DNA Transcription - Genetics
1. Be able to identify:
Ribose vs. Deoxyribose:
Ribose is a sugar found in RNA with a hydroxyl group (-OH) at the 2' carbon. Deoxyribose, found in DNA, lacks this hydroxyl group and has only a hydrogen (-H) at the 2' carbon.Purines vs. Pyrimidines:
Purines (double-ring structures): Adenine (A), Guanine (G).
Pyrimidines (single-ring structures): Cytosine (C), Thymine (T in DNA), Uracil (U in RNA).
5’ vs. 3’ end of ssDNA strands:
The 5' end has a phosphate group attached to the 5' carbon of the sugar.
The 3' end has a hydroxyl (-OH) group attached to the 3' carbon of the sugar.
5’ vs. 3’ ends of dsDNA molecule:
In double-stranded DNA (dsDNA), the two strands run antiparallel:One strand runs 5' → 3'.
The complementary strand runs 3' → 5'.
5’ vs. 3’ end of a single nucleotide:
The 5' end is the phosphate group.
The 3' end is the hydroxyl (-OH) group on the sugar.
Covalent vs. Non-covalent bonds in ssDNA:
Covalent bonds: Phosphodiester bonds link nucleotides in a single strand.
Non-covalent bonds: Do not exist in ssDNA; hydrogen bonds hold the two strands together in dsDNA.
Function of each carbon in ribose sugar (1' to 5'):
1' carbon: Bonds to the nitrogenous base.
2' carbon: Determines whether it’s ribose (-OH) or deoxyribose (-H).
3' carbon: Bonds to the next nucleotide via a phosphodiester bond.
4' carbon: Stabilizes the sugar ring structure.
5' carbon: Bonds to the phosphate group.
2. What are the 3 parts of a nucleotide building block for DNA?
A nitrogenous base (A, T, C, G).
A deoxyribose sugar.
A phosphate group.
3. If I were to synthesize DNA, where on ribose will the next new base be added or attached?
The new base is added to the 3' hydroxyl (-OH) group of the sugar via a phosphodiester bond.
4. What two other individuals’ work contributed to Watson and Crick’s 1963 model of DNA?
Rosalind Franklin (X-ray crystallography images of DNA).
Maurice Wilkins (collaborated on X-ray diffraction data).
5. How many backbones in dsDNA? What two molecules is the backbone made of? Is the backbone covalently bonded? What is ‘antiparallel’ regarding the backbone?
Backbones: Two.
Molecules: Sugar (deoxyribose) and phosphate groups.
Covalently bonded: Yes, via phosphodiester bonds.
Antiparallel: The two strands run in opposite directions: one 5' → 3', the other 3' → 5'.
6. In ssDNA, what type of bond holds the nucleotides together in a strand?
Phosphodiester bonds (covalent bonds).
7. In dsDNA, what type of bond holds the two strands together in a double-helix?
Hydrogen bonds between complementary nitrogenous bases.
8. Where does the energy come from to synthesize DNA?
Energy comes from the hydrolysis of the high-energy phosphate bonds in deoxynucleoside triphosphates (dNTPs).
9. What conditions separate the double helix into ssDNA: in PCR vs. in a cell?
PCR: Heat denatures the DNA strands.
Cell: Helicase enzyme separates the strands during replication.
10. TELs (telomeres):
How are telomeres protected? Special protein complexes (e.g., shelterin) prevent fusion and degradation.
Which strand is difficult to replicate? The lagging strand.
What enzyme replicates TELs? Telomerase.
What happens to TELs as we age? They shorten, leading to cellular aging and senescence.
11. What did Chargaff notice, regarding base pairs?
Chargaff's rules state that the amount of adenine (A) equals thymine (T), and the amount of cytosine (C) equals guanine (G).
12. Why does the double helix of DNA have a constant diameter, regardless of the sequence?
A purine always pairs with a pyrimidine (A with T, G with C), ensuring a constant diameter.
13. How many hydrogen bonds would form between the ssDNA sequence ATTG and its complement?
A-T pairs have 2 hydrogen bonds.
G-C pairs have 3 hydrogen bonds.
Sequence ATTG pairs with TAAC: 2 + 2 + 3 + 3 = 10 hydrogen bonds.
14. What is Tm? What 2 features of a primer molecule affect Tm?
Tm (melting temperature): The temperature at which half of the DNA duplex separates into single strands.
Features affecting Tm:
GC content (more GC = higher Tm).
Primer length (longer primers = higher Tm).
15. What are other words for “anneal” – what does this mean?
Synonyms: Hybridize, bind.
Meaning: Re-joining of complementary DNA or RNA strands after separation.
16. What nm wavelength of light does DNA (and RNA) absorb?
260 nm.
17. What is the overall charge of the DNA molecule, and what part of its structure causes this charge?
Charge: Negative.
Cause: Phosphate groups in the backbone.
Movement during electrophoresis: Towards the positive electrode (anode).
18. Know the different names for the two strands of DNA:
Coding strand (sense strand): Matches the RNA sequence (except T for U).
Template strand (antisense strand): Used as a template for RNA synthesis.
19. How many base pairs is 6.72 kb?
6,720 base pairs.
20. How many base pairs in the human genome in an egg or sperm? A somatic cell?
Egg or sperm (haploid): ~3 billion base pairs.
Somatic cell (diploid): ~6 billion base pairs.
21. What percent similar are two random human genomes?
Approximately 99.9% similar (0.1% different).
22. How many types of genomes are in an animal cell? A plant cell? Name them.
Animal cell: Two genomes (nuclear, mitochondrial).
Plant cell: Three genomes (nuclear, mitochondrial, chloroplast).
1. What is cpDNA, what is mtDNA? Can organelles live independently?
cpDNA (chloroplast DNA): Found in chloroplasts, involved in photosynthesis.
mtDNA (mitochondrial DNA): Found in mitochondria, involved in energy production.
Can organelles live independently? No, they depend on nuclear genes for many proteins.
2. How many mitochondria are in a cell? How many mtDNA genomes per mitochondrion?
Mitochondria per cell: Varies, ~100–10,000.
mtDNA genomes per mitochondrion: 2–10 copies.
3. What is heteroplasmy, and how could that affect inheritance of mitochondrial diseases?
Heteroplasmy: The presence of both normal and mutated mtDNA within a cell.
Effect on inheritance: The proportion of mutated mtDNA determines whether the disease manifests and its severity.