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2.1.3 Nucleotides and Nucleic Acids (DNA Replication (Evidence (Meselson…
2.1.3 Nucleotides and Nucleic Acids
Nucleotides
molecule consisting of a five carbon sugar, a phosphate group, and a nitrogenous base
monomer from which nucleic acids (DNA and RNA) are made
become phosphorylated when they contain more than one phosphate group
ADP (adenosine diphosphate) structure
ATP (adenosine triphosphate) structure
phosphate bonds are high energy bonds, as they release a lot of energy when broken; the more phosphate bonds a molecule has, the more energy it can release
regulate metabolic pathways e.g. by ATP, ADP and AMP
component of coenzymes
NADP in photosynthesis
NAD in respiration
FAD and coenzyme A in respiration
polynucleotides: phosphodiester bond between sugar residue (hydroxyl group) and phosphate group; broken when polynucleotides break down, and are formed when polynucleotides are synthesised
polynucleotide: large molecule containing many nucleotides
DNA
Structure:
polymer made up of repeating nucleotide monomera
one molecule of DNA consists of two polynucleotide strands
strands are antiparallel as they run in opposite directions; joined by hydrogen bonds
nucleotide consist of a phosphate group, deoxyribose (pentose sugar), and one of Adenine,
Thymine
, Cytosine, Guanine (nitrogenous bases)
double
helix for stability; twisting of double strands around imaginary axis
Purines
Adenine, Guanine
Two nitrogenous containing rings (bigger)
Pyrimidines
Thymine, Cytosine
One nitrogenous containing ring (smaller)
Hydrogen Bonds
antiparallel strands are joined via hydrogen bonds
Adenine and Thymine form two hydrogen bonds
Guanine and Cytosine form three hydrogen bonds
Purine and pyrimidine always bind, so rungs of DNA "ladder" are the same length (as purines are longer than pyrmiadines)
allow molecule to unzip for transcription and replication
Antiparallel Strands
one strand is in the 5' to 3' end (leading strand), and the other strand is in the 3' to 5' end (lagging strand)
5' end is where phosphate group is attached to 5th carbon
3' end is where the phosphate group is attached to 3rd carbon
Eukaryotes
majority of genome is in the nucleus
large molecule of DNA is wrapped tightly around histone proteins into chromosomes; each chromosome is one molecule of DNA
loop of DNA without histone proteins in mitochondria and chloroplasts
Prokaryotes
DNA is in a loop free floating in the cytoplasm; no nucleus
not wound around histone proteins; naked DNA
store information to code for proteins
Synthesis and Breakdown of Polynucleotides
synthesised in condensation reactions, when a phosphodiester bond is formed and two water molecules are lost
broken down in hydrolysis reactions, when a phosphodiester bond is broken, and two water molecules are broken down
RNA
Structure:
nucleotide consist of a phosphate group,
ribose
(pentose sugar), and one of Adenine,
Uracil
, Cytosine, Guanine (nitrogenous bases)
single
stranded
shorter chain
mRNA (messenger), tRNA (transfer), rRNA (ribosomal)
3 types:
mRNA
messenger RNA
least stable
straight, single helix
tRNA
transfer RNA
not very stable but more than mRNA
folded, clover shape
carry specific amino acids
rRNA
ribosomal RNA
found in ribosomes
fold into 3D shape to form scaffold on which ribosomal proteins assemble
used for protein synthesis; does not store information
DNA Replication
semi-conservative replication: how DNA replicates, resulting in two new molecules, each of which contains one old strand and one new strand; one strand is conserved in each molecule
DNA is self replicating; replicated before cell division, in interphase so daughter cells have the right amount of DNA; each chromosome is copied in eukaryotes
DNA molecule unwinds; double helix is untwisted, catalysed by gyrase enzyme
DNA molecule unzips; hydrogen bonds between nitrogenous bases are broken; catalysed by DNA helicase enzyme; results in two single strands of DNA with exposed bases
Free phosphorylated nucleotides present in the nucleoplasm bind to exposed bases via complementary base pairing; catalysed by DNA polymerase enzyme; bind in 5' to 3' direction
Leading strand is synthesised continuously, and lagging strand is synthesised in short fragments (Okazaki fragments); short fragments are later joined by ligase enzymes
Activated nucleotides are hydrolysed to release extra phosphate groups and supply energy to make phosphodiester bonds between sugar of one nucleotide and phosphate group of next nucleotide
Evidence
Meselson and Stahl, 1958
Mutations: random and spontaneous; can be good or bad or silent; wrong nucleotide inserted, and genetic code is changed; point mutation
Genetic Code
Triplet: DNA code is read in groups of three; three bases code for an amino acid
Non-overlapping: read from the start codon in triplets; if a base is added or deleted, it caused a frame shift, as every codon is altered, therefore every amino acid is also altered
Degenerate: more than one base triplet for each amino acid, except methionine and tryptophan; reduce effect of point mutations as different base sequence may still code for same amino acid
Universal: present in almost all living organisms; same three bases code for same amino acids
gene determines sequence of amino acids in polypeptide (primary structure of protein); if primary structure of a protein is correct, it will have the right folding and shape as a secondary, tertiary and quaternary protein; e.g. in an enzyme active site, in antibodies, in receptors on cells
Transcription
process of making mRNA from a DNA template
Gene unwinds and unzips; hydrogen bonds between complementary nucleotide bases break
Temporary hydrogen bonds form between RNA nucleotides and complementary unpaired DNA bases; catalysed by RNA polymerase enzyme; happens only on one strand (template strand)
mRNA produced is a complementary to the template strand, and a copy of the other strand (coding strand)
mRNA passes out of the nu0cleus via a nuclear pore and attaches to a ribosome
Translation
formation of a protein at the ribosomes by assembling amino acids into a particular sequence according to coded instructions carried from DNA to ribosome by mRNA; ATP is needed for protein synthesis
tRNA molecules bring amino acids and find place on anticodon to bind via temporary hydrogen binding to to complementary codon on mRNA
Ribosomes move along the length of the mRNA code and read it; when two amino acids are adjacent to each other, they are joined as peptide bonds form between them
After polypeptide is assembled, mRNA is broken down and component molecules can be recycled into new lengths of mRNA with different codon sequences
Chaperone proteins in the cell help fold polypeptide into correct tertiary structure to carry out its specific function
Sammer Sheikh