W1 Flashcards
Bacteriophages
Viruses that infect bacteria, used in the Hershey-Chase experiment to demonstrate DNA is the genetic material by labeling DNA with radioactive phosphorus.
Chargaff’s Rules
DNA has equal amounts of adenine and thymine, and equal amounts of cytosine and guanine, suggesting complementary base pairing.
DNA Structure
Watson and Crick proposed a double helix model with two antiparallel strands held by hydrogen bonds between base pairs (A-T, G-C).
Base Pairing Rules
Adenine pairs with Thymine (2 hydrogen bonds), Guanine pairs with Cytosine (3 hydrogen bonds), ensuring a uniform helical structure.
DNA Polymerase
Enzyme responsible for synthesizing new DNA strands by adding nucleotides in the 5’ to 3’ direction, requiring an RNA primer to start replication.
Leading vs. Lagging Strand
Leading strand is synthesized continuously, while the lagging strand is synthesized in short Okazaki fragments that are later joined by DNA ligase.
Replication Fork
Y-shaped region where DNA unwinds for replication, with helicase breaking hydrogen bonds and topoisomerase preventing supercoiling.
Telomeres & Telomerase
Telomeres are repetitive sequences at chromosome ends that protect DNA; telomerase extends them in germ cells to prevent degradation.
Nucleosome
The basic unit of chromatin, consisting of DNA wrapped around histone proteins, allowing for DNA packaging inside the nucleus.
Heterochromatin vs. Euchromatin
Heterochromatin is tightly packed and transcriptionally inactive, while euchromatin is loosely packed and active in gene expression.
Transcription
Synthesis of RNA from a DNA template by RNA polymerase, producing a complementary mRNA strand.
RNA Processing
Eukaryotic mRNA undergoes splicing (removing introns), 5’ capping, and 3’ polyadenylation before translation.
Translation
Conversion of mRNA codons into an amino acid sequence at the ribosome, facilitated by tRNA and rRNA.
Codon and Anticodon
Codons are three-nucleotide sequences in mRNA specifying amino acids, while anticodons on tRNA pair with them to ensure correct protein synthesis.
tRNA Function
Transfers specific amino acids to the ribosome during translation, ensuring correct protein synthesis based on mRNA codons.
Genetic Code Redundancy
The genetic code is degenerate, meaning multiple codons can specify the same amino acid, reducing the effect of mutations.
Post-Translational Modification
Chemical modifications like phosphorylation, glycosylation, and proteolytic cleavage alter protein function after translation.
Whole-Genome Shotgun Sequencing
A rapid sequencing technique that randomly fragments DNA, sequences the pieces, and assembles them computationally.
Bioinformatics
The application of computational tools to analyze biological data, including genome sequencing and functional annotation.
Gene Annotation
the plotting of genes onto genome assemblies, and indexing their genomic coordinates
Proteomics
the study of proteins
what they do and sht
Genome Size and Gene Density
Larger eukaryotic genomes have lower gene density and contain more noncoding DNA, including introns and regulatory elements.
Multigene Families
Groups of closely related genes arising from duplication, which can evolve new functions (e.g., hemoglobin gene family).
similar genes in different species coming from common ancestor
Transposable Elements
Mobile DNA sequences (like LINEs and SINEs) that can relocate within the genome, influencing gene regulation and evolution.
Genome Evolution
Driven by mutations, gene duplications, chromosomal rearrangements, and transposable elements, leading to genetic diversity.
Comparative Genomics
Compares genome sequences across species to understand evolutionary relationships and gene conservation.
PCR (Polymerase Chain Reaction)
A method to amplify DNA sequences using heat cycles, primers, DNA polymerase (Taq), and nucleotides.
Mendelian Cross Tables
Used to predict inheritance patterns using dominant and recessive alleles, often represented in Punnett squares.
Template vs. Coding Strand
The template strand of DNA is used for mRNA synthesis, while the coding strand has the same sequence as the mRNA (except T/U).
Mutation Effects on Pathways
Mutations can disrupt enzymes in metabolic pathways, leading to genetic disorders like PKU or albinism.
what is the difference between southern blot and western blot
southern blot is for DNA
western blot is for Proteins
How is the DNA transferred from gel to blot
by using a wick and having the liquid bring the DNA upwards.
How is a specific sequence labeled on a southern blot?
you break the DNA strands apart and let a probe bind to it, which is radioactive as a marker.
How do you make the bands visible after adding the marker?
you add an Xray film that will change color when it gets irradiated.
what is RFLP
Restiction fragment length polymorphism
its the analysis of southernblotting. different genes will have different lengths on the blot or might not even be able to bind to the probe if a restiction site is on the dna sequence where the probe would bind to.
needs restriction sites to be different between types
what is Allele Specific PCR
using primers to find dna sequences
specific wild type and mutant primers on top of primers that bind to both
what is HRM (high resolution melting)
using the difference in denaturation temperature to figure out if the sequence has more or less bonds. if an at bond changes to CG the denaturation temperature goes up, if it changes to AG there wont be any bonds. denaturation temperature is determined by adding fluorescense which turns off when the DNA is denatured.
sanger sequencing
random nucleotides die zorgen dat verlengen stopt
illumina sequencing
add 1 fluorescent nucleotide at a time and look at it
but millions of different pieces of dna at the same time
Nanopore long read sequencing
door een eiwit met een gat een lang stuk dna halen en verschillen in electrische verstoringen het dna sequencen
Multiplex Ligation-dependent Probe Amplification
2 probes om dezelfde streng, ligase plakt ze aan elkaar en je bekijkt de lengte met capilaire electrophorese
paracentrische inversie vs pericentrische inversie
paracentrische inversie: deel van het chromosoom draait om binnen 1 van de 2 armen
pericentrische inversie: deel van het chromosoom draait om binnen beide armen
wat is monosomie
een “paar” van 1 chromosoom
wat is trisomie
een “paar” van 3 chromosomen
translocatie
crossing over but to the wrong chromosome
non-disjunctie
wanneer de chromosomen gesplits worden en er een chromosoom niet gesplitst wordt
zorgt voor 3:1 inplaats van 2:2
onafhankelijke overerving
genen op verschillende chromosomen
linkage equilibrium
wanneer 2 allelen ver weg zitten van elkaar op hetzelfde chromosoom spelen ze alsof ze op andere chromosomen zitten omdat de kans op crossing over zo hoog is
linkage disequilibrium
wanneer 2 allelen dicht bij elkaar zitten op hetzelfde chromosoom worden ze vaak samen overgebracht met crossing over
wat is Karyotypering
analysing chromosomes by taking a picture and counting them
fluorescence in situ hybidization
you put fluorescense thing on the dna of a gene to see where it is on the chromosome
comparative genome hybidization
make dna of sample fluorescent, bind it to reference dna, more binding than normal = copy.
less = deletion
https://www.youtube.com/watch?v=bRML0PkH-wE
transformatie
conjugatie
transductie
transformatie - dna van buiten naar binnen brengen
conjugatie - dna delen met pilus
transductie - dna van virus naar bacterie
how to fungi reproduce
the 1n haploid fungus can create spores asexually or through scent, find a mate and grow towards it and when they touch they can mate and create 2n diploid gametes that split into spores
wat is AFLP
AFLP Amplified fragment length polymorphism
pcr op SSR marker
RAPD
RAPD random amplified polymorphic DNA. random primer pcr to amplify unknown genomes
16S analysis
16S analyse
all bacteria and archaea have the 16s gene that creates 16S rRNA. 16S analysis uses a primer that binds to 16S dna and sequences the pcr product.
dPCR
digital pcr, divide the sample into thousands, fluorescent dna, quantification to original dna levels. because sample pieces are tiny they either have or don’t have amplification which is used to calculate the original concentration.
ddPCR
droplet digital pcr, turning the sample into tiny droplets and putting it in oil
physical partitioning
dPCR
letting sample flow into thousands of very tiny wells
real time PCR
measure how much DNA is in your sample while it’s PCRing by having fluorescent probes that have exonuclease and get destroyed and become fluorescent when being destroyed and measuring it after every cycle.
you can measure the original amount of dna but its pretty shit at it compared to dPCR
also can just use sybrgreen and make the nucleotides green
RNAseq
cut rna in pieces, make cDNA, sequence cDNA with next generation sequencing.
you also label each piece with a “barcode” sequence of 14 nucleotides put together with ligase.
poly A tail is needed to make cDNA because the reverse transcriptase primers bind to it if you dont want ribosomal rna (which is most of it)
microarray
lots of wells with each different oglionucleotides on the bottom, cDNA from RNA is paired with fluorescent probe, cy3 and cy5 refer to green and red fluorescence used to differ different DNA, when its run some will light red green or yellow (both) and this can be used to analyse the rna or dna.
when comparing sick and healthy you make the healthy persons dna green and the sick person’s dna red.
if you put known rna probes at the bottom of the wells you can measure the expression thousands of different genes at the same time
QTL
snp, ssr of andere dna merker gebruiken en kijken welk fenotype welke marker ook heeft om uit te vinden waar ongeveer de genen bevinden die zorgen voor het fenotypen. word genomen van F2
quantitative trait locus
GWAS
alleen SNP’s
PCR met ARMS
3 primers. example:
1 forward primer 2 reverse primer where 1 binds to wildtype and 1 binds to a mutation.
one primer is longer than the other changing the product length
Amplification Refractory Mutation System
PCR met KASP
same as arms but uses fluorescense to know which primer
Kompetitive Allele Specific PCR
