Chapter 8 Flashcards
Draw the DNA bases and their H-bonding
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Draw the full DNA structure with sugar phosphate backbone
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What pieces make up a nucleotide
- Phosphate group
- Pentose sugar
- Nitrogenous base
What factors control and stabilize DNA structure?
- hydrogen bonding between complementary base pairs
- Base stacking and hydrophobic interactions
- The covalent phosphodiester bonds between the sugar molecules (ribose in RNA, deoxyribose in DNA) and the phosphate group in the DNA backbone
What are the defining differences between RNA and DNA
- Sugar Molecule:
* DNA =deoxyribose
* RNA= ribose - Number of Strands:
* DNA = double-stranded helix.
* RNA = single-stranded molecule. However, in some cases, it can fold back on itself to form complex secondary structures. - Function:
* DNA = genetic material, carrying the hereditary information of an
organism. It stores instructions for the synthesis of proteins and other molecules.
* RNA is involved in various cellular processes, including protein synthesis, gene regulation,
and the transmission of genetic information from DNA to proteins. There are several types
of RNA, each with its own specific function, such as messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). - Stability:
* DNA is more stable than RNA due to the presence of the methyl group on the deoxyribose sugar and the absence of the 2’-hydroxyl group found in ribose. This makes DNA less
prone to hydrolysis and degradation.
* RNA is relatively less stable and more prone to degradation, especially in alkaline `conditions
Define Chargraff’s rule
shows the complementarity of the DNA strands, with # of A = # of T and # of G = # of C
Describe the Sanger sequencing process and interpret experimental results
1) DNA Sequence For Chain Termination PCR:
- The DNA sequence of interest is used as a template for a special type of PCR called chain-termination PCR. Chain-termination PCR works just like standard PCR, but with one major difference: the addition of modified nucleotides (dNTPs) called dideoxyribonucleotides (ddNTPs)
2) Size Separation by Gel Electrophoresis:
- The chain-terminated oligonucleotides are separated by size via gel electrophoresis. In gel electrophoresis, DNA samples are loaded into one end of a gel matrix, and an electric current is applied; DNA is negatively charged, so the oligonucleotides will be pulled toward the positive electrode on the opposite side of the gel. Because all DNA fragments have the same charge per unit of mass, the speed at which the oligonucleotides move will be determined only by size.
3) Gel Analysis & Determination of DNA Sequence:
-In manual Sanger sequencing, the user reads all four lanes of the gel at once, moving bottom to top, using the lane to determine the identity of the terminal ddNTP for each band. For example, if the bottom band is found in the column corresponding to ddGTP, then the original sequence has a guanine (G) base.
What is the role of tRNAs?
tRNAs are responsible for carrying amino acids to the ribosome during translation
Each tRNA molecule is specific to one amino acid and has a binding site where that amino acid can be attached.
tRNA molecules have a specific three-nucleotide sequence called the anticodon. The anticodon is complementary to the codon (a three-nucleotide sequence) on the mRNA strand.
This ensures the correct amino acid is inserted at the right position in the growing polypeptide chain.
RNA can form into different structural levels like proteins. Describe these levels
Primary: nucleotides in a sequence
Secondary: folded chain of nucleotides with single-stranded and helical double-stranded regions.
Tertiary: pseodoknot folding
Quaternary: Can be either RNA-RNA interactions or RNA-protein interactions.
What is a palindromic sequence?
Regions of DNA that have inverted repeats
→ Self-complimentary sequence repeated in the opposite orientation of paired strand
→ When the self-complimentary sequence occurs in both strands of DNA, it’s a mirror repeat
Hairpins and cruciforms form in nucleic acids because of ____
palindromic sequences
How does the cell use DNA
methylation?
Methylated bases are useful
- for distinguishing self DNA from foreign
- For distinguishing between new DNA and old
- For modulating gene expression (epigenetics)
What do DNA mutations cause?
Aging and pathogenesis.
Hydrolysis of N-beta-glycosyl bond
between the base and pentose
causes loss of base, or creation of a
DNA lesion (aka AP: apurinic,
apyrimidinic)
- Purines are lost at a higher rate
than pyrimidines
- Deamination (loss of exocyclic amino group)
- UV radiation
What does H bonding between base pairs in DNA allow for?
Width Conservation
It also creates minor and major
groove
- Chargaff’s rules= A+G = T+C
- “The sum of purine bases is
equal to the sum of pyrimidine
bases”
What are the different types of RNA and what do they do?
rRNAs make up the ribosome,
- mRNAs give the info for protein
synthesis to the ribosome
- tRNAs are adaptor molecules that
decipher mRNA and translate it into
amino acids
