DNA structure, RNA structure

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Molecular biology

• Unit 2
• By Pallavi Bohra

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Nucleic acid

• Nucleic acids allow organisms to transfer genetic
  information from one generation to the next. 
• First discovered by Friedrich Miescher from the
  nuclei of the pus cell from discarded surgical
  bandages and called it nuclein.
• There are two types of nucleic acids
  deoxyribonucleic acid, better known as DNA and
  ribonucleic acid, better known as RNA.
• When a cell divides, its DNA is copied and passed
  from one cell generation to the next generation.

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Nucleic acid continue..

• Nucleic acids are composed of nucleotide
  monomers.
• Nucleotides contain three parts.
• A Nitrogenous Base
• A Five-Carbon Sugar
• A Phosphate Group
• DNA consists of the four nitrogenous
  bases adenine (A), guanine (G), cytosine (C),
  and thymine (T).

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Nucleic acid continue.

• DNA and RNA each consists of four different
  nucleotides.
• All nucleotides have a common structure
  a phosphate group linked by a phosphoester bond
  to a pentose (a five-carbon sugar molecule) that
  in turn is linked to an organic base.
• In RNA, the pentose is ribose in DNA, it
  is deoxyribose.
• The bases adenine, guanine, and cytosine are
  found in both DNA and RNA thymine is found only
  in DNA, and uracil is found only in RNA.

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Nucleosides and nucleotides
Base Ribonucleoside Deoxyribonucleoside
Adenine Adenosine (A) deoxyadenosin (dA),
Guanine Guanosine (G) deoxyguanosine (dG)
Cytosine Cytidine (C) deoxycytidine(dC)
Uracil Uridine (U) deoxyuridine(dU)
Thymine Ribothymine (T) Deoxythymidine(dT)
Base Ribonucleotide Deoxynucleotide
Adenine AMP,ADP,ATP dAMP,dADP,dATP
Guanine GMP,GDP,GTP dGMP,dGDP,dGTP
Cytosine CMP,CDP,CTP dCMP,dCDP,dCTP
Uracil UMP,UDP,UTP dUMP,dUDP,dUTP
Thymine rTMPTDP,TTP dTMP,dTDP,dTTP
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Chemical structure of ATP
ATP -gt ADP P energy, orATP -gt AMP 2P
energy
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Polynucleotide

• Polynucleotide formed by condensation of two or
  more nucleotides.
• Occurs between the alcohol of a 5 phosphate of
  one nucleotide and 3-hydroxyl of a second with
  the elimination of H2O, forming a phosphodiester
  bond.
• The primary structure of DNA and RNA proceeds in
  5 to 3 direction.
• Common presentation 5-pGpApTpC-3

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Polynucleotide
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Watson and crick model

• In 1953 using x-ray diffraction
• Nobel prize
• Watson and crick ds helix model describe the
  features of B form of DNA
• Other forms are A and Z

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Watson and crick model
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DNA double helix
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Types of DNA
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Types of DNA

• B- DNA
• The B-form of DNA is the most common form of
  DNA. 
• The B-DNA when compared to the A-DNA is more
  narrower and elongated. 
• The major groove is wider and is more accessible
  to proteins. 
• The minor groove is narrow.  
• Helix diameter  23.7 Å
• Rise per Base pair  3.4 Å 
• Base-pair per helical turn 10 

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Types of DNA

• A- DNA
• A-form of DNA are shorter and wider than the
  B-DNA.
• Most of the RNA and RNA-DNA duplex are found
  in this form. 
• The major groove is deep and narrow and is not
  easily accessible to proteins. 
• The minor groove is wide, shallow is accessible
  to proteins. 
• The base pairs are tilted to the helical axis. 
• Helix diameter 25.5 Å
• Rise per base pair 2.3 Å
• Base pair per helical turn  11

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Types of DNA

• Z-DNA
• Z-form of DNA has left handed sense. 
• This structure of DNA is more narrower and
  elongated than A or B helix. Major groove is not
  prominent.
• The minor groove is narrow. 
• The base pairs are nearly perpendicular to helix
  axis. 
• Helix Diameter 18.4 Å
• Rise per base pair 3.8 Å 
• Base pair per helical turn  12

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Types of DNA
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DNA Biological Functions

• Proteins
• DNA carries the codes for proteins. However, the
  actual protein differs a lot from the codes
  present on the DNA. The basic steps include
• Transcription
• Translation
• DNA replication
• DNA inheritance

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RNA

• RNA- Ribonucleic acid, a nucleic acid present in
  all living cells. Its principal role is to act as
  a messenger carrying instructions from DNA for
  controlling the synthesis of proteins, although
  in some viruses RNA rather than DNA carries the
  genetic information.

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RNA structure
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RNA type Functions
mRNA Carries genetic information copied from DNA in form of three base code
tRNA Transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation.
rRNA In the cytoplasm, ribosomal RNA and protein combine to form a nucleoprotein called a ribosome. The ribosome binds mRNA and carries out protein synthesis. 
SnRNA Found with nucleus of eukaryotic cells. Involve in RNA splicing and maintain the telomeres.
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RNA type Functions
Small silencing RNA 20-30 nt. First discovered in 1993 Regulate biological pathways Types-SiRNA, miRNA, and Piwi-interacting RNA
Tm RNA Only found in bacteria Recognizes ribosomes that have trouble translating or reading an mRNA, unfinished protein that may detrimental to the cell. TmRNA help in destructing or proteolysis of these unfinished RNA or protein .
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rRNA
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mRNA
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tRNA
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RNA silencing

• RNA interfence- RNA silencing-post-transcriptional
  gene silencing or RNA interference  gene
  silencing, effects by which the expression of one
  or more genes is down regulated or entirely
  suppressed by small RNAs- si,mi and pi RNA

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Function of SiRNA

• Potential to be used for therapeutic purposes
  where disease-causing genes are selectively
  targeted and suppressed.
• Eg. Cancer, HIV infection and hepatitis.

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Ribozymes

• Ribozymes (ribonucleic acid enzymes), also
  termed catalytic RNA, are RNA molecules that are
  capable of catalyzing specific biochemical
  reactions, similar to the action of
  protein enzymes.
• 1982 discovery
• Ribozymes demonstrated that RNA can be both
  genetic material (like DNA) and a
  biological catalyst (like protein enzymes).
• Contributed to the RNA world hypothesis, which
  suggests that RNA may have been important in the
  evolution for its self-replicating systems.
• Discovered by Sidney Altman and Thomas Czech, who
  were awarded the Nobel Prize in Chemistry in
  1989.

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Ribozymes

• Function
• Ribozymes function (as part of the large subunit
  ribosomal RNA) to link amino acids during protein
  synthesis.
• Includes  RNA splicing- spliceosome
• Hammerhead ribozymes
• VS ribozymes
• Leadzymes
• Hairpin ribozymes

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spliceosome