Molecular biology 2 - nucleic acids Flashcards
Function of nucleic acids
protein synthesis and transmit genetic information
Which part of the nucleic acid is charged and has a direction (polarity)?
The phosphodiester backbone
Standard direction of nucleic acid strand
5’ to 3’
Structure of DNA
2 complementary strands joined by complementary base pairing which form a double helix around a central axis
Function of nucleases
enzymes that cleave/digest nucleic acid
Name of enzymes that digest DNA
deoxyribonucleases
Name of enzymes that hydrolyse RNA
ribonucleases
What are endonucleases?
enzymes that are able to cleave internal phosphodiester bonds
What are exonucleases?
Enzymes able to hydrolyse a nucleotide phosphodiester bond only when it is present at the terminal of the nucleic acid
Name of the classes of endonucleases that recognise specific sequences in DNA
restriction endonucleases (recognition site 4-6 bp long)
Outline of protein synthesis
- In the nucleus, DNA unzips by H bonds splitting to expose the base pairs on the template strand.
- Transcription - DNA polymerase copies base sequence in template strand to produce mRNA.
- Translation - mRNA is translated by tRNA, using ribosomes as a functional support.
What does DNA provide a template for?
DNA replication and transcription
Why do the number of base pairs / length of DNA increase for more complex organisms?
More complex organisms require more proteins.
Which bonds are broken during DNA denaturation?
Hydrogen bonds (no covalent bonds are broken)
How can the DNA double helix be denatured?
Using extremes of temperature and pH
What is the reversal of DNA denaturation?
Annealing (renaturation) - the 2 strands spontaneously rewind
How can annealing occur?
When the temperature/pH is returned to the normal range, the H bonds reform via complementary base pairing
Definition for the melting point of DNA
The temperature at which half the DNA is denatured (separated into single strands)
How does the composition of base pairs affect DNA melting point?
The higher its content of G=-C base pairs, the higher the melting point.
At the site of DNA where strand separation is initiated for DNA replication / transcription, which base pairs are most abundant?
A=T base pairs (only 2 H bonds so easier to break)
Order of abundance for 3 types of RNA
rRNA (80%), tRNA (15%), mRNA (5%)
Function of mRNA
Transfers information of the amino acid sequence of a polypeptide from DNA to ribosomes for translation.
Which strand of DNA is mRNA complementary to?
Template strand
Which strand of DNA is mRNA identical to (except T->U)?
Coding strand
Name of base triplets in mRNA that code for an amino acid
codon
Structure of tRNA
Hairpin structure with an amino acid arm and an anticodon arm (complementary to mRNA codon)
Function of tRNA
Carries each amino acid to the ribosome (one specific tRNA for each amino acid)
Sequence of translation
- mRNA binds to ribosome
- tRNA with a complementary anticodon to the mRNA codon aligns with mRNA by complementary base pairing
- Each type of tRNA carries a specific amino acid
- amino acids are covalently joined (peptide bond) by the ribosome to form a polypeptide.
Structure of ribosomes
small and large subunits made of proteins and rRNA
Genome definition
whole genetic information within a single cell nucleus
How many possible tRNA molecules / base triplets exist?
64 (4^3)
Key features of the genetic code
degenerate, unambiguous (one codon will code for only one amino acid), nonoverlapping, not punctuated (no skipping)
What is meant by the genetic code being degenerate?
More than one codon can code for the same amino acid (as there are 64 codons but only 20 amino acids)
Which base differs between degenerate codons?
3rd base position (wobble position)
What is the wobble hypothesis?
A different base can be present in the 3rd base position but not the1st/2nd position
What is the first amino acid in polypeptides?
Methionine (AUG is start codon)
What signals the end of translation?
When a termination codon (UAA, UAG, UGA) is reached in mRNA.
Name of tRNA molecule once an amino acid has bound
aminoacyl-tRNA
Which ribosome subunit does the mRNA and tRNA bind to?
The small subunit. Then the large subunit will bind.
What is a mutation?
Permanent alternation in a DNA (gene) sequence
Causes of mutations
- spontaneous, low frequency errors in DNA synthesis
- chemical mutagens
- ionising radiation
Name of mutation in which one base is switched for another
substitution
Types of substitution mutations
conservative mutation, non-conservative mutation, no mutation
what is a conservative mutation?
A type of substitution when one amino acid is replaced by one with similar properties
What is a non-conservative mutation?
A type of substitution in which an amino acid is replaced by one with different properties
How can a substitution be a silent mutation?
If the substitution occurs in the 3rd position of the codon this might not change the amino acid (degenerate, wobble hypothesis)
How can a mutation change the length of the polypeptide?
A stop codon may be introduced or removed. A premature termination truncates the chain whereas a delayed termination elongates the polypeptide.
Effect of insertion/deletion mutations
causes a frameshift which synthesises a protein with a different amino acid sequence downstream of the mutation. A stop codon may also be prematurely introduced or removed.
Cause of sickle cell anaemia
single amino acid substitution (Glu -> Val) at position 6 in each beta chain of Hb due to a single base substitution.
What type of substitution mutation causes sickle cell anaemia?
Non-conservative mutation because the amino acids have different properties (R group of valine is neutral whereas glutamate has a negative charge)
How does the non-conservative substitution of Glu to Val in sickle cell anaemia alter Hb?
Hb has 2 fewer negative charges (substitution occurs in each beta chain) which produces a hydrophobic patch on Hb surface, causing the molecules to aggregate into bundles of fibres.
Effects of sickle cell anaemia
Hb content of blood is about half the normal value because sickled cells are fragile and easily rupture (results in anaemia). Abnormal shape of sickled cells blocks capillaries causing pain and interfering with organ function.
Symptoms of sickle cell anaemia
weak, dizzy, increased pulse, shortness of breath
