Nucleic acids

Question 1

DNA

Answer 1

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

Question 2

DNA nucleotides

Answer 2

made up of deoxyribose sugar, a phosphate ( backbone)
and a purine or pyrimidine base

purines : adenine & guanine
pyrimidines : cytosine & thymine

Question 3

full name of 4 nuclotides in DNA & the 2 important aspects of them

Answer 3

• Deoxyadenosine triphosphate (dATP)
• Deoxyguanosine triphosphate (dGTP)
• Deoxycytidine triphosphate (dCTP)
• Deoxythymidine triphosphate (dTTP)

triohosphate = 3 phosphate groups

1. when phosphodiester bonds forms between 2 nucleotides along the backbone 2 phosphate groups leave ( we can test these groups)
2. hydroxyl group is required for phosphate of the following nucleotide to bind

Question 4

phosphodiester bonds & hydrogen bonds

Answer 4

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

Question 5

requirements for complimentary strands

Answer 5

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

Question 6

why does DNA twist

Answer 6

the bases are hydrophobic ( 10 Bases per turn)
the sugar- phosphate back bone is hydrophilic
- back bone form noncovalent bonds with surrounding water molecules

Question 7

Calculating percentage of nuclotides

Answer 7

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%

Question 8

RNA

Answer 8

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

Question 9

folding of RNA

Answer 9

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

Question 10

mRNA

Answer 10

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

Question 11

long vs short nucleic acids

Answer 11

> 200 = long

< 200 = short

Question 12

tRNA

Answer 12

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

Question 13

rRNA

Answer 13

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

Question 14

non coding RNA

Answer 14

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

Question 15

short non coding RNA

Answer 15

• 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

Question 16

long noncoding RNA

Answer 16

• 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

Question 17

miRNA

Answer 17

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

Question 18

siRNA

Answer 18

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

Question 19

piRNA

Answer 19

piwi-interacting RNA
• piRNAs are derived from successive Argonaute cleavage of long ncRNAs
• Function in the germline to regulate transposition activity and chromatin state

Question 20

PASR and tiRNA

Answer 20

• Transcribed from promotors and transcription start sites and may be
involved in regulating gene expression

Question 21

Argonaute Proteins

Answer 21

Proteins of the RNA-induced
silencing complex (RISC)

Question 22

RISC

Answer 22

The complex responsible for the gene silencing process known as RNA interference

Question 23

Circulating Nucleic Acids

Answer 23

• 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