Lecture 14 - Nucleotides and Nucleic Acids

focus: RNA

What sugar is found in RNA, and how does it affect stability?

RNA contains ribose, which has a 2'-OH group, making it less stable than DNA and susceptible to base hydrolysis.

Why is DNA more chemically stable than RNA?

DNA lacks a 2'-OH group on its sugar, preventing base-catalyzed hydrolysis.

Is RNA always single-stranded?

Yes, but it can fold into secondary structures (e.g., hairpins) with base-paired regions.

Q4: Does A = U and G = C in RNA?

No, because RNA is single-stranded and only complementary to one DNA strand.

How does RNA relate to its DNA template?

RNA is complementary to the template strand and has the same sequence as the non-template (coding) strand.

What are examples of RNA secondary and tertiary structures?

• Secondary: hairpins, cloverleaf (tRNA);

• Tertiary: folded RNAs with non-Watson-Crick base pairs (e.g., G-U)

• some of these structures have catalytic properties (ex. hammerhead ribozyme from plant viruses)

What is a ribozyme?

A catalytic RNA molecule, e.g., the hammerhead ribozyme in plant viruses.

What are the four major types of RNA?

1. mRNA

2. tRNA

3. rRNA

4. miRNA

What is the function of mRNA?

Carries the genetic message from DNA to ribosomes for translation into protein.

What is the 5' cap of mRNA and its function?

A 7-methylguanosine triphosphate linked to a 2’-methylated ribonucleoside; it aids ribosome recognition and protects from degradation.

What is the function of the poly-A tail in mRNA?

It stabilizes mRNA and helps ribosome recognition; typically 20–250 adenines long.

What is the function of tRNA?

Carries amino acids and matches them to codons during translation via the anticodon loop.

What are key features of tRNA?

~73–93 nucleotides, cloverleaf structure, ACC at 3′ end (AA attachment site), and anticodon region.

What is the function of rRNA?

Forms the core of ribosomes, catalyzes protein synthesis, and provides structural support.

What are the components of eukaryotic ribosomes?

• 60S subunit: 5S, 5.8S, 28S rRNAs + ~50 proteins

• 40S subunit: 18S rRNA + ~30 proteins
  Together = 80S ribosome

What does the 'S' stand for in ribosomal subunits?

Sedimentation coefficient; a measure of particle speed in a centrifugal field (not additive).

What is miRNA and its function?

Small RNAs (~22 nt) that bind to mRNAs to inhibit their translation or promote degradation.

How do miRNAs regulate gene expression?

By base pairing with complementary mRNAs to silence or degrade them, preventing overproduction of proteins.

Why does DNA use thymine instead of uracil?

Deamination of cytosine produces uracil. If DNA used U, repair enzymes couldn’t distinguish real vs. mutated bases.

What is depurination?

Loss of a purine base (A or G) from DNA’s phosphodiester backbone; occurs frequently and requires constant repair.

What are the effects of UV light on DNA?

Causes thymine dimers (cyclobutane and 6-4 photoproducts), leading to mutations.

• cyclobutane thymine dimer has 2 covalent bonds

• 6-4 photoproduct has 1 covalent bond

What are other sources of DNA damage?

• Ionizing radiation (X-rays)

• Oxidative damage (H₂O₂, free radicals, compounds with unpaired electrons)

• Chemicals (nitrous acid, alkylating agents, base analogs like AZT)

Why are mutations linked to cancer?

Mutations can disrupt genes controlling cell growth, leading to uncontrolled division and tumor formation.

How are all major RNA types produced in the cell?

They are produced by transcription, a process where one DNA strand is copied into a complementary RNA strand.

In what ways do the different types of RNA vary?

They differ in size, function, and general stability.

What are the features of the guanine cap

• 7-Methylguanosine (guanine with methyl attached)

• triphosphate on 5’ instead of 3’OH

  • 5’, 5’ - triphosphate linkage

• At 2’, instead of OH, it’s sometimes methylated giving OCH3

What are mutations?

Mutations are changes in the DNA base sequence, such as replacements, deletions, or insertions of bases.

Why are mutations significant in biology?

They alter genetic information and play important roles in processes like aging and cancer.

What is deamination, and how does it relate to mutations?

Deamination is the loss of an amino group from a base, such as cytosine (C) turning into uracil (U).

How does the cell deal with C → U mutations?

DNA repair enzymes recognize and remove uracil, replacing it with cytosine to preserve correct genetic information.

How does the rate of depurination in RNA compare to that in DNA?

Depurination occurs much more slowly in RNA than in DNA.

What are mutagenic agents and how do they relate to cancer?

Mutagenic agents are chemicals that cause mutations in DNA. They are often carcinogens because mutations can disrupt genes that regulate cell growth.

Why are multiple mutations often found in tumor cells?

Tumor cells usually contain two or more mutations in genes that control growth, which can lead to uncontrolled cell division and tumor formation.