WEEK 3 Flashcards
genome
the entirety of an organisms hereditary information. Usually DNA, but an exception is some viruses only have RNA
Human genome
22, 000 genes and 3 billion base pairs per genome, two genomes (maternal and paternal) each with 23 chromosomes. So around 6 billion base pairs all together.
bacteriophages
viruses that infect bacteria (genome is only 48 000 base pairs)
How many base pairs in E. Coli genome?
4.6 million base pairs
How many base pairs in mitochondrial DNA?
16 000 base pairs
Why is mitochondrial DNA so small?
Some has gone into nuclear DNA also potentially evolution (use it or lose it, the host cell does many things for mitochondria so it needs less functional DNA)
Genome size has nothing to do with…
size or complexity! Salamanders have 90 000 million base pairs, clearly we are more complex than salamanders.
The number of protein encoding genes…
does not reflect complexity or size of organism either
How much of our genome encodes for protein?
1.5%
How much of our DNA is unique and how much of it is repetitive?
50-50
What composes repeated sequences of DNA?
TRANSPOSONS and REPEATS
. LINEs - long interspersed nuclear elements (more than 500 bp)
. SINEs - short interspersed nuclear elements (less than 500 bp and often highly conserved)
. Retroviral like elements
. DNA only Transposon Fossils
. simple sequence repeats - like GAG repeated hundreds of times
. segmental duplications - thousands of bp (or more) that are repeated
What is unique DNA composed of?
. non-repetitive DNA that is neither in introns nor codons - includes promotoers and non-protein encoding genes
. Introns - regions that are spliced out of RNA
. Protein-coding regions - genes that are transcribed and have some protein coding regions
How long is the DNA in each human cell?
2 metres unpackaged
Karyotype
artificial array of paired chromosomes in a numerical order-diagnostic aid OR you could do chromosome painting hybridization
FISH
Fluorescence in situ hybridization
Detects presence of a specific sequence. A probe binds to a target sequence and you see fluorescence.
Chromatin is…?
Dynamic. It can be condensed, decondensed, and moved around.
What is each chromosome made of?
Each chromosome contains a single, long, linear DNA molecule and associated proteins—called chromatin.
Sister chromatids
Two double strands of DNA tied together into one chromosome. Splitting them will create separate chromosomes.
Levels of organization of chromatin
- DNA double helix
- Nucleosome core particle
- Nucleosome filament
- 30 nm fibre
- Looped domains
- Metaphase chromosome
How much is DNA compressed in prokaryotes?
DNA is condensed through twisting and folding about 1000 X and is complexed with proteins.
Which enzyme is responsible for the supercoiling of DNA?
topoisomerase
total length of DNA in human body
2 x 10^10 km
Nucleosome
nucleosome core particle + H1 + linker DNA
How many times does DNA wrap around core particle?
1.8 times, approx. 146 bp
How long is linker DNA?
Around 80 bp
When is DNA decondensed?
When genes are being expressed. There is not enough room in the nucleus for everything to be unpacked so only the parts that need to be transcribed are unraveled.
Histones
Small, positively charged proteins (attract negative phosphates on DNA) that are rich in lysine and arginine.
H1
like a paperclip; clips DNA onto nucleosome core particle. Necessary for a stable interaction.
Four core histone proteins
H2A, H2B, H3, and H4
What is an octamer core
8 protein complex that is found at the centre of the nucleosome core particle. Two of each of the four core histone proteins (H2A, H2B, H3, H4)
DNA molecule that has been packaged into a mitotic chromosome is ….. than its extended length
10 000 times shorter
Cohesion rings
involved in making loops of chromatin which are anchored to the nuclear matrix/scaffold.
Packing and unpacking DNA requires…
ATP
Heterochromatin
highly condensed (30 nm fibre or even more condensed) chromatin. Usually found at the periphery of the nucleus.
- meiotic and mitotic chromosomes
- centromeres and telomeres
- Barr body
Barr body
An inactivated X chromosome. One of the X chromosomes in each cell in human females is entirely composed of heterochromatin (half of the cells one is activated in the other half the other is activated).
Heterochromatic regions of interphase chromosomes are areas where…
gene expression is suppressed
Euchromatin
relatively uncondensed chromatin, regions where genes tend to be expressed
Transcription Factories
Regions of the nucleus where you have a lot of substrates and lots of enzymes for transcription.
DNA replication is…
semi-conservative. Each new daughter cell has one parental strand and one newly synthesized strand.
Rules for DNA synthesis
- DNA is antiparallel
- New DNA is synthesized from 5’ to 3’
- The template is read 3’ to 5’
Where does DNA replication start?
Areas rich in As and Ts which are only held together by two hydrogen bonds (less energy to pull apart). Always starts in the same location on DNA, place that is recognized by specific proteins.
Origin of replication
Where DNA replication starts. Single origin in bacterial DNA but multiple in eukaryotic
DNA synthesis is catalyzed by…
DNA polymerase
dNTPs
deoxynucleoside triphosphates; what DNA is synthesized from.
NTPs
ribonuceloside triphosphates; what RNA is synthesized from.
Nucleotides are linked by…
phosphodiester bonds
Type of DNA growth in many linear viruses
Unidirectional growth of single strands from TWO starting points (no lagging strands)
Type of DNA growth in some plasmids
Unidirectional growth of single strands from ONE starting point (one leading, one lagging strand). Has a replication fork. Leading strand and replication fork go in same direction.
Type of DNA synthesis in eukaryotes and some bacteria
Bidirectional growth from one starting point. One origin, two replication forks (two leading and two lagging strands).
Leading strand is replicated…. while lagging strand is replicated…
continuously
discontinuously
INGREDIENTS FOR DNA SYNTHESIS
- Origin of replication
- Primers
- NTPs
- ATP
- DNA polymerase
- Accessory proteins
