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STRUCTURE OF NUCLEIC ACID (RNA) & PROTEIN SYNTHESIS (RNA STRUCTURE…
STRUCTURE OF NUCLEIC ACID (RNA) & PROTEIN SYNTHESIS
CENTRAL DOGMA
unidirectional
flow of
genetic information
from
DNA through RNA
to
polypeptide
involving genes (specific sequence of nucleotides in DNA that codes for RNA molecule or polypeptide)
Gene in DNA is replicated
occurs in nucleus
Ref. DNA replication
Gene undergoes transcription:
genetic information is passed on from DNA to mRNA via transcription
where bases in the DNA template are copied onto a complementary sequence of bases in mRNA
identifying what to be transcripted (TRANSCRIPTION UNIT) : gene to be transcribed is preceded by promotor (promotor likes upstream) and followed by terminator sequence
promotor: information regulates transcription
non-coding
terminator: information end transcription
only one DNA strand serves as template for transcription
template/antisense/non-coding strand
non template strand: coding/nontemplate/sense strand
region undergoing transcription: transcription bubble
occurs in nucleus
mRNA undergoes translation
genetic information is passed on from mRNA to polypeptide via translation
occurs in cytoplasm
requires energy (ref. cell structure - high amount of mitochondria likely found in that area)
PREPARATION
INITIATION
ELONGATION
TERMINATION
trigger: ribosome reaches stop codon on mRNA (UAG, UAA, UGA)
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Aminoacyl-tRNA binding
Peptide bond formation
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initator tRNA already bonded to start codon at P site
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prokaryotes
mRNA binding site (small subunit) binds to Shine-Dalgarno sequence on 5' end of mRNA
Start codon AUG (codes for methionine) is positioned on P site
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shine-dalgarno sequence lies upstream of start codon
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eukaryotes
initator tRNA carrying methionine binds to small subunit
mRNA binding site on small subunit binds to finders sequence on 5' end of mRNA
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on P site
amino acid activation
Attachment of amino acid to tRNA
catalysed by aminoacyl-tRNA synthetase
requires energy (from hydrolysis of ATP)
20 possible amino acids
20 tRNA (at least)
20 aminoacyl-tRNA synthetase (at least) - (ref. enzyme specificity)
process: each amino acid binds (covalent) to tRNA amino acid binding site (ref. structure of RNA)
carboxyl group of amino acid binds at 3' end: can form a peptide bond (free NH3 group) with carboxyl end of growing chain (ref. amino acid structure)
forming aminoacyl-tRNA
how (FYI): tRNA 3' end (ribonucleoside monophosphate with A group) bonded to OH group in COOH of amino acid
NH3 group bonded to COOH group of
previous
amino acid in peptide bond
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ester bond between first tRNA and amino acid broken - COOH group used to bond to 2nd amino acid
post-translational events
polypeptides folded into 3D conformation
helped by chaperone proteins
polypeptides from ribosomes on RER
enter cisternae by channel proteins (due to signal peptide) and folded (ref. cell structure)
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polypeptides from free ribosomes (spontaneously fold during synthesis)
remain in cytoplasm or transported into organelles for cellular functions
GENETIC CODE
3 nucleotide bases (codon) are read in mRNA (translation)
one codon codes for one amino acid
function
degenerate and no ambiguity
codon allows 4 ribonucleotide bases to specify 20 amino acids (due to their order)
more than one codon codes for same amino acid (degenerate)
codons coding for one amino acid only codes for that amino acid
universal (for same amino acid in all organisms)
non-overlapping
mRNA is read sequentially - all genetic information is translated into amino acid
many ribosomes translate an mRNA simultaneously
forms polyribosome/ polysome (add pic of electron microgrpah)
function: translate many copies of polypeptide quickly
prokaryotes: transcription and translation are almost simultaneous
(because mRNA doesn't need to move to cytoplasm - no membrane bound organelles (nuclear envelope) - so ribosomes immediately translate the still-growing mRNA
INITIATION (process)
ELONGATION
TERMINATION
RNA polymerase reaches terminator sequence
newly formed mRNA is released
DNA rewinds
RNA polymerase dissociates from DNA
prokaryotes
after transcription of terminator sequence
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eukaryotes
RNA polymerase transcribes terminator sequence
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(EUKARYOTES) PROCESSING OF mRNA TRANSCRIPT
pre-mRNA (newly formed transcript) undergoes post-transcriptional modification to form mature mRNA
happens in nucleus
MODIFICATIONS
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only eukaryotes
prokaryotes don't have introns (non-coding regions)
eukaryotes contain exons (expressed sequences) and introns (intervening sequences) only exons expressed
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RNA polymerase moves along the template strand from 3' to 5'
by
complementary base pairing
free ribonucleoside triphosphates complementary to DNA nucleotides are matched up to DNA template
ribonucleoside triphosphate are joined by phosphodiester bonds catalysed by RNA polymerase
forming mRNA that elongates in a 5' to 3' direction
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hydrolysis of 2 phosphate groups in incoming ribonucleoside triphosphate (forming ribonucleoside monophosphate) provides energy for formation of phosphodiester bonds
occurs by RNA polymerase
recognises template by promotor
unwinds double helix in front of it to expose nucleotides
catalyses the formation of phosphodiester bonds between neighbouring RNA nucleotides to form mRNA
EUKARYOTES
general transcription factors
bind to
TATA box
on promotor
general transcription factors recruits RNA polymerase (for correct positioning)
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why TATA box? only 2 hydrogen bonds (easier to break)
general transcription factors occur in all cells --> needed to form transcription initiation complex for transcription of all actively expressed genes
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PROKARYOTES
sigma factor (part of bacterial RNA polymerase) recognises promotor (Pribnow box)
RNA polymerase bind to DNA at promotor
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Eukaryotes
mRNA
RNA polymerase II
for transcription
tRNA
RNA polymerase III
rRNA
RNA polymerase I
Prokaryotes
one RNA polymerase to transcribe all RNA
ref. pg 10 (differences between RNA polymerase and DNA)
preserve genetic information for future generations
RNA STRUCTURE
polymer of ribonucleotides (ribose sugar) joined by phosphodiester bonds
single-stranded
looped regions due to intramolecular complementary base pairing (eg: transfer RNA)
ribose sugar - phosphate backbone
nitrogenous bases:
purines:
adenine
guanine
pyrimidines
uracil
cytosine
TYPES
messenger RNA (mRNA)
FUNCTION: carries genetic information from DNA in nucleus to ribosomes in cytoplasm
specific genetic sequences (shorter than DNA)
less stable than DNA (short-lived) as they are degraded once they have been translated
structured in codons (set of 3 nucleotides) that codes for specific amino acids
in euk, transcribed by RNA polymerase II
transfer RNA (tRNA)
folds upon itself through complementary base pairing to form a 'clover leaf shape'
3' end has an amino acid binding site
FUNCTION: bring amino acids to mRNA for protein synthesis
structured in anti-codons (3 nucleotides complementary to codon on mRNA)
allows for specificity in amino acids
20 different tRNA (variation)
in euk, transcribed by RNA polymerase III
ribosomal RNA (rRNA)
transcribed from rRNA genes in nucleolus region of nucleus (ref. cell structure)
forms ribosomes subunits by complexing with ribosomal proteins
subunits transported out of nucleus to cytoplasm to be assembled into functional ribosomes (where subunits bind together - triggered by binding of mrNA) during translation
in euk, transcribed by RNA polymerase I
part of ribosome (RIBOSOME STRUCTURE)
RIBOSOME STRUCTURE
small subunit
mRNA binding site
large subunit
3 tRNA binding sites
peptidyl tRNA site (P site)
holds tRNA carrying growing polypeptide
aminoacyl-tRNA site (A site)
holds tRNA carrying next amino acid to be added
exit site (E site)
ref: DNA vs RNA structure (pg 6)
COMPLEMENTARY BASE PAIRING
where complementary bases on nucleotides (A-T/U, C-G) are bonded together (ref. DNA replication)
AT 2 hydrogen bonds, CG 3 hydrogen bonds
transcription
ensures accurate replication of genetic information
process: mRNA is formed as free ribonucleotides bond to DNA via complementary base pairing
translation
DNA replication (ref. DNA replication)
parental DNA strands are templates for identical copies of daughter DNA
MUTATION
GENE MUTATION
identified by a change in gene's nucleotide base sequence
results in mutated mRNA
codes for different amino acid --> abnormal protein
results in physical changes
types
insertions or deletions
causes frame shift mutation
alters reading frame of mRNA
since number of nucleotides read is no longer multiples of 3
eg: AUG AAA CGC, A is deleted
becomes AUG AAC GC
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causes primary structure of protein (type number sequence of amino acid) to change
producing non-functional proteins
substitution
when one nucleotide is substituted for another
big effects
when base causes new codon to be a stop codon (terminates transcription early)
codes for a different amino acid
insignificant change
codes for a different amino acid with similar properties (folding - tertiary structure unchanged)
no change
substitution transforms original codon into a codon coding for the same amino acid (due to degeneracy)
CHROMOSOMAL MUTATION
change in number of chromosomes
defects in chromosome separation in cell division
mitosis
only daughter cells of parental cell with abnormal chromosome number is aneuploidy
aneuploidy in somatic (non-reproductive cells)
meiosis I
gametes have polyploidy (one has extra homologous chromosome one has one less homologous chromosome)
after further division in meiosis II
all gametes have aneuploidy --> all cells have abnormal chromosome number and whole organism is aneuploidy
forming aneuploidy
extra or missing chromosome (+!/-1)
forming polyploidy
more than 2 sets of homologous chromosomes due to non-disjunction of all chromosomes (in meiosis I)
results in
Down syndrome (trisomy 21) - 47 chromosomes instead of 46 in zygotes
Turner syndrome (45 chromosomes instead of 46)
change in structure of chromosomes (gene loci)
during prophase I of meiosis (intertwining of homologous chromosomes in crossing over)
translocation
part of chromosome detaches and rejoins at a different point on either homologous chromosome (gene loci changes)
forms fusion gene coding for a chimeric protein (persistently active - cell divides uncontrollably
introduces new enchancer - increases rate of expression of gene
duplication
part of chromosome replicates (repeated genes)
repetition of genetic material
inversion
2 breaks in a chromosome, part of chromosome inverts and reinserts back into chromosome (flipped around)
affects gene expression if it happens on a coding region --> results in expression of genes that aren't normally expressed
deletion
loss of portion of chromosome
loss of genes
GENETIC VARIATION
through gene reshuffling
meiosis
crossing over
independent assortment
random mating
random fusion of gametes
through mutation
gene mutation
change in DNA nucleotide sequence
forms new alleles
chromosomal aberration
duplication
creates redundancy
since it doesn't need to perform the basic functions the original gene needs to, it can be used to evolve into new genes or functions
random mutations to duplicated gene occurs (gene mutation)
causes it to be non-functional
causes new structure and function
GENETIC DISEASES
DOWN SYNDROME
due to chromosomal aberration (duplication)
failure of separation of homologous chromosome 21 during anaphase I of meiosis
forming an aneuploidy (abnormal gamete with an extra chromosome 21)
ie non-disjunction in anaphase I of meiosis I
effects
mental retardation
characteristic facial features
heart defects - below average lifespan
sexually undeveloped and sterile
SICKLE CELL ANEMIA
due to gene mutation (substitution)
valine coded for instead of glutamic acid
Haemoglobin S instead of haemoglobin A produced (ref. proteins)
valine is hydrophobic while glutamic acid is hydrophilic
HbS less soluble than HbA
homozygous recessive
effect
deoxygenated HbS precipitates out of solution to form rigid fibres
causes sickle cell shape in red blood cells
which is less efficient in carrying oxygen compared to HbA
which are more fragile and haemolyse readily
which may accumulate in blood vessels and prevent blood circulation - depriving organs of oxygen