2.1.3 - Nucleotides and Nucleic Acids Flashcards
What is a nucleotide made of
Pentose monosaccharide
Phosphate Group PO4 2-
Nitrogenous base
Phosphodiester bonds
Formed in a condensation reaction between nucleotides
Phosphate group at 5’ forms covalent bond with hydroxyl group 3’ (H2O)
Forms a long, strong sugar-phosphate backbone with a base attached to each sugar
Difference between ribose and deoxyribose
Deoxyribose doesn’t have an oxygen atom at 2’
Bases
Adenine
Cytosine
Guanine
Thymine/ uracil
Pyrimidines
Smaller bases
Single carbon ring structures
Thymine/ Cytosine
Purine
Larger bases
Double carbon ring structures
Adenine/ Guanine
How do bases pair up
A purine with a pyramidine
Cytosine pairs with guanine - 3 H bonds
Adenine pairs with thymine (uracil - RNA) - 2 H bonds
Structure of DNA
Hydrogen bonding between complementary bases
Double helix composed of two twisted antiparallel strands (phosphate group 5’ - OH 3’/ OH 3’ - phosphate group 5’)
Each strand is a polynucleotide
Why are polynucleotide chains parallel
Complementary base pairing rule:
When a small pyramidine base binds to a larger purine base a constant distance between the DNA ‘backbones’
There will also always be equal amounts of A, T, C, G
Types of RNA
Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA)
mRNA
Carries the code held in the genes to the ribosomes where the code is used to manufacture proteins
tRNA
Transports amino acids to the ribosomes
rRNA
Makes up the ribosomes along w/ protein complexes
Phosophorylated nucleotides
ADP and ATP
Contain a pentose sugar (ribose)
A nitrogenous base (adenine)
2/ 3 inorganic phosphates
Semi conservative replication
One old strand and one new strand
Process of semi-conservation replication
Helicase causes the DNA to untwist and breaks the hydrogen bonds between bases
Polynucleotides with exposed bases act as new template for new double strands
Free DNA nucleotide bases pair with their complementary bases - H bonds
DNA polymerase catalyses the formation of phosphodiester bonds between the nucleotides and also checks base pairing
Sugar phosphate backbone reforms
Each new molecule then twists to form it’s double helix
Purpose of DNA replication
Genetic info needs to be conserved with accuracy so each cell from cell division has the correct amount of genes
Continuous replication
DNA polymerase binds to the end of a strand
Free DNA nucleotides added without any breaks
This occurs in the leading strand (3’ to 5’)
Discontinuous replication
DNA polymerase cannot bind to the end of a strand (5’- 3’)
Free DNA nucleotides are added in sections (Okazaki fragments)
Sections are later joined by DNA ligase
Mutations
Incorrect sequences may occur in the newly-copied strand
Errors happen randomly and spontaneously
Leads to change in the sequence of bases
Codon
Triplet of bases that code for an amino acid
Genetic code
Triplet code
Genetic code is universal
All organisms use this same code
Degenerate code
64 different codons possible (444) but only 20 amino acids
An amino acid can be coded for by more than one codon
Non-overlapping
DNA base sequence is read from base 1 not base 2 or 3
Nature of genetic code
Triplet code
Non-overlapping
Degenerate
Universal
Synthesis of polypeptide
Transcription
Translation
Transcription
Conversion of the genetic code to a sequence of nucleotides in mRNA
Reading the code and producing a messenger molecule to carry the code out to the cytoplasm
Translation
Converting the code in mRNA to a sequence of amino acids
Gene
A length of DNA that codes for one polypeptide
Start codon
Signals the start of a sequence that codes for a protein
Stop codons
There are 3 codons that do not code for any amino acids and signal the end of a sequence
Process of transcription
DNA strands separate (same process as replication)
Sense strand contains code for protein (5’ to 3’)
Free RNA nucleotides base pair to complementary bases exposed on antisense/ template strand (3’ to 5’) - used to build copy of coding strand
RNA polymerase joins bases to form single-strand RNA (phosphodiester bonds)
mRNA detaches from DNA template and strands reform helix. mRNA leaves through nuclear pores and enters cytoplasm
Process of translation
mRNA enters ribosomal groove and binds to small subunit in ribosomes
tRNA molecule carrying amino acid binds to mRNA start codon and another binds to next mRNA codon with complementary anti codons (max. 2) - these form H bonds
Peptidyl transferase causes a peptide bond to form between amino acids
Ribosome moves along mRNA, releasing first tRNA
Process stops when ribosome reaches end of mRNA with stop codon and detaches
Conservative model
Proposed that that the original DNA served as a complete template so that the resulting DNA was completely new
Dispersive model
Proposed that the two new DNA molecules had part new and part old DNA interspersed throughout them
Transcription unit
Comprises of at least one gene but often more
mRNA vs complementary DNA sequence
They’re the same but T is replaced by U
How many base pairs are there in one full turn of the DNA double helix
10
Why is the double helix structure of DNA important
Keep DNA stable
Enables it to fit much info in a small space
Protects bases in the middle
Role of DNA ligase
Joins sugar-phosphate backbone of DNA
Catalyses formation of phosphodiester bonds
Joins promoter to gene and promoter and gene to plasmids
How is the replication fork formed
When the helicase starts to break H bonds between the bases on the two antiparallel strands
Okazaki fragments
Short single stranded DNA molecule complementary to DNA on lagging strand
Do start codons code for an amino acid
Yes only stop codons do not
DNA polymerase
Reads in the 3’ to 5’ direction and builds in the 5’ to 3’ direction
DNA extraction procedure
Grind sample in pestle and mortar - break cell wall
Add detergent - breaks down csm
Add salt - breaks H bonds between DNA and water
Add protease - breaks down histones
Add ethanol - causes DNA to ppt out of sol to be collected using a glass rod
What types of activity does the cell require energy for
Synthesis e.g protein
Transport
Movement - sliding filament model
What makes ATP a good immediate energy store
The interconversion of ATP and ADP is constantly happening so not much ATP is required
Properties of ATP
Small - moves easily in and out of cells
Water-soluble - energy requiring processes happen in aq
Easily regenerated
Releases energy is small quantities - energy not wasted as heat
Contains bonds between phosphates w/ intermediate energy - large enough to meet needs of cellular reactions
