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Lecture 4

BIO130H1 Lecture 4: Week 2 - Introduction to Nucleic Acids _ Proteins

Course Code
Melody Neumann

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Week 2 - Introduction to Nucleic Acids & Proteins
Introduction to Nucleic Acids & Proteins
Lecture outline:
1) Introduction to nucleic acids (finish from last week)
2) Molecular Interactions
3) Properties of nucleic acids
4) Intro to proteins
5) Amino acid structure
6) Protein structure
77-79 (from last week); 393-397; 33-42 (chemistry review); 50- 63; 70-72
Molecular Interactions
Interactions between individual molecules usually mediated by noncovalent
1.Electrostatic attractions
oppositely charged ions
strong in the absence of water
2.Hydrogen bonds
special forms of polar interaction
strongest when in straight orientation
directly across
3.van der Waals attractions
not weakened by water, dynamic, attractions moving through the
molecules all the time
4.Hydrophobic force
Individually, very weak forces--BUT can pile up to generate strong
bindings between molecules
force hydrophobic molecules
Nucleic acid chains
1) DNA is synthesized from deoxyribonucleoside
triphosphates, otherwise known as: dNTPs
deoxyribose -AND base - triphosphate
2) RNA is synthesized from ribonucleoside
triphosphates, or: NTPs
3) Nucleotides are linked by: phosphodiester
OH on the 3’ linked to a phosphate
through to the 5’ of the next nucleotide
gives the directionality of the molecule
Base Pairing
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The H bonds are straight
1) Holds the DNA double helix together
2) A-T has 2 H bonds; G-C has 3 H
�Three forces that keep DNA together…
1.H bonds (represented by the dashed
2.Van der Waals attraction
stacking attractions
a weak force, but can be
3.hydrophobic interactions
DNA is always surrounded by
backbone is polar, hydrophilic
the base rings are hydrophobic
so bases will be forced into the middle of the DNA structure, while the
backbones are on the outside -- stabilize the DNA
DNA Structure
the second strand is antiparallel (from 3’ to 5’)
major groove allows access to base groups without ripping DNA apart (protein-DNA
DNA backbone negatively charged
base stacking contributes to the stability
1)The strands in a double helix are antiparallel
This means that one strand is 5 --3’ while its partner is 3 ’’’’’’’’’’’’’’’’’’’’’’’’’’ ’ ’
the only way that the double helix can form a stable entity
2) What are the two ends of the DNA strand composed of?
5’ = Phosphate group (PO4-)
3’ =hydroxyl group(OH-)
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The sequence of the two strands are: complementary
The strands can be:unzipped
eg. under high temperature--denaturation--cool down -- renaturation
This is important for:
DNA replication
RNA synthesis
Introduction to Protein Structure
Primary (sequence)
AA sequence
linear order connected together
Secondary (local folding)
a helix, beta-sheet
Tertiary (long-range folding)
3D structure
Quaternary (multimeric organization)
(not all proteins have this )
multiple polypeptide chains
e.g. hemoglobin
Multiprotein complexes
molecular machines
e.g. eukaryotic transcription apparatus
e.g. protein code of a virus
Protein Structure
1) Proteins are composed of amino acids
2) The amino acid side-chain, or R group is variable, and determines the type of
amino acid
3) 4 major categories of amino acids:
Polar charged
Polar uncharged
unique properties
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