Lecture 2 Intro to Nucleic Acids & Proteins
Nucleic Acid Chains
1. DNA is synthesized from deoxyribonucleoside triphosphates, otherwise known as:
dNTP’s – things that are used to make this linear structure. 2 phosphates get
removed during this process.
2. RNA is synthesized from ribonucleoside triphosphates, or: NTP’s
3. Nucleotides are linked by: phosphodiester bonds (through phosphate groups)
- DNA is double stranded while RNA is single stranded – in order for
replication & transmission of info contained in DNA strand, it needs to be
double-stranded. Basis of exactly how those strands together is mediated
through process called base pairing – ensures that base opposite of it in
opposing strand is specific base b/c not all bases are complementary to each
1. Holds DNA double helix together
2. A-T – 2 H-bonds
G-C – 3 H-bonds
- H-bonds form, helping to keep 2 strands together
- Strands run anti-parallel
3 forces that keep DNA together:
1. H-bonds – dipole-dipole interactions with each other
2. Van der Waals – are induced dipoles (slight variation in positive &
negative charge) – clouds of e- that when they come near each other
induce dipoles in each other.
3. Hydrophobic interactions – tendency to avoid water – stacking b/w bases
which are very hydrophobic particularly ring structure – tend to like to
stack in certain way.
- Info is always read 5’ to 3’ – DNA is composed of 2 antiparallel strands.
Has ladder-like structure. Same info present on 1 strand is on other b/c of
complementarity of bases & this redundancy is extremely important for
preservation of info.
- DNA structure is organized into double helix – ladder twists around itself
forming major groove & minor groove. Interactions with turns of helix
make DNA more stable.
1. Strands in double helix are antiparallel (go in opposite direction) – this means that 1 strand is 5’ 3’ while
its partner is 3’ 5’
2. What are 2 ends of DNA strand composed of? 5’ = P, 3’ = OH
Sequence of 2 strands are: complementary. Strands can be unzipped (reversible – can be reannealed).
This is important for: DNA replication (making copy of DNA), protein synthesis (i.e. making RNA copy
1. Heating denatures double-stranded DNA by: disrupting H-bonds b/w bases (specifically those H-bonds
mediating base pairing holding 2 strands together)
2. Temp at which DNA denatures is called: T M 3. Denaturation of DNA is reversible process
1) Why is T oM DNA rich in G-C base pairs higher than T of DMA rich in A-T base pairs? G-C have 3 H-
bonds; A-T have 2
2) Why do high temp organisms such as bacteria around undersea vents have G-C rich genomes? DNA would
Intro to Protein Structure
Primary (sequence) - AA sequence
Secondary (local folding) - a-helix, B-sheet
Tertiary (long-range folding) - 3D structure
Quaternary (multimeric organization)
Supramolecular (large-scale assembly) - protein assemblies
1. Proteins are composed of AA
2. AA side-chain or R group is variable & determines type of AA (only part of
entire AA that varies – analogous to base in nucleotide)
3. 4 major categories of AA: basic (positively charged AA), acidic (negatively
charged), uncharged polar (1s with hydroxyl groups on them), non-polar
Mutational steps b/w codons
1) What is min # of mutational steps b/w AA? - # mutations b/w codons for different AA’s
2) How many mutational steps required to get from a codon for proline to one for cysteine, minimum? 2 (CCG
3) … maximum? 3 (CCG UGC)
1. Groups of AA’s with similar properties tend to be clustered in codon table.
2. Codons of AA’s with similar properties tend to have fewer mutational steps b/w them.
3. 1 random mutation in codon is less likely to result in dramatic change in AA properties than 2 random
Synthesis of Proteins
- Reactions of carbonyl group with amino group of next AA in
condensation reaction that forms peptide bond (molecule of
water is lost).
- Proteins also have direction: go from N-terminus (where amine
group is hanging off) to C-terminus (where carboxyl group is
hanging off). Side chains are always attached to alpha-C –
never connected to C attached to peptide bond.
1. Why are properties of AA side chains important? Folding & function – properties of side chain determine
property of protein as whole (3D structure determines function)
2. What kind of covalent bond connects AA in chain to form proteins?