding on to the 3’ end, to make the bulk of the new DNA
DNA polymerase I.
RNA primers are removed and replaced with DNA by DNA polymerase I.
DNA Ligase
The gaps between DNA fragments are sealed by ligase
Operon
Only found in prokaryotes. A collection of genes with one promoter. A typical operon consists of a promoter, an operator and two or more structural genes.
Shine-Dalgarno sequence
The polypurine sequence AGGAGG centered about 10 bp before the AUG initiation codon on bacterial mRNA. Is a ribosomal binding site - helps to recruit the ribosome to the mRNA and start the protein synthesis.
Phosphatase
Can hydrolyse a terminal ester bond linking a phosphate to a terminal nucleotide in a nucleotide chain - cuts off the phosphate.
Centromere
Specialized DNA sequence of a chromosome that links a pair of sister chromatids. Constricted region of a chromosome that includes the site of attachment (the kinetochore) to the mitotic or meiotic spindle. It consists of unique DNA sequences and proteins not found anywhere else in the chromosome.
Bacteriophage
A bacterial virus
Codon
Combination of 3 nucleotides, codes for an amino acid
Active site
Is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. Consists of residues that form temporary bonds with the substrate (binding site) and residues that catalyse a reaction of that substrate (catalytic site).
cDNA
Complementary DNA, doubled stranded DNA which is synthesized from RNA. Can be used to express eukaryotic genes in prokaryotes.
When researchers want to express a specific protein in a cell that does not normally express that protein (i.e., a heterologous expression), they will transfer the cDNA encoding the protein to the recipient cell.
Cloning
Insertion of an insert to the host cell, which can be replicated.
LacZ
Gene that encodes β-galactosidase which cleaves lactose into glucose and galactose.
Replication fork
During replication, when the helicase is separating the two DNA strands, the DNA-helicase complex is called the replication fork.
Vector
Often a plasmid, DNA (often derived from a plasmid or a bacteriophage genome) that can be used to propagate an incorporated DNA sequence in a host cell; vectors contain selectable markers and replication origins to allow identification and maintenance of the vector in the host.
Plasmid
Circular, extrachromosomal DNA. It is autonomous and can replicate itself.
Insert
A piece of DNA inserted into a larger DNA vector, such as a plasmid, through recombinant DNA techniques.
Transcription factor
Can bind DNA (at the promoter region) to regulate the rate at which specific target genes are transcribed. Transcription factors are also encoded by genes, which can be regulated by other transcription factors, etc. The activities of transcription factors in a cell can therefore be considered an internal representation of the environment. Can act as both activators and repressors to either increase or decrease the transcription rate.
