Flashcards in Nucleotides&NucleicAcids_Molecules Deck (69):
What are nucleotides?
- "Energy rich" compounds
- Sends out chemical signals
- Act as enzyme cofactors
What are nucleic acids?
- Part of DNA and RNA
- Polymers of nucleotides
What are the components of nucleotides?
1) Nitrogenous "base"
2) Sugar (ribose or deoxyribose)
Name the four Nitrogenous "bases"
What are the two kinds of bases?
What are the 2 purine bases?
What are the 2 pyrimidine bases?
Thymine (DNA) or Uracil (in RNA -> No CH3)
What is the ribose made of?
What are the different forms of ribose?
Straight chain (simple)
- Can be rearranged to either.
What is a nucleoside?
Base + Sugar
What happens to the OH in the phosphate usually?
usually ionised and loses H+ to form O-
What does the structural backbone of DNA consist of?
Alternating phosphate and 2-deoxyribose resides that are held together by phosphodiester bonds involving Carbon 3 and Carbon 5 of the sugar
What does Carbon 1 of the ribose in DNA do?
Forms a beta - N- glycosidic bond with one of the four bases.
What does the ends of DNA strand have?
One end: Has a free hydroxyl group at C - 5 of the last 2-deoxyribose.
Other end: has a free hydroxyl group at C-3
By convention, which terminus is where?
The 5' terminus of a DNA (or RNA) strand is written at the left end and the 3' terminus at the right hand
THEREFORE: Tetranucloetide ACTG
5' -> 3'
N terminus -> C terminus
With four different bases how many possibility are there of different trinucleotides?
4^3 = 64
What can nucleotides do?
1) Act as Energy Carriers
2) Act as Enzyme Cofactors
What are examples of nucleotides that act as energy carriers?
ATP (Adenosine Triphosphate)
ADP, AMP (Adenosine Diphosphate, Adenosine Monophosphate)
What is the main energy exchange reactions in cells relating to ATP and ADP?
ATP ADP + PO4
ADP AMP + PO4
What is this process "ATP ADP + PO4
ADP AMP + PO4" called?
What are examples of nucleotides that act as enzyme cofactors?
1) Nicotinamide adenine dinucleotide
2) Nictotinamide adenine dinucleotide phosphate
3) Flavin adenine dinucleotide
4) Flavin mononucleotide (FMN)
What are the two forms of NAD or NADP?
Oxidised: NAD+ and NADP+
Reduced: NADH and NADPH
What is NAD and NADP derived from?
Derived from Niacin
What is FAD and FMN derived from?
Derived from Riboflavin
How are nucleotides linked to form strand of DNA or RNA?
Phosphates linked to 2 sugars. Phosphodiester linkages present => Linking PO4 at 5' end to 3' OH of next molecule
What is a specific quality of DNA or RNA chains?
Have polarity due to the distinct ends (5' and 3' end)
Who provided the 3D structure of DNA?
Crick and Watson in 1950
What is Chagaff's rules?
Different organisms have different amount of DNA but:
no. of [A] = no. of [T]
no. of [G] = no. of [C]
What is unique about Chagaff's rules?
Stays constant for each organism over time, across all tissues
What does X ray diffraction do?
Predict Double helix and the 2 periodicities (3.4 Angstrom and 34 Angstrom)
What is the space occupied by a single nucleotide unit?
3.4 Angstrom units same as each subunit of DNA
Name the base pairing
A - T basepair (2 H bonds)
G - C basepair (3 H bonds)
What are the structure of DNA strand
2 anti-parallel DNA strands
What is 3.4 Angstroms?
Distance between base pairs
What are properties of a double helix?
1) 3.4 Angstrom per basepair
2) 10 basepairs per turn (10 - 11 in aqueous solution)
3) 2 antiparallel strands
What are prominent features of the double helix?
1) Two strands of the double helix have opposite polarity, meaning they run in opp. direction. (antiparallel)
2) The 2-deoxyribose/phosphate backbones of the two strands form two ridges on the surface of the molecule. (phosphate group negative charge)
3) Bases face inward to the helix axis but their edges are exposed
4) In each of the two strands, successive bases lie flat, one on top of the other
5) Bases in opp. strands interact by H bonds
6) Double strand is wounded into a right handed helix
What happens when the bases of the double helix face inward to the helix axis but edges exposed?
Form lining of two grooves (major and minor) that are framed by the ridges of the sugar-phosphate backbone.
Because the N-glycosidic bonds are not exactly opposite each other, the grooves are unequal size.
What are the flat surfaces to the bases?
What do successive bases in a strand form?
Numerous van der Waals interactions
What is the key enzyme that facilitates DNA replication?
What are the two steps of DNA replication?
1) Double helix unwinds to produce two single strands. This requires ATP dependent enzymes to break the H bonds between bases. DNA unwinding creates the replication fork (place where new DNA strand is synthesised)
2) A new complementary strand if synthesised for each of the two old strands.
Why is DNA replication known as semiconservative?
One strand in the daughter molecule is always old (template strand) and the other strand is newly synthesised.
What does DNA polymerase do?
Synthesis new DNA strand stepwise, nucleotide by nucleotide, in the 5' -> 3' direction.
What direction does the enzyme go when while synthesising new strand in the 5' -> 3' direction?
Enzyme moves along template strand in 3' -> 5' direction
What unwinds the DNA strand?
How does the double helix disintegrates?
At high temperature (melting temperature) and enzymes
Which base pair unravels more easily under melting temperature?
A - T rich sections of the DNA unravel more easily than G - C rich regions.
What does heat denaturation do?
Decreases viscosity of DNA solutions because the single strand are more flexible
What temperature does DNA start to denature?
85 degree - 95 degree
What is the difference between RNA and DNA?
RNA usually single stranded
RNA contains ribose and uracil
What is the use of RNA?
Genetic material of RNA virus
Function: e.g. Translation machinery (rRNA and tRNA)
Controlling gene expression (miRNA)
Gene expression (mRNA) - copy of 1 gene for translation by ribosomes
What type of structure does many functional RNA have?
Where do base pairs form in RNA?
form base pair internally
Which type of RNA is translated into protein?
What is a major constituent of ribosome?
Ribosomal RNA (rRNA)
What is tRNA
Small cytoplasmic RNA that bind AA covalently and deliver them to the ribosome for protein synthesis
How is RNA synthesised?
by RNA polymerase which contains a sigma subunit that recognises transcriptional start sites and the core enzyme synthesis RNA.
Human Genomes are usually made of?
What are viruses usually made of?
RNA virus (e.g. HIV)
What is bacteria made of?
1 large circle of DNA - chromosome
What is the size of a bacteria?
500 kb - 6mb plus smaller circular plasmids
(1 gene - 1000 bases)
How many genes are in a bacteria and how far are the gaps between the genes?
500 - 600 genes and the genes are tightly packed. The gap of 20 - 200 bases between genes
Mitochondria has what form of DNA and how large?
Linear chromosome has what form of DNA and how large?
3gb x 2 in total -> huge
25k genes (huge spaces between genes)
What are the genes in linear chromosome interrupted by?
Humans have how many pairs of chromosome?
What is the average length of human chromosome?
1.3 x 10^8 bp
What are the properties of chromatin?
1) Need very tight packing - 5 order of magnitude
2) Wrap DNA around 5 histones (H1, H2A, H2B, H3, H4)