Stuff Flashcards
Purines?
Adenine, Guanine (Purines have a short name, and long base- 2 rings)
What does 5’- 3’ mean?
The 5’ and 3’ mean “five prime” and “three prime”, which indicate the carbon numbers in the DNA’s sugar backbone. The 5’ carbon has a phosphate group attached to it and the 3’ carbon a hydroxyl group. This asymmetry gives a DNA strand a “direction”. For example, DNA polymerase works in a 5’ -> 3’ direction, that is, it adds nucleotides to the 3’ end of the molecule (the -OH group), thus advancing to that direction.
Major and Minor grooves?
The strand backbones are closer together on one side of the helix than on the other. The major groove occurs where the backbones are far apart, the minor groove occurs where they are close together.
Single strand binding protein?
Single-strand binding protein (SSBP) binds to and stabalizes the single strand to keep DNA unwound.
Primase?
Type of RNA polymerase, catalyses the synthesis of the Primer
Exonuclease?
Removes nucleotides from the end of a strand. Can go in either direction along the DNA.
Ligase
Joins ends of a single DNA strand by making new phosphate bonds
Gyrase
Gyrase (a topoisomerase) relaxes supercoils produced when the molecule is twisted during replication. Also facilitates unwinding at the beginning of replication.
Telomerase
Telomerase:- Uses a short RNA template to add short DNA repeats to the short ends of the linear chromosomes when the last primer is removed using the RNA template.
rRNA
Ribosomal RNA: With ribosomal proteins, makes up the ribosomes, the organelles that translate the mRNA.
snRNA
Small nuclear RNA: With proteins, forms complexes that are used in RNA processing in eukaryotes. (NOT found in prokaryotes.)
GPPP cap?
At the 5’ end, a cap is added consisting of a modified GTP (guanosine triphosphate). This occurs at the beginning of transcription. The 5’ cap is used as a recognition signal for ribosomes to bind to the mRNA.
AA*AA?
At the 3’ end, a poly(A) tail of 150 or more adenine nucleotides is added. The tail plays a role in the stability of the mRNA.
Splicing?
The intron loops out as snRNPs (small nuclear ribonucleoprotein particles, complexes of snRNAs and proteins) bind to form the SPLICESOME
The intron is excised, and the exons are then spliced together.
The resulting mature mRNA may then exit the nucleus and be translated in the cytoplasm.
How is a ribosome made up?
Whole thing:- 80s
P, A site
Small subunit:- 40S (18S rRNA + 30 ribosomal proteins)
Large subunit:- 60S (28S rRNA,5.8S rRNA, 5S rRNA + 50 ribosomal proteins)
tRNA
All tRNA’s have CCA at the 3’ end to which the aa attaches
At the other end of the tRNA is the anticodon which, during translation, reads the matching codon on the mRNA
Adding an aa to tRNA
An enzyme called AMINOACYL-t RNA SYNTHETASE adds the correct amino acid to its tRNA.
This process is called AMINOACYLATION or ‘charging’.
Since there are 20 amino acids, there are 20 aminoacyl- tRNA synthetases.
All tRNAs with the same amino acid are charged by the same enzyme, even though the tRNA sequences, including anticodons, differ
Process of adding aa to tRNA
AA and enzyme join by way of ATP AA loses two phosphate groups and binds to aa as AMP uncharged tRNA binds aa tRNA leaves molecule enzyme returns to original shape
Initiation of translation?
Small ribosomal subunit binds to mRNA at start codon region
Termination of translation?
No anticodon on tRNA matches stop codon
RELEASE FACTOR binds to stop codon
Peptidyl transferase is triggered, causing release of polypeptide from tRNA, tRNA is ejected.
Polysomes
Several ribosomes can translate a mRNA at the same time, forming a polysome.
STOP codons
UAA
UAG
UGA
Degenerate
In most cases more than one codon per aa
ORF
An open reading frame (ORF) is a string of SENSE codons starting with the start codon ATG and flanked at the 3’ end by a stop codon.
Histones: DNA ratio
1:1
Histone facts
Small, highly positively charged, high degree of conservation (little evolution)
The Nucleosome (Level 1 of packaging)
Four core histones (H2A x2) 28Kda, (H2B x 2) 28Kda, (H3 x2) 30Kda, (H4x2) 22Kda
H1- 24Kda
146bp of DNA left handed supercoil
DNA path:- 1.8 superhelical turns
How is the Nucleosome formed?
H3,H4:- heterodimer, tetramer, histone handshake, horseshoe
H2A, H2B form Dimer, above and below H3, H4
H1:- Dyad axis, locks DNA in place
Histones are responsible for maintaining shape and structure of nucleosome
Histone variants:- H2A.Z
Non-cannonical variants of histones-representing one or a few aa different
Histone H2AZ is a variant of histone H2A, and is used to mediate the thermosensory response, and is essential to perceive the ambient temperature. Nucleosome occupancy of H2A.Z decreases with temperature, and in vitro assays show that H2A.Z-containing nucleosomes wrap DNA more tightly than canonical H2A nucleosomes in Arabidopsis.
Level 2: The 10nm fibre
Two nucleosomes bind together
20-30 bp
Beads on a string
6-7
Level 3:- The 30nm Solenoid
6 nucleosomes, 10nm fibre wrapping around it
H1 essential
40
Level 4:- 300nm Solenoid
Looped
Each loop contains 60-100 bp DNA tethered by nonhistone scaffold proteins
680
Level 5:- 700nM fibre
Coiled Coil
10^4
This one looks like a flower
Level 6:- Metaphase chromosome
1400nm
Telomeres
Protect genome (don’t code for anything)
Centromere
Repeating sequences, mediates chromosome cohesion, spindle attachment, Chromosome segregation
Constituative Heterochromatin
Part of Telomeres and Centromeres
Highly repeated sequences
Permenantly heterochromatic
Facultive Heterochromatin
Either H or E
Not consistent
X chromosomes
Regulated and often associated with morphogenesis or diffrentiation
Nonpolar aa
Glycine, Alanine, Proline (also cyclic), Valine, Leucine, Isoleucine
Aromatic
Phenylaline, Tyrosine, Tryptophan
Polar,uncharged
Aspargenine, Glutamine, Serine, Threonine
Sulfer containing
Methlonine, Cystine
Charged
Asparate, Glutamate
Negative
Arginine, Lysine, Histidine
Positive
