Biochem - Molecular (DNA Basics) Flashcards
Pg. 66 in First Aid 2014 Sections include: -Chromatin structure -Nucleotides
What is the purpose of chromatin?
DNA exists in the condensed, chromatin form in order to fit into the nucleus
What forms the nucleosome “bead” in chromatin structure? What are the electric charges of these components?
Negatively charged DNA loops twice around positively charged histone octamer to form nucleosome “bead”; Think: “beads on a string”
In what 2 amino acids are histones rich?
Histones are rich in the amino acids lysine and arginine
What stabilizes the chromatin fiber, and how?
H1 binds to the nucleosome and to “linker DNA”, thereby stabilizing the chromatin fiber
What happens to DNA in mitosis?
In mitosis, DNA condenses to form chromosomes
What occurs during S phase?
DNA and histone synthesis occur during S phase
Which histone(s) is (are) inside the nucleosome core of chromatin?
H1 is the only histone that is not in the nucleosome core; Nucleosome core histones H2A, H2B, H3, H4 (each x2)
Describe heterochromatin in terms of condensation, transcription, and sterics. How does it appear on EM?
Condensed, appears darker on EM. Transcriptionally inactive, sterically inaccessible; Think: “HeteroChromatin = Highly Condensed”
Describe euchromatin in terms of condensation, transcription, and sterics. How does it appear on EM?
Less condensed, appears lighter on EM. Transcriptionally active, sterically accessible; Think: “Eu = true, ‘truly transcribed’”, “Euchromatin is Expressed”
What is the mechanism of DNA methylation, and when does it occur? What does this allow?
Template strand cytosine and adenosine are methylated in DNA replication, which allows mismatch repair enzymes to distinguish between old and new strands in prokaryotes
What type of DNA methylation represses transcription?
DNA methylation at CpG islands represses transcription; Think: “CpG Methylation Makes DNA Mute”
What effect(s) does histone methylation have?
Usually reversible represses DNA transcription, but can activate it in some cases; Think: “histone Methylation Mostly Makes DNA Mute”
What effect(s) does histone acetylation have?
Relaxes DNA coiling, allowing from transcription; Think: “histone Acetylation makes DNA Active”
Which nucleotides are the purines versus pyrimidines? How many rings does each have?
PURines (A,G) - 2 rings; PYrimidines (C, T, U) - 1 ring; Think: “PURe As Gold & CUT the PY (pie)”
What functional group distinguishes thymine?
Thymine has a methyl; Think: “THYmine has a meTHYl”
From what other nucleotide is uracil made, and how?
Deamination of cytosine makes uracil
In which nucleic acid is uracil versus thymine found?
Uracil found in RNA; Thymine in DNA
Which nucleotide bonds in DNA are stronger, and why?
G-C bond (3 H bonds) stronger than A-T bond (2 H bonds)
What is a consequence of high G-C content in DNA?
High G-C content –> High melting temperature of DNA; Think: “C-G bonds are like Crazy Glue”
What 3 amino acids are necessary for purine synthesis?
Amino acids necessary for purine synthesis: Glycine, Aspartate, Glutamine; Think: “GAG”
What is a nucleoside versus nucleotide?
NucleoSide = base + (deoxy)ribose (Sugar); NucleoTides = base + (deoxy)ribose + phosphaTe
What links nucleotides?
Linked by 3’-5’ phosphodiester bond
Draw the structure of Purines (A, G) & associate aspects of this structure with the following 5 requirements for purine synthesis: (1) Aspartate (2) CO2 (3) Glutamine (4) Glycine (5) N10-Formyl tetrahydrofolate.
See p. 33 in First Aid 2017 for visual at top
Draw the structure of Pyrimidines & associate aspects of this structure with the following 2 requirements for pyrimidine synthesis: (1) Carbamoyl phosphate (2) Aspartate.
See p. 33 in First Aid 2017 for visual at top
Draw the chromatin structure.
See p. 32 in First Aid 2017 for visual at top left
What are Barr bodies, and of what type of chromatin are they composed?
Barr bodies (inactive X chromosomes) are heterochromatin
What is located at the 5’ versus 3’ end of a 3’-5’ phosphodiester bond, and what purpose does each serve?
5’ end of incoming nucleotide bears the triphosphate (energy source for the bond). Triphosphate bond is target of 3’ hydroxyl attack.
