KH 01 Flashcards
What are 3 informational biopolymers?
DNA, RNA and protein
What is a polymer?
A covalent bond-linked chain of monomers
What is a sequence?
The order of the different kinds of monomer units in the polymer chain. It’s the information in an informational biopolymer. Different sequence = different information
In the case of DNA, RNA and protein, what would be the information?
The DNA sequence, the RNA sequence and the protein sequence
What are the 2 elements that form the common generic structure of informational biopolymers?
A common element (shared by all the different monomers) and a characteristic element (that makes each monomer different from the others)
What is the polymer backbone?
The common element of informational biopolymers “linked” by covalent bonding between monomers
What do the characteristic elements form that protrude form the polymer backbone?
Side-chains
If the monomer has one joining site in the common element, how many monomer units can be joined together?
Only two monomer units. It can only form a dimer (no other joining sites are exposed at the common element’s ends, there is no further chain growth)
If the monomer has two joining site in the common element, how many monomer units can be joined together?
Potentially infinite monomer units. We can make linear polymers (joining sites are exposed at the common element’s ends, further chain growth is possible)
If the monomer has three joining site in the common element, how many monomer units can be joined together?
Potentially infinite monomer units. We can make branched polymers.
Can cells make branched polymers?
Yes (ex: complex carbohydrates)
Can informational biopolymers make branched polymers?
No. Informational biopolymers are always linear and have two joining sites
Packaging and handling of (1) molecules may be more efficient than of (2) molecules
- Linear
- Branched
(this is a good thing for scientific progress because it would have been harder to determine the structures if they had been branched)
In most cases, how many ends do linear informational biopolymers have?
2 ends, but in some cases, the two ends can be joined, giving an unbranched circular molecule (ex: viruses)
Are the monomers in informational biopolymers symmetric?
No, they are asymmetric. The two joining sites are different (there is an “A” end and a “B” end. A can only join with B, B can only join with A)
Is the informational polymer symmetric?
Like the monomers, the polymer is asymmetric. The “A” end and the “B” end are also chemically distinct
Polymer growth is…?
Unidirectional. For DNA, RNA and protein, growth of the chain occurs only at one end
What is the convention when showing biopolymer representations on a sheet of paper and depicting polymer growth?
Polymer chain growth is depicted in the rightward direction. New monomers are added at the right end
What is the typical chain length of DNA?
About 1000 to 100 million nucleotides
What is the typical chain length of RNA?
About 20 to 10 000 nucleotides
What are the nucleic acids’ (DNA, RNA) monomers?
Nucleotides
What are the proteins’ monomers?
Amino acids
What is the typical chain length of protein?
About 100 to 1000 amino acids
What are the nucleotides’ polymers?
Nucleic acids
What are the amino acids’ polymers?
Protein
What is the characteristic element in nucleotides?
A heterocyclic base (ex: adenine)
What is the common element that form the polymer backbone in nucleotides?
A pentose sugar phosphate (ex: ribose)
What are the 2 joining sites on the nucleotide’s common element?
The 5’ phosphate (the acid in “nucleic acid”, has a negative charge) and the 3’ hydroxyl (OH)
Nucleic acid polymer growth is always by addition of monomers to which end?
The 3’ end
What charge do nucleic acids have?
A strong negative charge
The monomer polarity is reflected in the polymer, so we speak of the ___ end and the ___ end of a nucleic acid chain.
5’ end, 3’ end
What is the pentose sugar phosphate found in DNA?
Deoxyribose
What is the pentose sugar phosphate found in RNA?
Ribose
What is deoxyribose missing compared to ribose?
The 2’ hydroxyl (OH)
Why does DNA have a greater stability than RNA?
Because DNA’s deoxyribose is missing the 2’ - OH, which makes it much more resistant to chain cleavage by hydrolysis (more stable in water)
What is the name of the bond that links the pentose sugar phosphate to the heterocyclic base?
The N-glycosidic bond
What are the 2 purines?
Adenine and Guanine
What are the 3 pyrimidines?
Uracil, Thymine and Cytosine
Which pyrimidine is only found in RNA?
Uracil
Which pyrimidine is only found in DNA?
Thymine
What is the advantage of having thymine instead of uracil in DNA?
Thymine makes some chemical damage easier to repair
Between purines and pyrimidines, which contain a pair of fused rings?
Purines
Between purines and pyrimidines, which contain only a single ring?
Pyrimidines
What is the bond between adjacent nucleotides?
A phosphodiester bond (diester because the phosphate is joined in an ester linkage to the 5’ OH of the downstream nucleotide and in another ester linkage to the 3’ OH of the upstream nucleotide)
What is the characteristic element in amino acids?
The amino acid side chain (R)
What is the common element that forms the polymer backbone in amino acids?
The alpha carbon liked to a COOH (carboxyl) group and a NH2 (amino group)
What stereoisomers of amino acids are used in protein synthesis?
The L stereoisomers (not the D)
What are the 2 joining sites on the amino acid’s common element?
The amino (NH2) group and the carboxyl (COOH) group
The monomer polarity is reflected in the polymer, so we speak of the _____ and the _____ end of a protein.
amino terminus, carboxyl terminus / amino end, carboxyl end
Protein polymer growth is always by addition of monomers to which end?
The carboxyl (COOH) end
How many amino acid side chains are there?
20
What are the main 3 classes of amino acids?
Hydrophobic (8 amino acids), hydrophilic (9 amino acids), and special (3 amino acids). Their chemical properties define them.
What is the bond between adjacent amino acids?
A peptide bond
How do the nucleic acids’ monomers have to be in order to be incorporated into the growing polymer chain?
“Energized”. They have to be in the form of high-energy nucleoside triphosphates (NTPs)
What happens when the monomers are in the form of nucleoside triphosphates (NTPs) and are about to be incorporated into the growing polymer chain?
The outer 2 phosphates are “kicked out”
How do the proteins’ monomers have to be in order to be incorporated into the growing polymer chain?
“Energized”. They have to be in the form of high-energy amino acyl-tRNA esters
What happens when the monomers are in the form of amino acyl-tRNA esters and are about to be incorporated into the growing polymer chain?
The tRNA molecule is “kicked out”
Can energized monomers join a growing chain by themselves?
No, the linkage reaction is catalyzed by a specific enzyme
What are the respective templates of the biopolymers DNA, RNA and protein?
DNA, DNA, mRNA
What are the respective enzymes of the biopolymers DNA, RNA and protein?
DNA polymerase, RNA polymerase, ribosome
The enzyme is associated with a _____ biopolymer that directs the enzyme to incorporate the correct flavor monomer.
template
How are DNA strands held together?
By H-bonds between complementary bases (Watson-Crick base pairs)
DNA is generally in a ____-handed helix named “B” DNA
right
Are the two DNA strands parallel or antiparallel?
Antiparallel
RNA and protein usually exist as single polymer chains, but how does DNA exist?
As double-stranded, duplex DNA
What can DNA-binding proteins do?
Make contact with base-pairs at the major or minor grooves and identify specific sequences without having to separate the strands
How are sugar-phosphate backbones and base-pairs placed in the DNA structure?
Sugar-phosphate backbones are on the outside and base-pairs are stacked on the inside
How do we call DNA strand separation?
Denaturation
How does DNA strand separation occur?
By breaking the H-bonds that link the DNA strands together (ex: by heat, melting)
What is renaturation?
Denatured DNA strands can accurately re-form base-paired duplex DNA by formation of H-bonds between complementary base-pair sequences
DNA denaturation and renaturation are important during which biological processes?
DNA replication and transcription. They are also exploited in many experimental techniques in molecular biology and genomics
What do we call the temperature at which the DNA is one-half melted?
The Tm
What does the Tm depend on?
Its base composition
DNA with a higher proportion of ___ base-pairs has a higher Tm (it takes a higher temperature to have the DNA one-half melted)
G-C
Why does it take less energy to separate an A-T base-pair than a C-G base-pair?
Because A-T base-pairs have 2 H-bonds whereas C-G base-pairs have 3.
Why is DNA like spaghetti?
Because it can bend about its long axis. This is an important property in DNA-protein interactions and in the folding of DNA into compact condensed structures
Why do we call the link between adjacent nucleotides a phosphoDIESTER bond?
Because the phosphate is joined in an ester linkage to the 5’ OH of the downstream nucleotide and in another ester linkage to the 3’ OH of the upstream nucleotide
What does upstream mean in biology?
The opposite direction in which a template DNA strand is transcribed
What does downstream mean in biology?
The direction in which a template DNA strand is transcribed
What do nucleoside triphosphate (NTPs) include in DNA?
Adenosine triphosphate (ATP), cytidine triphosphate (CTP), guanosine triphosphate (GTP) and uridine triphosphate (UTP)
What do nucleoside triphosphate (NTPs) include in RNA?
Deoxyadenosine triphosphate (ATP), deoxycytidine triphosphate (CTP), deoxyguanosine triphosphate (GTP) and deoxyuridine triphosphate (UTP)
