Nucleic Acid L2 Flashcards
DNA = deoxyribonucleic acid
EXPLAIN
- polymer of deoxyribonucleotides,
- nt = nucleotide
WHAT JOINS THE SUGARS AND PHOSPHATES IN DNA?
PHOSPHODIESTER bonds join sugars & phosphates
5’ TO 3’
Explain the DNA PRIMARY STRUCTURE
- Sugars’ carbons are designated 1’,2’,3’,4’,5’
- BASE joins to the 1’ carbon
- PHOSPHATE to the 5’ carbon
- NEXT nt to the 3’ carbon
So DNA has a 5’ and 3’ terminus
(like proteins have ‘ends’) - In DNA, ribose lacks O at 2’ carbon, hence DEOXY!
What does phosphate groups?
Note phosphate groups
“bridge” 3’OH of one nt
to 5‘C of next nt =
phosphodiester bond
Explain why is DNA is an ACID?
Phosphate groups
ionised (pKa low),
- so carry negative
charge at physiological pH
Is the “backbone” of DNA hydrophobic or hydrophilic?
- Covalent “backbone”
of DNA is hydrophilic. - Consists of alternating
sugar-phosphates.
Writing Conventions: NA sequences
- Bases symbolised by first letter, A,C,G,T, U in RNA
- Phosphate groups are symbolised P which circled
- ALWAYS write NA in 5’ to 3’ direction
Sequence of <50 nt = ?
- Sequence of <50 nt = oligonucleotide (oligo)
- Longer = polynucleotide
- Even longer = nucleic acid
What is the structure of DNA?
PRIMARY VS SECONDARY STRUCTURE?
- Like protein structure, it is useful to describe NA
structure in terms of hierarchical levels of complexity:
- PRIMARY STRUCTURE = sequence of nts from 5’ to 3’
e.g., ATCGTTTACAT, etc. - SECONDARY STRUCTURE of DNA involves TWO STRANDS running ANTIPARALLEL, DEVELOPMENT OF MOFEL EXPLAINS:
- Chemistry
- Physical measurements
- DNA’s ability to carry genetic information
Chemistry (& Chargaff) OF DNA = 6
- HYDROPHOBIC BASES , & HYDROPHILIC CHARGED
BACKBONE OF PHOSPHATES AND SUGARS - All DNA contains SAME AMOUNT OF PHOSPHATE,
PENTOSE SUGAR, BUT DIFFERENT AMOUNTS OF BASES. - ALL DNA, regardless of species, shows that:
SUM OF PURINES = SUM OF PYRIMIDINES , A+G = T+C and amount of A = amount of T, & C = G … - Exact base composition varies with species
- Base composition of DNA from different cells in a specimen is identical
- Base composition does not change with age,
nutritional status, environment,
Physical Measurements
- X-ray measurements show regular structure:
Helix with complete turn every 3.4nm, diameter ± 2nm.
Density measurements: Helix must have TWO chains.
DNA as a Carrier of Genetic Information
TRANSFORMATION
DNA as a Carrier of Genetic Information:
What caused the change from a nonlethal R strain to the lethal S strain?
- DNA from the ruptured S strain cells was transferred to the R strain.
- This process is TRANSFORMATION, uptake of DNA from outside the bacteria, that integrates into the bacterial cell’s chromosome.
Bonds in the Double Helix:
- Watson & Crick proposed 2 POLYNUCLEOTIDE CHAINS COULD ASSOCIATE BY HYDROGEN BONDING BETWEEN BASE PAIRS.
- Hydrogen bonds:
HYDROGEN atom
shared between TWO
OTHER ATOMS, BOTH
ELECTRONEGATIVE
(such as O & N)
Understanding Hydrogen Bonds in DNA….
- Hydrogen bonds are STRONGEST WHEN THE THREE ATOMS ARE IN A STRAIGHT LINE …..
- The bases in DNA hydrogen bond to form specific pairs known as COMPLEMENTARY BASE PAIRS:
A with T and C with G
Explain Hydrogen bonds form between
complementary bases
A=T and G=C
A purine with a pyrimidine
A large base with a small
Are Other Pairings Possible?
- Two fully extended chains could form H-bonded base
paired complex - essentially a STEP LADDER STRUCTURE
2.BUT this is ENERGETICALLY UNFAVOURABLE - hydrophobic planes of bases prefer to be in closer contact with
each other rather than with water
Double bonds of bases make pyrimidines & purines EXPLAIN
(nearly flat) planar …
In water, hydrophobic groups cluster together …
“hydrophobic interactions”
Such hydrophobic interactions
(stacking), as well as van der Waals forces & dipole-dipole interactions stabilise 3-D structure of nucleic acids.
This minimises contact with water
Remember, H bonds between complementary
base pairs also stabilise the DNA double helix.
Remember, H bonds between complementary
base pairs also stabilise the DNA double helix.
Explain The DNA structure:
Protein Interact where?
Bases project?
2 strands held together by?
Orientations of the 2 strands are…?
Strands are …?
- The sugar -phosphate
backbone is on the
outside (proteins interact). - The bases project into the inside of the double helix.
- The two strands are held
together by many
hydrogen bonds &
hydrophobic interactions
between bases. - The orientations of the
two strands are
antiparallel: 5’
-3’ directions are opposite. - Strands are
complementary:
C=G, A=T
Helix is held together mainly by two sets of forces:
- H-bonding between base pairs &
- hydrophobic
“stacking” interactions of bases.
explain the Structure of the HELIX? = 4
- Specificity that maintains base sequence is contributed entirely by H BONDING BETWEEN COMPLEMENTARY BASE PAIRS.
- BASE STACKING increases DNA STABILITY.
- ‘10 bases’ make a COMPLETE TURN in the Watson-Crick
model. - A ‘RIGHT’ -handed helix with a MAJOR AND MINOR groove.
What are the Grooves of the Helix?
- The helix
has a WIDE & a NARROW groove - Grooves ALLOW IONS & PROTEINS to INTERACT WITH DNA.
What about the Helix?
- An EXTENDED STEP LADDER can be CONVERTED to A HELIX by A SIMPLE TWIST.
- Bases are STACKED NEATLY ON TOP OF ONE ANOTHER IN THE DOUBLE HELIX, GIVING A CONSISTENT DIAMETER TO THE HELIX… CELL CAN DETECT CHANGES.
DNA in the Cell
- B FORM OF DNA MOST STABLE UNDER PHYSIOLOGICAL CONDITIONS.
——-Two other variants have been
identified in the lab, A & Z forms:
- A FORM is favoured in solutions devoid (almost) of water, so not our cells.
- Z FORM is a “ZIGZAG”, there is evidence short tracts of DNA can take on this shape in cells.
DNA is flexible EXPLAIN….
DNA has several configurations.
There is rotation around the sugar-base bond, the C1’ – N glycosidic bond.
Model of DNA as a Double Helix….
The specificity of base pairing permits duplication of genetic information - DNA replication.
Base pairs are always purine with a pyrimidine, so large with small, maintaining the helix
diameter… useful for
monitoring DNA integrity,
which is vital.
DNA can also base pair
with RNA: C-G & A-U,
antiparallel!
