Nucleic acids Flashcards
DNA
single molecule of DNA is a polymer consisting of a backbone & side groups arranged in a variable sequence
the polymer is synthesized from monomers of nuclotides
DNA nucleotides
made up of deoxyribose sugar, a phosphate ( backbone)
and a purine or pyrimidine base
purines : adenine & guanine
pyrimidines : cytosine & thymine
full name of 4 nuclotides in DNA & the 2 important aspects of them
- Deoxyadenosine triphosphate (dATP)
- Deoxyguanosine triphosphate (dGTP)
- Deoxycytidine triphosphate (dCTP)
- Deoxythymidine triphosphate (dTTP)
triohosphate = 3 phosphate groups
- when phosphodiester bonds forms between 2 nucleotides along the backbone 2 phosphate groups leave ( we can test these groups)
- hydroxyl group is required for phosphate of the following nucleotide to bind
phosphodiester bonds & hydrogen bonds
nucleotides are joined by phosphdiester bonds that link the 5’ phosphate group of one to the 3’ hydroxyl group of the next
hydrogen bonds attach the base pairs of complimentary strands
- 2 hydrogen bonds attach adenine to thymine
- 3 hydrogen bonds attach cytosine to guanine
requirements for complimentary strands
when the base pairing of A & T as well as G & C line up
and the two strands run opposite to each other with a free hydroxyl group at each end
why does DNA twist
the bases are hydrophobic ( 10 Bases per turn)
the sugar- phosphate back bone is hydrophilic
- back bone form noncovalent bonds with surrounding water molecules
Calculating percentage of nuclotides
number of purine bases= number of pyrimidine bases
- A+G = T=C
due to base pairing
%A = %T
%G= %C
ex. if % of thymine is 20% what are the others
A= T so A= 20%
thats 40% so 60% is left over
60/2 = 30% each
G= 30%
C=30%
RNA
ribose sugar
uracil instead of thymine
exists mostly as a single- stranded polymer that is much shorter than DNA
- mRNA is usually straight but other RNA can have different folded structures
folding of RNA
RNA conformations are NOT random structures, and the folding mechanism of RNA molecules is complex
• The secondary structure adopted by an RNA molecule is related to its nucleotide sequence
• RNA molecules fold sequentially from 5’ to 3’ to form stable sub-motifs dictated by their primary sequence
ex. hairpin loop which is a precursor to miRNAs
RNA may adopt further tertiary folding
RNA has potential to fold into a number of different conformations, but usually only 1 is functional
the folding process is influenced by
- Ions
- Cofactors
- Proteins
Once an RNA molecule adopts a conformation that is favoured by its immediate cellular environment, it rarely switches
RNA will further interact with other RNA or protein molecules to form complex quaternary structures such as ribonucleoproteins which are essential to certain cellular processess
mRNA
messenger RNA is the only type of coding RNA
initial connection between the info stored in DNA & production of a protein responsible for the phenotype
if a lot of protein is needed there will be lots of mRNA
mRNA is typically linear
consists of codons
long vs short nucleic acids
> 200 = long
< 200 = short
tRNA
transfer RNA
non-coding
translation of info from nucleic acids to protein requires reading mRNA by ribosomes, using adaptor molecules - tRNA
relatively short, single stranded
there is at least one tRNA for each amino acid
rRNA
Ribosomal RNA
makes up ribosomes
non coding
important structural & functional part of the ribosomes - cellular organelles where proteins are synthesized
Majority of RNA is rRNA
non coding RNA
we use to think that the main transcription of DNA was to form proteins
but exon for coding proteins only occupies 1-2% of base pairs in the genome
- we thought the rest of the genome was “junk”
recently we discovered that
- almost the entire genome is transcribed
- trasncription takes place in both directions ( sense & antisense)
- the same genomic region can serve as a template for many non-overlapping or overlapping transcription units
- most transcription units do NOT result in a protein product
short non coding RNA
- rRNA - ribosomal RNA
- tRNA – transfer RNA
- miRNA – micro RNA
- siRNA – small interfering RNA
- piRNA – piwi-interacting RNA
- PASR - Promotor-associated RNA
- tiRNA – Transcription initiation RNA
long noncoding RNA
- These long chain RNAs could be 5’capped, 3’ polyadenylated and spliced like mRNAs
- Reported functions vary and include:
- Modulation of chromatin architecture
- Regulation of gene expression
- Precursors to some short chain ncRNAs
miRNA
micro RNA
small
regulate translation
each strand has an imperfect complimentary strand miRNA*
mature miRNA detaches from it partner & is incorporated into the RNA induced silencing complex ( RISC)
RISC is responsible for the gene silencing process known as RNA interference
miRNA pairs with the 3’ untranslated region of mRNA leading to
either:
• Repression of protein translation
• mRNA degradation
miRNAs modulate gene expression and are involved in many biological processes including development and cell differentiation They have been shown to regulate: • Cell proliferation • Apoptosis • Maturation
• Aberrant expression of miRNA’s has been reported for many diseases involving the cardiovascular, neurologic, musculoskeletal,
endocrinologic and immunologic systems. They have also been implicated in carcinogenesis.
• The presence of miRNAs in plasma and serum make them attractive candidate biomarkers for disease and monitoring
siRNA
Small Interfering RNA
Produced by Dicer cleavage of perfectly complementary double-stranded RNA molecules
Form complexes with Argonaute proteins and are involved in:
• Gene regulation
• Transposon control
• Viral defense
piRNA
piwi-interacting RNA
• piRNAs are derived from successive Argonaute cleavage of long ncRNAs
• Function in the germline to regulate transposition activity and chromatin state
PASR and tiRNA
• Transcribed from promotors and transcription start sites and may be
involved in regulating gene expression
Argonaute Proteins
Proteins of the RNA-induced silencing complex (RISC)
RISC
The complex responsible for the gene silencing process known as RNA interference
Circulating Nucleic Acids
- Nucleic acids can be confined within cellular boundaries but can also be found present in the blood circulation
- Cell-free DNA and RNA molecules exist in plasma of healthy humans
DNA, RNA, miRNA and methylated DNA sequences have been found:
• Derived from tumors in cancer patients
• Derived from a fetus in pregnant women
• Derived from transplant donors in transplant recipients
• Derived from traumatized tissues in patients suffering from acute pathologies
can be healthy or can tell about something that is wrong
