Section 1 Flashcards
What type of polymers are DNA, RNA and proteins?
informational biopolymers
What is a informational Polymer?
Polymers: Covalent bond-linked chain of monomers
Informational: more than 1 kind of monomers, order of them IS the information
All monomers have common element (forms the backbone by covalent bonding of common element) + characteristic element
How many joining sites are needed for different polymers?
The joining sites on the common elements react together and bond
1 joining site = max 2 monomers in polymers
2 joining sites = linear polymers
3 joining sites = branched polymers (complex carbs)
*Informational polymers are LINEAR
Why are informational polymers always linear?
It is more efficient for handling and packaging (DNA has a huge length so need efficient use of space)
Most cases, have 2 ends but can be circular (but still unbranched) ex: genomic DNA of some bacteria and some virus such as E.coli
How does the joining sites configuration affect the growth?
Assymetry of the monomers → assymetry of the polymer
(2 different joining sites)
growth occurs only at one end/ unidirectional (right end by convention)
What are the 2 major information biopolymer monomer units?
nucleotides (nucleic acids, DNA, RNA) and amino acids (proteins)
DNA = longest chains, then RNA, then proteins
What is the structure of nucleotides?
Characteristic element: heterocyclic base (A, C, G, T) attached to the 1’ Carbon of the ring
Common element: pentose sugar phosphate
for DNA → Deoxyribose
for RNA → Ribose
What are the joining sites nucleotides?
5’ phosphate (ACID in “nucleic acid”, doubly Negatively charged on 2 O)
3’ OH (hydroxyl)
*We talk of 5’ end and 3’ end
Addition of monomers ALWAYS to the 3’ end.
What is the difference between DNA and RNA nucleotides?
The pentose sugar differs at C 2’
Ribose: OH attach to 2’ (RNA)
2-Deoxyribose: only H attached to 2’ (DNA)
*Absence of 2’-OH makes DNA much more resistant to chain cleavage by hydrolysis (more stable)
Which are the heterocyclic bases of nucleotides?
PURINES (A, G) = double cyclic rings (9C)
PYRIMIDINES (U (in RNA), T (in DNA), C) = Single ring (6C)
What is the difference between U and T?
There is a methyl on 5’ C in T, and not in U
*T in DNA instead of U makes chemical damage easier to repair
How do we call the bond between the heterocyclic base and the common element?
N-glycosidic bond (bonded to a sugar on the 1’C)
What is the name of the bonds between nucleotides?
Phosphodiester bond
Because phosphate is joined in an ester to the 5’OH and to the 3’OH
What are the monomers of proteins?
What are their structure?
Amino acids (Only L stereomers, not D)
Common element: H2N - CH - COOH
Joining sites: H2N (amino group/n-terminus) and COOH (carboxyl group)
Always adds onto Carboxyl group
Characteristic element: R side chain
Which are the different classes of amino acid side chains? (How many of each?)
20 different side chains total
- Hydrophobes (8)
- Hydrophilic (acidic and basic, 9)
- Special (3)
How do we call the link between adjacent amino acids?
peptide bond
O=C (plus rest of chains) - NH
COOH end is chained to just C=O when in chain
What are Nucleotide monomers named in the form of high-energy?
nucleoside triphosphate (NTPs) = chain of 3 phophates - pentose - base
The outer phosphates are kicked-out when NTP is incorporated in the chain (energizing group is on the 5’ end)
*Revoir ATP, CTP, GTP, UTP
What are amino acid monomers in the form of high-energy? (needed to incorporate the chain)
amino acyl-tRNA esters
high energy ester bond on the C-terminus!
tRNA bonded to the single bonded O of the COOH group
tRNA molecule is kicked-out when the next amino acid is incorporated at the end of a growing protein chain (they add to the c-terminus)
Can energized monomers join a growing chain by themselves?
No, reaction needs to be canalized by specific enzymes
Which biopolymer is associated with which template and enzyme?
B: DNA, T: DNA, E: DNA polymerase
B: RNA, T: DNA, E: RNA polymerase
B: protein, T: mRNA, E: ribosome
How are the 2 antiparallel DNA strands held together?
By Watson-Crick base pairs
2H bonds between A&T
3H bonds betwen C&G
*Bases are stacked on the inside
How are base-pairs «read» in interior of DNA?
By DNA-binding protein binding to major or minor grooves and identify specific sequence without separating the strands
Groove = space between curls of the backbone?
How is strand separation called? What is used for?
It is called melting or denaturation
Done by breaking individually weak H-bonds
When they re-associate = renaturation
Important for replication and transcription
What is Tm? How does the composition of DNA affects it?
Temperature at which 1/2 of DNA is melted
Depends on composition
Higher G-C proportion = higher Tm bc more H-bonds, so more energy needed to separe the strands
Why is it important that DNA can bend?
Important in DNA-protein interaction and in folding DNA into compact structures
Can bend easily bc no H-bonds alond the backbone
Which protein is responsible for bending DNA?
TATA box-binding protein
By what chain of structure do gene develop to generate organisms?
DNA —> RNA —> protein (def of Physiology)
What is the definition of replication?
Making a perfect copy of DNA
DNA —> DNA
What is transcription?
Rewriting in a different nucleotide font (deoxyribose = DNA font, ribose = RNA font)
DNA —> RNA
What is translation?
rewriting in a different language (nucleotide —> amino acid)
for protein synthesis (mRNA —> Protein)
What type of molecule are RNA polymerase and DNA polymerase?
What is the composition of ribosomes?
RNA pol and DNA pol: proteins
ribosomes: protein + RNA
How does the process of Transcription work?
Direct interaction of template with rNTP (nucleoside triphosphate)
Base waits for perfect Watson-Crick base pair nucleotide to attach to the specific base by H-bond
When right Watson-Crick base pair attached by H-bond, Polymerization happens
Polymerization: 3’-OH attacks alpha phosphate, beta and gamma diphosphate are dropped from rNTP
What is the transcription bubble? How the Transcription work?
RNA polymerase causes helicase (local unwinding of duplex DNA) —> exposes template DNA strand
Transcription bubble is the local unwond part of DNA
Unwoumded strand = template strand
Transcription bubble moves UNIDIRECTIONALLY along DNA with RNA polymerase
After transcription, re-forming of the duplex behind polymerase, «kicks out» the newly-synthesized RNA strands
How do the starting site and stop site of RNA polymerase work?
Sites are on the template strand
Starting: promotors (specific DNA sequences facilitate the intial binding of RNA polymerase to DNA
Stopping: Certain DNA sequences destabilize the attachement of RNA polymerase to the DNA so it falls off and releases RNA chain
What is helicase?
Helicase is the process of unwinding DNA duplex locally to expose template
What direction is the new strand synthesized? (on template and growing chain)
Addition to the 3’-end of the growing chain
Template read from 3’ to 5’ bc anti-parallel
By direct interaction (Watson-Crick base pairing)
What are the differences between DNA transcription anfd DNA replication?
Tr monomers = rNTP, Rep monomers = dNTP (ribose and deoxyribose)
Transcription: Start and stop sites on template
Replication: Start sites (origins), but no stop sites
Transcription: new strand (RNA) separates from template
Replication: new strand (DNA) never separates from template
Transcription: Only 1 strand is a template
Replication: 2 strands independently serve as templates
How is called protein synthesis?
Translation
1 language (nucleotides) to another (amino acids)