Nucleic Acids and DNA Flashcards
What are some of the cellular activities performed by proteins?
Catalyze metabolic reactions, build cellular structures, and send/receive signals.
What is the function of the building blocks of DNA?
Storage of genetic information
What is the function of the building blocks of RNA?
carrier of genetic information + structural components of tRNA, ribosomes, spliceosomes, etc.
What are the functions of energy metabolism?
ATP, GTP, and perform biochemical work
What is the function of cellular signalling?
second messengers in the form of cAMP etc
What is the linear polymer of deoxyribonucleotides?
DNA
What is the linear polymer of ribonucleotides?
RNA
What are nucleotides composed of?
phosphate, pentose sugar (5 carbon) and nitrogenous base
What is the difference between nucleotides and nucleoside?
Nucleotides consist of phosphates, sugar, and base while nucleoside only has sugar and base (i.e. no phosphate group).
What makes up an adenosine?
Ribose and adenine
What are some differences between pyrimidine and purine?
Pyrimidines have single ring and smaller structure. Purines have double ring and larger structure.
What are the five types of nitrogenous bases? What are considered pyrimidines and purines?
Thymine, cytosine and uracil are types of pyrimidines. Adenine and guanine are types of purines.
What are two types of pentose sugars? Differentiate between the two.
Ribose has OH group at #2 carbon and is a building block of Ribonucleic acid. While 2-deoxyribose lacks OH group at the #2 carbon (only has H) and is a building block of deoxyribonucleic acid.
What is the difference between pyrimidines and purines in terms of the connection between nitrogen and carbon of ribose sugar.
In pyrimidines, nitrogen 1 is connected to the 1’ carbon of the ribose sugar. In purines, nitrogen 9 is connected to the 1’ carbon of the ribose sugar.
What forms when a sugar phosphate is added to a base such as guanine?
Nucleotide
Where does nucleotides attach on the structure of the ribose (sugar)?
Through 5’ and 3’ carbons
How does polymerization occur?
Polymerization occurs via formation of 3’ to 5’ phosphodiester bonds.
In what direction does DNA get synthesized?
In the 5’ -> 3’ direction
What is an enzyme catalyzed condensation reaction?
When 3’ carbon of the first nucleotide attacks the 5’ carbon of the second nucelotide.
How does nucleotides polymerize?
Nucleotide1 is about to polymerize nucleotide 2. Then 3’ OH of the nucleotide 1 attacks the 5’ phosphates of nucleotide 2. Afterwards, 3’-5’ phosphodiester bond connects nucleotide 1 and 2. Then when Nucleotide 3 is about to polymerize, 3’ OH of the nucleotide 2 attacks the phosphates of nucleotide 3. Therefore, nucleotide 3 is now incorporated into the polymerize nucleotides.
Where does incoming nucleotides get added?
Incoming nucleotides always gets added to the 3’ end of the already existing poly-nucleotide.
What is the alternating chains of sugar and phosphate called?
Sugar-phosphate backbone.
What is true about the 5’ end of the linear polynucleotide?
They will always have 3 phosphates attached.
How are nitrogenous bases forms a pair?
Bia hydrogen bonds
What are the Watson Crick base pairing?
Adenine pairs with thymine (or uracil), guanine pairs with a cytosine, and purine pairs with pyrimidines.
What holds the two strands of DNA together,i.e., what makes double stranded DNA?
Base-pairing of nitrogenous bases between two strands of DNA holds the strands together.
How are the two strands of DNA held and why is that?
Two strands of DNA are held antiparallel to each other with respect to their 5’-3’ polarity.
What is on the outside and inside of a double stranded DNA?
Sugar-phosphate backbone on the outside and nitrogenous bases inside.
What is the distance between the two C1’ carbons in a base-pair?
10.85 A or 1.085 nm
What hold DNA strands together?
Hydrogen bonds
What is the difference between C-G pair and A-T pair?
C-G pair has one more hydrogen bond compared to A-T pair, therefore, it takes more energy to break apart a CG pair.
What is denaturation?
It is when hydrogen bonds break with heat
What is true about the species living in extremely high temperatures in terms of % GC of genome?
They may have higher % GC
An organism’s genome is 15% Adenine. What is the % Guanine fro this organism?
15% A = 15% T, so AT = 30%
100% - 30% AT = 70% GC
70% GC / 2 = 35% G, 35% C
What is used as a template to ‘copy’ DNA?
A single strand of parental DNA
In what direction should the nucleotide sequence be written?
5’ to 3’
What did Levene deciphered about the DNA structure?
DNA contains equal proportions of deoxyribose, nitrogenous bases, and phosphates
What did Chargaff decipher about the DNA structure?
number of adenine = number of thymine, number of guanine = number of cytosine
What did Franklin and Wilkins decipher about the DNA strcuture?
X-ray diffraction shows DNA structure is double helix
What did Watson and Crick decipher about the DNA structure?
Deduced the double helical structure of DNA
What is the distance per one turn of double helix? What is the distance between adjacent base-pairs? How many bases are there per turn?
3.4 nm is the distance per one turn, 0.34 nm is the distance between adjacent pairs, therefore, there are 10 bases per turn of double helix.
What are the 3 structural variants of double stranded DNA?
A, B, and Z
Describe the structure of A-DNA
- right handed
- short and broad
- <75% humidity
Describe the structure of B-DNA
- right handed
- longer and thinner
- physiological conditions
Describe the structure of Z-DNA
- left handed
- elongated and slim
- function unknown
What angle does a major groove have? How about minor groove?
257, 103
At what angle does DNA rotate while the next base pair gets attached on top?
36 degrees
Where are the different ‘shapes’ of nucleotides exposed?
On the minor and major grooves
What is the purpose of the major and minor grooves for proteins?
They become binding points for proteins
How is the chemical composition of RNA similar to DNA?
Sugar-phosphate backbone with nitrogenous bases attached to sugars
What are the differences of RNA compared to DNA?
- Pyrimidine uracil instead of thymine
- Sugar is ribose, not deoxyribose; the sugar has a OH group on the 2’ carbon
- Exists as a single stranded molecule with extensive secondary structures
- Not for storage
- Some RNA has catalytic activity
How are secondary structures formed using RNA?
When bases within the same molecule of single stranded RNA base-pair with one another
