Biological Molecules Nucleic acids and Proteins

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Biological Molecules Nucleic acids and Proteins

• Cell Biology
• Lecture 4

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Nucleic acids

• Informational macromolecule
• Deoxyribonucleic acid (DNA) is the genetic
  material
• Ribonucleic acid (RNA)
• Messenger RNA (mRNA) carries information from DNA
  to the ribosomes
• Ribosomal RNA (rRNA) and transfer RNA (tRNA) are
  involved in protein synthesis
• RNAs involved in regulation of gene expression
  and processing and transport of RNAs and proteins

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Nucleic acids

• DNA and RNA are polymers of nucleotides
• Nucleotides consist of
• Purine and pyrimidine bases
• Purines adenine (A) and guanine (G)
• Pyrimidines cytosine (C) and thymine(T)
• RNA has uracil (U) in place of thymine
• 5 C sugar (5 phosphorylated)
• D-Ribose (RNA)
• D-2deoxyrobose (DNA)
• Phosphate 1-3 phosphate at 5C of sugar

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Nitrogenous bases

• Structures are meaningful
• Reactive centers?

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Base pairing Hydrogen bonding

• Hydrogen bonding btw complementary bases is the
  basis for double stranded DNA structure

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Backbone

• Sugar phosphodiester forms the backbone
• Ribose for RNA
• 2-deoxyribose for DNA
• Nucleosidecovalent bonding of C1 of sugar and a
  base
• Naming Guanosine, Adenosine, cytidine and
  Thymidine, Uridine
• Nucelotide Nuceloside5phosphate (1-3)
• Naming
• Adenosine monophosphate (AMP)
• Adenosine diphosphate (ADP)
• Adenosine triphosphate (ATP)
• Can you name the others?

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Phosphodiester bond formation

• DNA polymerases catalyze the rxn
• uses complementary dNTPs
• dehydration reaction between
• 3-OH of new strand and
• 5-phosphate of incoming dNTP
• synthesis is 5?3
• covalent bond is called phosphodiester
• there is always a 5-phosphate and a 3-OH that
  gives the DNA its polar sense (5?3)
• complementary strands are anti-parallel

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Phosphodiester bond formation

• DNA polymerases catalyze the rxn
• uses complementary dNTPs
• dehydration reaction between
• 3-OH of new strand and
• 5-phosphate of incoming dNTP
• synthesis is 5?3
• covalent bond is called phosphodiester
• there is always a 5-phosphate and a 3-OH that
  gives the DNA its polar sense (5?3)
• complementary strands are anti-parallel

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DNA is an antiparallel helix

• Geometry of bases and their spacial arrangement
  to form H-bond cause helix structure of dDNA
• In B-form right handed dDNA
• pairing bases stack in the centre
• backbone intertwined
• creates minor and major grooves
• 0.34 nm (3.4 A) rise per base pair
• one full helix turn houses 10 nucleotides

Major groove
34 A
20 A
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Central dogma

• Complementary base pairing allows one strand of
  DNA to act as a template for synthesis of a
  complementary DNA or RNA strand
• DNA is transcribed to pass genetic information to
  RNA
• The information in RNA is present in a triplet
  code where every three bases stands for one of
  the 20 amino acids
• Translation mRNA codes for protein
• This flow of information from DNA to protein is
  called central dogma in cell biology
• Information flow DNA?mRNA?Protein

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Central dogma and mutations
GAG?GUG

• The DNA contains the instructions for the
  sequence of amino acids in each protein
• The order of amino acids in a protein determines
  its shape and function
• Errors or faults, ie mutations, in the DNA can
  change the amino acid sequence and function of
  the encoded protein
• Sickle cell anaemia is due to one nucleotide
  change affecting hemoglobin ? reduced O2 carrying
  capacity

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Proteins

• Proteins are the most diverse of all
  macromolecules
• Each cell contains several thousand different
  proteins
• Proteins direct virtually all activities of the
  cell
• Functions of proteins include
• Enzymes
• Structural components (e.g. keratin, collagen)
• Motility (e.g. actin)
• Regulatory (e.g. transcription factors)
• Transport (e.g. Na-K-ATPase)
• Receptors (e.g. insulin receptors)
• Transport and storage of small molecules (e.g.
  O2)
• Transmit information between cells (protein
  hormones),
• Defense against infection (antibodies)

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Amino acids

• Polymers of 20 different amino acids.
• Each amino acid consists of the a carbon bonded
  to a carboxyl group (COO-), an amino group
  (NH3), a hydrogen, and a distinctive side chain
  (R)

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Amino acids

• Amino acids are grouped based on characteristics
  of the side chains
• Nonpolar side chains
• Polar side chains
• Side chains with charged basic groups
• Acidic side chains terminating in carboxyl groups

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Nonpolar amino acides

• 10 aa have nonpolar R-groups (hydrophobic)
• Simplest is glycine (RH)
• 2 contain S and two have cyclic side chains
• Nonpolar aa tend to be burried in the hydrophobic
  core of proteins

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Polar amino acides

• 5 aa have polar R-groups either OH or NH2
  (hydrophilic)
• Partial charge H-bond formation with water
• Polar aa tend to appear on the surface of
  proteins

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Charged amino acids

• 3 aa have positively charged NH2 groups (basic)
• Full charge H-bond and ionic bond
• Like Polar aa tend to appear on the surface of
  proteins
• Might take part in catalytic core of enzymes

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Charged amino acids

• 2 aa have negatively charged COO- group (acidic)
• Full charge H-bond and ionic bond
• tend to appear on the surface of proteins or
  enzyme catalytic core

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Peptide bond formation

• Polypeptides chains of amino acids joined by
  peptide bonds
• Number of aas varied
• oxytocin 9 aa,
• insulin 51 aa, titin (connectin) 34,350 aas
• Average 400-500 aa
• One end of a polypeptide terminates in an a amino
  group (N terminus)
• other end is an a carboxyl group (C terminus)

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Protein structure

• Sequence of amino acids in a protein is
  determined by the order of nucleotide bases in a
  gene (Primary structure)
• One can deduce aa sequence from the sequence of
  nucleotides in the gene (or mRNA)
• 3-D conformation is critical to proteins function
• What determines the 3-D structure of proteins?

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Protein secondary structure
Christian B. Anfinsen (1957)

• 3-D structure is a result of interactions between
  the amino acids
• Christian Anfinsen denatured ribonuclease (RNase)
  by heat treatment breaks H-bonds
• If the treatment was mild, the proteins would
  return to their normal shape at room temperature
• This would mean that the information for folding
  the protein is in its primary sequence (how could
  he test?)

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Protein secondary structure

• Secondary structure regular arrangement of amino
  acids within localized regions
• There are 2 types of secondary structure
• The polypeptide can coil in a spiral helix shape
• The polypeptide can fold to form a ß pleated
  sheet (parallel or antiparallel)
• Both are held together by hydrogen bonds between
  the CO and NH groups of peptide bonds

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Protein Tertiary structure

• Observation
• Similarly disrupting the disulfide bonds (S-S)
  using chemical denaturing agents (eg.
  ß-mercaptoethanol) denatures proteins (-SH forms)
• Incubation under oxygen refolded the RNase back
  to its functional conformation (ie enzyme gained
  capacity to degrade RNA)
• indicates a higher level of structure important
  for function that relies on covalent S-S bridge
  (tertiary structure)

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Protein Tertiary structure

• Tertiary structure folding of secondary
  structural elements to form a 3-D arrangement
• 2 elements connected by loops and less ordered
  aas
• interactions btw the side chains of amino acids
  in different regions of protein stabilizes the 3
  structure
• Covalent bonds (S-S bridge)
• Hydrophobic and hydrophilic interactions
• In most proteins this results in domains, the
  basic units of tertiary structure

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Protein Quaternary structure

• Quaternary structure consists of interactions
  between different polypeptide chains
• In multi-subunit enzymes
• Hemoglobin, for example, is composed of four
  polypeptide chains

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Protein structure Summary
Campbell Reece, 2002
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Can you meet these objectives?

• Distinguish among nucleosides, nucleotides and
  nucleic acids?
• Explain the structure of DNA?
• List some functions of proteins in cells?
• Describe and distinguish between amino acids?
• Discuss the levels of protein structure and
  organization of proteins?