Molecular biology Flashcards
Explain the 5’ - 3’ / 3’ - 5’ directionality concept.
Directionality is the orientation of a single nucleic acid NA strand.
In a strand, one end contains a PO4 on the 5th C of a pentose, and the other end contains an OH on the 3rd C of the pentose.
Palindrome
dsDNA with the same sequence on both complementary strands
Does the base pairing have to be perfect for primer-dimer formation?
No
are nucleic acids in solution linear?
NA are usually base-paired in solution. Either intra- or inter-molecularly.
What is the difference between DNA and RNA pentoses?
Why is DNA called “deoxyribonucleic”?
DNA contains an H on the 2nd C of the pentose
RNA contains an OH (hydroxil).
The 2’ group in DNA is deoxygenised (i.e. deoxyribonucleic acid).
Wha it is the structural base of all nucleic acids?
What is a nuceloside?
What is a nucelotide?
NTP (nucleoside triphosphate), i.e. 3 phophates and a nuceloside.
A nuceloside is a pentose + nitrogenous base.
A nucelotide is a pentose + nirogenous base + one phosphate group.
Briefly explain RNA alkaline hydrolisis.
Phosphodiester bonds are broken by OH-
Three requiemens for DNA synthesis?
1) base-pairing at the 3’ end
2) 3’ must have an OH
3) ssDNA template downstream of this site
What is an oligonucleotide?
A short NA sequence (note: a primer is an oligonucelotide)
Briefly explain DNA acid hydrolisis.
1) excess H+ attacks N7 of A-G
2) O- in breaks phosphodiester bond
What does DNA and RNA stand for?
deoxyribonucleic acid and ribonucleic acid, respectively
Chargaff’s rule
- DNA should have a 1:1 stoichiometric ratio of purine and pyrimidine bases
- the amount of G should be equal to C and the amount of A should be equal to T
Polarity of nucelcic acids
Nucelic acids are hydrophobic, thus, they are more likely to bind with each other than with water. Consequently, in solution they bind together.
B form of DNA: definition
Double-stranded, right-handed with antiparallel strands.
The most biologically important form of DNA.
B form DNA: structural description
- *1)** Contains major and minor grooves.
- *2)** distance between adjacent bases is 0.34 nm.
- *3)** 1.9 nm in diameter.
- *4) 10** bases per complete turn.
Major grooves in DNA: definition and biochemical importance
Definition: Portions in which backbone is widely separated.
Biochemical importance: They allow protein binding
Major grooves in DNA: definition and biochemical importance
Definition: Portions in which backbone is widely separated.
Biochemical importance: They allow protein binding
Chargaff’s rule
- DNA should have a 1:1 stoichiometric ratio of purine and pyrimidine bases
- the amount of G should be equal to C and the amount of A should be equal to T
Protein - DNA interactions: mechanism
- exocyclical groups (i.e. gorups outside the pentose) recognized by protein
- sequence-specific
Double helix: bonding
Covalent:
1) Phosphodiester bonds: betwee pentoses; forms sugar-phosphate backbone
2) Glycosidic bonds: between bases and pentoses
Non-covalent:
3) Hydrogen bonds: between paired bases
4) Base-stacking: between adjacent bases
5) Shell of hydration: between phosphodiester backbone and water; stabilizes double helix and increases solubility
Differnces between A RNA and B DNA
RNA (A-form):
1) major groove is narrow and deep.
2) more compact than DNA B form
3) 11 bases per complete turn.
4) U instead of T
5) Can occasionally have G-U pairs
Pseudoknots
Pseudoknots are secondary structures in RNA characterized by having at least two stem loops
RNA secondary stuctures
RNA almost always forms secondary sructures, making it structurally similar to proteins
RNA has to unfold for translation
Pseudoknots
Pseudoknots are secondary structures in RNA characterized by having at least two stem loops
Chaperones and RNA
Chaperones are proteins that alter RNA structure and they are very important for RNa functionality
B form DNA: structural description
- *1)** Contains major and minor grooves.
- *2)** distance between adjacent bases is 0.34 nm.
- *3)** 1.9 nm in diameter.
- *4) 10** bases per complete turn.
Types of nucleic acid duplexes and order in strength
RNA:RNA > RNA:DNA > DNA:DNA
DNA:RNA duplexes: function
Transcription and DNA replication
RNA:RNA duplexes: function
RNA:RNA duplexes regulate gene expression
miRNA (micro RNA): function and mechanism
1) silences gene expression
2) miRNA binds to a RNA gene
RNA editing: definition and three types
1) post-transcriptional alteration of RNA sequences
2) insertion, deletion, substiution
Antiparalellism
Two strands parallel to each other but runing in opposite directions
tmRNA: name, function/mechanism
1) transfer-messenger RNA.
2) translates into an amino acid sequence that targets an improper protein or mRNA for degradation
Chaperones and RNA
Chaperones are proteins that alter RNA structure and they are very important for RNa functionality