Exam 2 Study Guide - Nucleic Acids Flashcards
The structure of a nucleotide.
A nitrogenous base (pyrimidine or purine), a pentose sugar, and 1+ phosphates
The difference between DNA and RNA: Structure
DNA (deoxyribonucleic acid)…2’ carbon in ribose sugar has only hydrogen atom, no oxygen “deoxy”; RNA (ribonucleic acid)
The difference between DNA and RNA: Function
DNA provides storage of genetic material; RNA has many roles in protein synthesis, gene expression, catalytic properties, etc.
Pyrimidines vs purines.
- Major pyrimidine bases: cytosine, thymine (only in DNA), uracil (only in RNA)
- Major purine bases: adenine and guanine
Nucleic acids: Structure
Hydrophilic and negatively charged, double helix formation
What does 5’ and 3’ mean?
Refers to the carbon atoms in a deoxyribose sugar that bind to the phosphate groups in DNA. DNA is always synthesized in the 5’ to 3’ direction and have antiparallel strands.
Structure of the phosphodiester bond
Nucleotides join together by links of phosphodiester bonds (5’ carbon is linked to the phosphate; the phosphate is linked to the 3’ carbon on the next nucleotide)
Base pairs: How are they connected
Hydrogen bonds between complementary strand of nucleic acids
Which bases bind?
A bonds to T (or U in RNA); G bonds to C
Base pairs: How many hydrogen bonds?
3 hydrogen bonds from between G and C; 2 hydrogen bonds form between A and T
B-form DNA: Basic structure and where it is found
Watson-Crick structure; most stable for a random-sequence DNA molecule (normal DNA found in humans)
A-form DNA: Basic structure and where it is found
Right-handed double helix with a wider helix (11 bp/turn), and a tilted plane; found in solutions devoid of water
Z-form DNA: Basic structure and where it is found
Left-handed helix (12 bp/turn) and a backbone with a zig-zag appearance (slender and elongated); found in archaea, bacteria, some eukaryotes
Palindromes
Region of DNA that is identical when read forward or backward (applied to region of DNA with inverted repeats)
Hairpin and cruciform
Form from the self-complementarity within each strand
Triplex DNAs
Form from Hoogsteen pairing (hydrogen bonding with a third DNA strand)
Tetraplex DNAs
Occur when four DNA strands pairs (readily occurs with DNA sequences with a very high proportion of G residues)
Messenger RNA
Portion of cellular RNA carrying the genetic information from DNA to the ribosome
Transfer RNA
Carries and transfers an amino acid (anti-codon) to the polypeptide chain (required for protein translation)
Ribosomal RNA
Ensures correct binding catalyzing the peptide bond (required for protein translation)
Denaturation
Melting of the double helix (disrupts hydrogen bonds and base-stacking interactions); caused by pH or temperature extremes
What is the Tm?
Temperature at which ½ of DNA is present as separated single strands
What factors affect the Tm?
G-C content can increase the melting temperature…pair has three hydrogen bonds making them more difficult to melt
Anneal
Process by which two strands spontaneously rewind when temperature or pH is returned to its normal range
Mutation
Alterations in DNA structure that produce permanent changes in the genetic information encoded
Deamination
Spontaneous loss of exocyclic amino groups (deamination of cytosine to uracil) uracil is recognized as foreign material and could be why DNA contains thymine instead
What are the effects of UV light?
Mutations: Cyclobutene pyrimidine dimers and/or 6-4 photoproduct
Ionizing radiation (X-rays and gamma rays)
Causes ring opening, base fragmentation, breaks in the covalent backbone of nucleic acids
ROS
Reactive oxygen species can damage DNA…cells have antioxidants that defend and destroy ROS
When DNA is run out on an agarose gel, the DNA moves toward the positive electrode. Explain why, include specifics about the structure of the molecule.
Nucleic acids are hydrophilic and negatively charged, due to its phosphate groups in the backbone. These phosphate groups have negatively charged oxygen atoms, giving DNA its negative charge. Therefore, when DNA is on an agarose gel, it will move toward the positive electrode, since it is the opposite charge (opposite charges attract each other).
Which scientist demonstrated base-pair property?
Erwin Chargaff
Provide 1 example of a nucleotide where the phosphate is not attached to the 5’ carbon.
One example is ribonucleoside (adenosine) 3’-monophosphates where the phosphate is attached to the 3’ carbon, hence its name. Ribonucleoside (adenosine) 3’-monophosphates is important because it’s the end product of RNA hydrolysis.
Double stranded nucleic acids are antiparallel. Use what you know about the structure of DNA to explain what this means.
Nucleotide subunits are held together by phosphodiester bonds, linking the 5’ end of one sugar to the 3’ end of the next, hence the 3’ and 5’ orientation. The double stranded nucleic acids are antiparallel because the structure of DNA is oriented with opposite polarities. The antiparallel direction allows the strands to twist around one another to form the DNA double helix. Lastly, the polarity within the antiparallel strands give rise to the major and minor grooves in the DNA structure.
What is a tautomer?
A tautomer is a structural isomer that can readily interconvert. Conversion occurs due to the relocation of a hydrogen atom within the compound. Examples are lactam, lactim, and double lactim.
