(Dr. Heinemann) (Unit C) Topic 14 Flashcards
Purines
- 2 rings
- Adenine (A) and Guanine (G)
Pyrimidines
- 1 ring
- Cytosine (C), Thymine (T), Uracil (U)
What are purines and pyrimidines?
Nitrogenous bases
What are the two major categories of nitrogenous bases?
- Purines
- Pyrimidines
What shapes are nitrogenous bases?
- Flat
- Hydrogen bonding groups on the outside
What types of bonds links nitrogenous bases together?
N-Glycosidic Bonds
2 major types of nucleic acids in humans
- Ribonucleic
- Deoxyribonucleic
Function:
DNA
- Holds genetic material
Function:
RNA
- Template from which proteins are produced (mRNA)
- Ribosome formation (rRNA)
- Catalyzing protein synthesis (rRNA)
- Carrying amino acids to growing peptide chain (tRNA)
- Gene regulation
- mRNA splicing
- Telomere maintenance
What are ribonucleotide/deoxyribonucleotide monomers comprised of?
- A monosaccharide
- A nitrogenous base
- A phosphate
What is the difference between Uracil and Thymine?
Uracil lacks a methyl group
Where are purines/pyrimidines joined to monosaccharides?
Joined to the anomeric (1’) carbon of ribose/deoxyribose
* Via N-Glycosidic Bond
Nucleoside
Nitrogenous base joined to a sugar
List:
The 5 common nucleosides
- Adenosine
- Guanosine
- Cytidine
- Thymidine
- Uridine
Where do phosphates attach to on a nitrogenous base?
Attached to the 5’ position of ribose/deoxyribose
What is the bond between phosphate and nitrogenous bases known as?
Phosphoester linkage
Nucleotide
Has 3 groups:
* A nitrogenous base
* A sugar
* A phosphate group
What is the notation of nucleotides?
- Nitrogenous base
- Number of phosphates
E.x. ADP (Adenosine Diphosphate)
- Sometimes deoxyribonucleotides will begin with a “d” (e.x. dTTP)
Polynucleotide structure
Phosphate group at 5’ carbon on one pentose, forms phosphoester bond with hydroxyl group at the 3’ position of another pentose
How are 5’ and 3’ ends determined in a polynucleotide?
- 5’ free carbon (not attached to anything) is 5’ end
- 3’ free carbon (not attached to anything) is 3’ end
How are polynucleotides conventionally written?
5’ to 3’
Oligonucleotides
“Short” (up to 200 base pairs)
True or False:
Double helices are usually right handed
True
What types of interactions between bases stabilize the double helix?
- Base stacking
- Base pairing
Base stacking
As bases are planar aromatic rings, they can stack on top of each other and tstasbilize via interactions (London forces)
Base pairing
Hydrogen bonding between chemical groups on edges of ring structure
What are the different types of base pairings?
- C and G: 3 bonds
- A and T: 2 bonds
What form of double helices do DNA usually form?
B-DNA double helix
What are certain features of B-DNA double helices?
- Narrow (2 nm or 20 angstroms wide)
- Long (1 human chromosome is 245 million base pairs)
- Distance between consecutive bases is around 0.34 nm
What are the two grooves in the sugarphosphate backbones known as?
- Major groove
- Minor groove
Major groove
The wider groove in B-DNA double helices
Minor groove
The narrower groove in B-DNA double helices
5 differences between RNA and DNA
- Ribose vs. Deoxyribose
- Uracil vs. Thymine
- Shorter (few thousand nucleotides, usually)
- Single stranded (folds into cocmplex 3D structures
- More likely to chemically modify nitrogenous bases
What can modified bases in RNA do?
Influence the secondary and tertiary structure of RNA
Tm
The melting temperature
* Temperature at which 50% of a specific dsDNA has become single stranded
What types of factors determines the Tm?
- Intrinsic factors
- Extrinsic factors
Intrinsic factors that affect Tm
- A:T / G:C ratio: More GC content, the higher Tm
- Length: Longer means higher Tm
- Degree of complementarity: Imperfect matches have lower Tm
Extrinsic factors that affect Tm
- Salt concentration: Increasing salt concentration increases Tm
- Organic solent concentration: Lowers Tm (reduces base stacking interactions)
- Hydrogen bonding compounds: Urea decreases Tm
- pH: Extreme pH decreases the Tm
(these do not need to be memorized, except for pH)
How is melting temperature approximated?
- 2 degrees Celsius for every AT
- 4 degrees Celsius for every GC
Chromatin
Organizes and packages DNA
Histones structure
- Fewer than 200 amino acids
- Many lysine and arginine residues
Nucleosome core particle
Wrapped DNA and histone core proteins
