Topic 1: Nucleic Acid and Protein Structure

What are the 3 main functions of DNA?

1. Stores information

2. Replicates faithfully (preservation of information)

3. Has ability to mutate (variability of information)

What do we need to make a functional RNA?

• 4 letters ATGC

• So we need 3 or more to make AA

• Info carried by base sequence 

  • 1 nuc can only make 4 types of AA

  • 2 nucleotides can be 16 types

  • 3 nucs can make 4^3 = 64

  • 4 can make 4^4 = 256. 

How do we know we need 3 or bases to make amino acids?

mixed synethic dna w AAA to find out its always 3 or more

What type of info does dna carry?

• coding for which proteins/diff rnas like trna/rrna etc

• regulatory signals/binding sites

How does DNA’s physical structure allow it to store information?

Base sequence = information

Bases inside protected by backbone

Double helix keeps info stable

How does DNA’s structure let it replicate faithfully?

Complementary pairing (A–T, G–C)

Each strand = template

Hydrogen bonds allow easy separation

How does DNA’s structure let it mutate?

Sequence can change

Replication errors

Damage to bases (UV, chemicals)

Why does the order of bases matter?

Order sets codons

Codons set amino acids

Amino acids set protein function

How do we know DNA is the hereditary material?

DNA transfers traits, stores information, replicates, and directs protein synthesis

What did Avery, MacLeod & McCarty (1944) show?

DNA transforms bacteria

Only DNA (not protein) transferred traits

First strong proof DNA = genetic material

What did Chargaff (1947) discover?

A = T, G = C

Suggested base pairing → DNA has structure suitable for coding

What did Watson, Crick & Franklin (1953) show?

Double helix model

Structure explains information storage + copying

What did Meselson & Stahl (1958) demonstrate?

Semi‑conservative replication

DNA copies itself in a predictable, heritable way

What did Crick, Nirenberg & others (1965) discover?

Genetic code (triplet codons)

Showed how DNA → RNA → protein

What is the central dogma?

info flows from dna → rna → protein.

Why is RNA made?

• Rna made to protect dna (original copy)

• more copies = more opportunities to replicate.

Can RNA ever synthesize back to DNA?

Yes.

• RNA virus (retrovirus, replicate dna) → major issue w rna.

Why can RNA bend but not DNA?

• Rna can bend bc ss

• Not dna bc dsdna

• If there is a knick in rna = dead

• if there is a knick in dna = ok bc ds so its more stable

Can protein ever reverse back to RNA?

No.

only rna can reverse back to dna.

What causes cancer from viruses?

retroviruses

What is a gene?

entire DNA sequence necessary for production of functional protein or RNA

What do regulatory sequences do?

act as signals or binding sites

Which strand makes the protein?

Sense/coding/nontemplate strand codes for the protein.

Which strand makes the strand that makes the protein?

antisnense/template/non-coding strand makes the sense strand which makes the proteins.

The DNA strands are…? (3)

• have polarity (bc sense antisense go in opp directions)

• complementary

• antiparallel

How do the 2 original strands make new daughter strands?

• two strands of a parental DNA separate and each

• template for daughter strands by complementary base pairing

Why is DNA double-stranded?

• bc one is an imprint/copy of the other

• replicates semiconservatively

What type of information do the strands keep when replicated?

only keeps infor for one strand

the other makes a complementary version of it

What are the 3 models of replication that were proposed?

Explain how the Meselson-Stahl experiment was conducted. (9)

• Grow E. coli in heavy nitrogen (^15N)

• All DNA becomes “heavy” because it contains ^15N atoms.

• Move the bacteria to normal nitrogen (^14N)

• New DNA strands made now contain ^14N (lighter).

• Extract DNA and spin it in CsCl solution

• When centrifuged, DNA separates by density:

• Heavy DNA (15N–15N) sinks lower.

• Light DNA (14N–14N) stays higher.

• Hybrid DNA (14N–15N) sits in between.

What were the results of the Meselson-Stahl experiment?

• Before transfer: only heavy DNA (15N–15N).

• After one generation: all DNA was hybrid (14N–15N)

  • one old heavy strand + one new light strand.

• After two generations: half hybrid (14N–15N), half light (14N–14N).

What did the pattern from the results of the Meselson-Stahl experiment mean?

Each new DNA molecule keeps one old strand and makes one new strand → semiconservative replication.

Information is preserved.

What happens if there is a mutation in ONE of the parental strands?

Would change the information on the strand and the daughter strands would be replicated using the wrong bases/wtv the mutation is.

What are the 4 types of mutations that can arise?

What happens if there is a mutation in the coding sequence?

change in AA —> possible alteration in protein product

What is colinearity of genes?

• Sequence of 3 DNA bases (a codon) codes for a single amino acid.

• 1st codon in the DNA translates to the 1st amino acid in the protein, the 2nd codon to the 2nd amino acid, and so on.

What happens if a promoter is mutated?

• Too little transcription

• Too much transcription

• Gene may turn off or on inappropriately

What happens if UTRs (5’ or 3’) are mutated?

• mRNA stability changes

• Translation efficiency changes

• Protein levels go up or down

What is the overall consequence of regulatory region mutations?

• change gene expression, not the protein

• Often more harmful than coding mutations

Why are mutations important?

results in formation of new alleles'

• Source of genetic variation

What can mutations change?

• Altered product (protein/RNA)

• No product (knockout)

• Altered regulation (regulatory sequence)

How do mutations lead to evolution?

• Mutations + selection → evolution

• Beneficial changes spread in populations

What are the 5 diff nitrogenous bases?

What type of sugar do DNA molecules have?

What type of sugar do RNA molecules have?

What is a nucleoside?

sugar + base

What is a nucleotide?

sugar + base + phosphate complex

What are the nucleosides called in DNA?

What are the nucleosides called in RNA?

What are covalent bonds?

sharing electrons to become stable

What are non covalent bonds?

• ionic (witin molecules),

• H-bonds = particle positive charge

• LDFs all mols have

• hydrophobic (some mols would rather interact with eo and not w the water)

What is uracil?

Uracil is demethylated Thymine.

• exists in RNA.

What determined that purines have 2 rings and pyrimidines have single rings?

Width determines # of rings

• so can have 3 across (1 purine +. 1 pyrimidine)

What ensures that only A bonds with T/U and G bonds with C?

hydrogen bonds.

CG = TB, AT = DB

What is a polypeptide chain?

nucleotide attaches to eo to make a long chain of nucleotides.

What is chargaffs rule?

#pur is same as #pyr. But (A+T is not equal to G+C)

Which bases are more abundant in the promoter sequence?

more A+T