test 3 biochem Flashcards
What are the function for nucleotides?
E for metabolism (ATP)
Enzyme cofactors (NAD+)
Signal transduction (cAMP)
Functions for nucleic acids?
Storage of genetic info (DNA)
Transmission of genetic info (mRNA)
processing of genetic info (ribozymes)
Protein synthesis (tRNA and rRNA)
What makes up a nucleotide?
-Nitrogeneous base ( AGCT in DNA, AUGC in RNA).
-A Pentose Sugar (deroxyribose in DNA and ribose in RNA).
-A phosphate Group.
differences between Purines and Pyrimidines
Purines: Larger bicyclic, always bind to pyrimidine. (A and G are purines)
Pyrimidines: Smaller. (DNA: C, T mostly) (RNA: C, U mostly)
How is the N - beta Glycosidic bond formed?
Why and what’s the purpose of it?
When the anomeric carbon (C1) of a sugar molecule (ribose or deoxyribose) reacts with a N atom (N1 in pyrimidines or N9 in purines) of a nitrogenous base.
This is crucial for forming structures like those in DNA and RNA.
What are the minor nucleosides in DNA?
Inosine ( made by de - aminating adenosine), provides richer genetic code
sometimes found in the wobble position of the anti codon in tRNA.
What is a phosphodiester bond?
A covalent linkage between the 5’ phosphate group of one nucleotide and the hydroxyl group (OH) attached to the 3’ carbon of the deoxyribose sugar in an adjacent nucleotide forming the sugar phosphate backbone of DNA and RNA.
Why is RNA readily hydrolyzed in alkaline conditions but not DNA?
DNA is relatively stable in alkaline conditions because it lacks the 2’-hydroxyl group present on the ribose sugar in RNA, which is crucial for the base-catalyzed hydrolysis that RNA undergoes.
RNA’s sugar, ribose, has a hydroxyl group (OH) at the 2’ position, making it susceptible to nucleophilic attack by the negatively charged oxygen from the hydroxyl group,
3 dimensional forms of DNA
A form (low water environments, not found in vivo)
B form (normal conformation in cells, watson and crick structure)
Z form (found occasionally in vivo, left handed double helix!, sequence dependent)
what is mRNA?
The code carrier for the sequence of proteins.
- It is synthesized using DNA template.
- contains ribose instead of deoxyribose.
- contains uracil instead of thymine.
- One mRNA may code for more than one protein.
- Together with tRNA transfers genetic information from DNA to proteins.
- They are usually longer than 3x the protein length.
double stranded RNA (dsRNA)
They are usually short and highly ordered
- follows 5’ - 3’ orientation.
- predominate but complimentarity where it is found.
- Palindromic sequences drive tRNA 2 structure.
DNA denaturation
The process where the double - stranded structure of DNA unwinds and separates into two single strands due to the breaking of hydrogen bonds between the base pairs.
- covalent bonds remain intact
- genetic code remain intact
- H Bonds are broken
- two strands separate
- Base stacking is lost
- UV absorbance increases (Hyperchromic effect)
Free nucleotides > ssDNA > dsDNA
- UV absorbance increases (Hyperchromic effect)
Denaturation can be induced by high temperature, or change in pH.
Denaturation may be reversible: annealing.
DNA denaturation is commonly monitored by UV spectrophotometry at 260 nm.
3 fundamental rules of replication
- it is semi conservative.
- begins at an origin and proceeds (usually) bidirectionally.
- Synthesis of a new DNA occurs in the 5’ - 3’ direction and is semidiscontinuous.
The Meselson - Stahl Experiment?
write in later. This is slide 14, remember that…
Potassium cyanide is a poison which combines with cytochrome c oxidasestart subscript, 3, end subscript to prevent binding of oxygen to the enzyme without altering the Km of the reaction. Which type of inhibition does this represent?
Competitive inhibition
Noncompetitive inhibition
Uncompetetive inhibition
Irreversible inhibition
Non competitive inhibition
Allosteric enzymes consist of multiple polypeptide chains. True or false
True
A recently diagnosed hypertensive patient has been prescribed an ACE inhibitor(Angiotensin convertase inhibitor) which is known to act by increasing the Km. No effect on Vmax is noticeable. What is the possible mechanism of inhibition of this drug?
Competitive inhibition
The activity of many enzymes, membrane transporters, and many other proteins can be quicky activated or inactivated by phosphorilation of specific amino acid residues. This regulation is called…
Covalent Modification
The compound that consists of ribose linked by an N-glycosidic bond to N-9 of adenine is:
A) a deoxyribonucleoside.
B) a purine nucleotide.
C) a pyrimidine nucleotide.
D) adenosine monophosphate.
E) adenosine
Adenosine
What is the difference between a ribonucleotide and a deoxyribonucleotide?
a deoxyribonucleotide has an —H instead of an —OH at C-2
(ribonucleotides contain ribose sugar, while deoxyribonucleotides contain deoxyribose, which lacks an oxygen atom at the 2’ position compared to ribose)
Tell me about Pentoses
Pentoses are always in the -furanose form. (Both in RNA and in DNA).
The phosphodiester bonds that link adjacent nucleotides in both RNA and DNA
A) always link A with T and G with C.
B) are susceptible to alkaline hydrolysis.
C) are uncharged at neutral pH.
D) form between the planar rings of adjacent bases.
E) join the 3’ hydroxyl of one nucleotide to the 5’ hydroxyl of the next.
E
The Meselson-Stahl experiment established that
DNA synthesis in coli proceeds by a semiconservative mechanism
What is an okazaki fragment?
segment of DNA that is an intermediate in the synthesis of the lagging strand
Which one of the following statements about enzymes that interact with DNA is true?
Many DNA polymerases have a proofreading 5’ to3’
coli DNA polymerase I is unusual in that it possesses only a 5’ ® 3’ exonucleolytic activity.
Endonucleases degrade circular but not linear DNA molecules.
Exonucleases degrade DNA at a free end.
Primases synthesize a short stretch of DNA to prime further synthesis.
Exonucleases degrade DNA at a free end.
E. Coli DNA poly III
is the principal DNA poly in chromosomal DNA replication
During the DNA replication, DNA Poly III synthesizes the leading strand and DNA poly I synthesizes the lagging strand
TRUE OR FALSE?
False. During DNA replication, DNA Poly III synthesizes BOTH the leading and lagging strands.
