Nucleotides And Nucleic Acids Flashcards
What is transformation?
A transfer of genetic material from one organism to another
E.g. Griffit bacteria mouse experiment
What is a bacteriophage?
A virus that infects bacteria
These virus’s transfer genetic material into host, which then replicate the virus
What is transcription?
DNA is copied into RNA
What is translation
Nucleic acid information is used to synthesize proteins
What do nucleotides play a role in?
Building blocks of nucleic acids (DNA/RNA)
Energy currency (ATP/GTP)
Mediator in signaling (GDP/GTP)
Structural component of many enzyme con factors and metabolic intermediates (NAD+. FADH2, UDP-glucose)
Nucleotides consist of:
A nitrogenous base (a purine or pyrimidine)
A pentode sugar (ribose or deoxyribose)
1 to 3 phosphates
How do you distinguish a Nucleoside from a nucleotide?
They lack phosphates
What are the pyrimidines?
Cytosine
Thymine
Uracil
What are the Purines?
Adenine and Guanine
How do you know a structure is a purine?
How do you know which is guanine?
Two rings
It has a carbonyl and a amino group while the adenine has an amino group where the carbonyl is at
How do you distinguish the pyrimidines?
One ring
Cytosine: has an amino group
Thymine: has a methyl group
How do you name the nucleotides?
- Start with the nucleoside name
- If it’s a deoxyribose, use the deoxy prefix
- Invite the number of phosphates as 5’ mono-, di- or tri- phosphates
How are nucleotides joined together?
A 3’-5’ phosphodiester bond
What are the two distinct ends of a nucleic acid?
3’ hydroxyl
5’ phosphate
In which direction are nucleic acids written?
In the 5’ to 3’ direction
What happens to RNA and DNA in basic solutions?
RNA is degraded to individual nucleotides
-2’ or 3’ monophosphates
DNA is stable since it lacks the 2’ OH
What methylated base do eukaryotes use?
Only methylcytosine
What do bacteria use to methylate base?
5-methycytosine
N6-metyhadeosine
When are bases methylated?
Only C’s followed by G’s can be methylated
Only A’s in the sequence GATC can be methylated
When can a cytosine be methylated?
When it is followed by a G
-60-90% of CpG’s are methylated
When can Adenosines be methylated?
When in the sequence GATC
What produces methylated bases?
Methylase
Bacteria: DAM (deoxyadenosine methylase)
Eukaryote: DNMT (DNA methytransferase )
Recognition site are palindromic!
What does palindromic mean?
Sequence is the same forwards no backwards
Why does methylation occur bacteria?
Controlling initiation of replication
Discrimination of self DNA (methylated) from foreign DNA (non-methylated)
Discriminate old and new strands in mismatch repair
Regulation of gene expression
-All DNA based
Why do eukaryotes methylate?
Regulation of chromatin structure and gene expression
What kind of gene expression does methylation allow?
Gene silencing
An epigenetic mechanism
E.g. Imprinting and X-chromosome inactivation
In what order is the DNA double helix stranded?
2 antiparallel strands
- one 5’-3’
The other 3’-5’
What complementary bases pair in a DNA helix?
G pairs with C
A pairs with T
- Through hydrogen bonds (the number of bonds differs)
- A purine way pairs with a pyrimidine
In DNA what side is oriented outward and what side is oriented inward?
Hydrophilic sugar-phosphate backbone is oriented outward
Hydrophobic bases stacked in the interior
How many bonds do the A-T and G-C complementary bases have?
AT:2
GC: 3
About how much stronger is a GC bond than an AT bond?
50% stronger
What is base stacking?
Interactions between stacked bases above and below through:
Van der walls
Hydrophobic
What does base stacking contribute to?
Major contribution to helical stability
What bases have the strongest and weakest base stacking?
Stacked GC bases are strongest
Stacked AT bases are weakest
What are Chargaff’s Rules?
A always = T
C always = G
Pyrimidines nucleotides (T+C) always = total amount of purine nucleotides (A+G)
(A+G)=(C+T)
More AT than GC
What is G-quadrupled DNA?
Guanine tetrads: 4 G's in a plane connected by hydrogen bonding Stabilized by a cation (k+) Stacks of 2 or more guanine tetrads Found physiologically in G-rich region E.g. Telomeres
Where can you find G-quadruplex DNA?
Telomeres
What kind of DNA is found physiologically?
B-form DNA
Which side contains the minor grove?
The side with the glycosidic bond
Where do DNA binding proteins bind?
Bind in the grooves making specific interactions with these atom
-usually the major groove
What do the bases in DNA provide for binding proteins?
H-bond donors (N-H0
Acceptors (N,O)
Methyl groups for hydrophobic interactions
How can you tell if DNA is plindromic DNA?
Reads the same 5’ to 3’ on complimentary strands
What’s an example of palindromic DNA?t
GACGTC
Why are DNA palindromes important?
They are recognition sequences for restriction endonucleases and some transcription factors
What is the difference between DNA palindromes in restriction endonucleases and transcription factors?
Restriction: palindrome not interrupted
Transcription: palindrome is often interrupted by a few bases
What is the recognition sequence for EcoRI (restriction endonuclease)
5’ GAATTC 3’
What is the recognition sequence for transcription factors such as Glucocotiocoid receptor binding site?
5’AGAACAnnnTGTTCT3’
The nnn is the interruption
What are inverted repeats?
When single-stranded may form a hairpin or a stem-loop structure
What are mirror repeats in DNA?
Repeats that are not repeats in the 5’ to 3’ direction
Why are mirror repeats important?
For the formation of triple stranded DNA
-aka Hoogsteen or H-DNA
What repeats facilitates in the H-DNA formation?
Repeat of a poly-purine:polypyrimidine tract
With what strand does the third strand interact with?
Major groove via base-specific hydrogen bonds
What are Direct repeats and inverted repeats are often involved in?
Structural chromosomal abnormalities
What are direct repeats DNA inverted repeats?
Direct repeats = deletion and duplications
Inverted repeats= inversions
Trinucleotide repeat expansions such are hungtintons Disease are associated with what kind of elemental symmetry?
Direct repeats
How re direct repeats and inverted repeats formed?
Unequal crossing-over in meiosis
How can we denature DNA?
(Def: bases are broken down)
Heat, high ph
AKA: melting
What tool can we use to follow denturation and renaturation of DNA?
UV spectrometry
What light does ssDNA absorb?
260 nm
How does the melting temperature of DNA increase?
With a higher content of GC
Does denaturation cause an increase in absorbance?
Yes
What is DNA hybridization?
Annealing of single-strand of DNA to a complementary strand of different DNA molecule
What is demination?
Loss of an exocyclic amino group
What is usually deaminated? How often does this occur?
Cytosine into uracil
1 every 10Mb per 24h
What enhance deamination?
Nitrous acid (HNO2)
What is depurination?
Los of the base from a nucleotide (usually a purine)
What does depurination lead to?
An apurinic site (AP site )
What are mutagens?
Physical, chemical, or biological agents that increase the rate of mutations
-may be carcinogens or teratogens
What are alkylating agents? What do they cause?
They add alkyl groups (methyl or ethyl) to bases
Cause mispairing
E.g. O6-methylguanine pairs with T instead of C
What are the addition of bulky group do to DNA?
Reword this q….
Benzo(a)Pyrenees’s
Found in col tar, tobacco smoke, charred food
Oxidized in cels and binds covalently to guanine, distorting the double helix
What are intercalating agents?
Flat, planar molecules that slide between the stacked bases of the double helix
What do intercalating agents do?
Distort double helix and increases separation of bases
- cause insertions and deletions during DNA replication
- frameshift mutations
What are some examples of radiation-induced DNA damage
X rays
UV
What do X-rays do to DNA?
Generate free radicals that cause DNA double-stranded breaks
What does UV generate?
Pyrimidine diners (thymidine diners)
-covalent bonds between adjacent pyrimidines in the same strand
What is the main example for oxidative damage?
Reactive oxygen species (ROS)
-Hydrogen peroxide (H2O2), Hydroxyl radicals (OH*), and superoxide radicals (O2-)
How are ROS generated?
Irradiation and from oxidative phosphorylation in the mitochondria
What are the main differences between RNA and DNA?
- Ribose
- Uracil instead of Thymine
- Single-stranded
- Intramolecular base-pairing
- Unstable
- Unusual bases may occur (tRNA)
What does intramolecular base pairing create in RNA?
Partially double-stranded structures
Either Watson-crick or Hoogsteen base-pairing
Wha is Inosine?
A deaminated adenosine
IS inosine a purine or pyrimidine?
Purine
What will inverted repeats form in RN?
A hairpin or stem-loop
How are complex RNA structures generated?
H-bonds and base stacking
