Struc of Nucleic Acids Flashcards
What are the functions of nucleotide?
- Energy for metabolism (Stoffwechsel) (ATP)
- Enzyme cofactors (NAD+)
- Signal transduction (cAMP)
What are the functions of nucleic acid?
- Storage of genetic info (DNA)
- Transmission of genetic info (mRNA)
- Processing of genetic information (ribozymes)
- Protein synthesis (tRNA and rRNA)
What is metabolism?
-bezeichnet man die gesamten chemischen und physikalischen Vorgänge der Umwandlung chemischer Stoffe bzw. Substrate (z. B. Nahrungsmittel und Sauerstoff) in Zwischenprodukte (Metaboliten) und Endprodukte im Organismus von Lebewesen
What are Enzyme?
- macromolecular biological catalysts
- > accelerate chemical reactions
- The molecules upon which enzymes may act are called substrates
What is signal transduction?
- process of transferring a signal throughout an organism, especially across or through a cell
- Signal transduction relies on proteins known as receptors, which wait for a chemical, physical, or electrical signal
How is a nucleotide structured?
- Nitrogeneous base (organischen Base (Purin oder Pyrimidinbase) mit einem heterozyklischen Ring oder Ringsystem)
- Pentose (a sugar)
- Phosphate
What is a heterocyclic compound or ring structure?
-a cyclic compound that has atoms of at least two different elements as members of its ring(s)
How is a nucleoside structured?
- Nitrogeneous base
- Pentose
How is a nucleobase structured?
-Nitrogeneous base
How is the phosphate group charged at neutral pH?
Where is it attached?
-Negatively charged at neutral pH
-Typically attached to 5’ position
-Nucleic acids are built using 5’-triphosphates
ATP, GTP, TTP, CTP
-Nucleic acids contain one phosphate moiety per nucleotide
-May be attached to other positions (5’; 2’; 3’; 2’, 3’)
Which forms does pentose have in nucleotides?
- β-D-ribofuranose in RNA
- β-2’-deoxy-D-ribofuranose in DNA (deoxy means without O in 2 carbon)
- Different puckered conformations of the sugar ring are possible
Give some facts about Nucleobases (derivates, molecule, structure, absorption)
- Derivatives of pyrimidine or purine
- Nitrogen-containing heteroaromatic (O, N, S) molecules
- Planar or almost planar structures (liegen auf einer ebene)
- Absorb UV light around 250–270 nm
Name some base which are counted as pyrimidine bases+ name pKa
- Cytosine is found in both DNA and RNA
- Thymine is found only in DNA
- Uracil is found only in RNA
- All are good H-bond donors and acceptors
- Cytosine pKa at N3 is 4.5
- Thymine pKa at N3 is 9.5
- Neutral molecules at pH 7
Draw the structure of cytosine, thymine and uracil
.
Name some base which are counted as purine bases+ name pKa
- Adenine and guanine are found in both RNA and DNA
- Also good H-bond donors and acceptors
- Adenine pKa at N1 is 3.8
- Guanine pKa at N7 is 2.4
- Neutral molecules at pH 7
Draw the structure of adenine and guanine
.
Where is the N-glycosidic bond attached in nucleotides?
-n nucleotides the pentose (Zucker) ring is attached to the nucleobase via N-glycosidic bond
-The bond is formed:
to position N1 (bottom right) in pyrimidines
to position N9 (bottom) in purines
-This bond is quite stable toward hydrolysis, especially in pyrimidines
-Bond cleavage is catalyzed by acid
The UV absorption of Nucleobase is due to? (danger of genetic material?)
- Absorption of UV light at 250–270 nm is due to π → π* electronic transitions
- Excited states of common nucleobases decay rapidly via radiationless transitions
- Effective photoprotection of genetic material
- No fluorescence (spontaneous emission) from nucleic acids
Give the nomenclature of nucleotide and Nucleic Acid
- Nucleoside, Nucleotide, Nucleic acid
-Purine:
-Adenine: (Deoxy)Adenosine, (Deoxy)Adenylate, (DNA)RNA
-Guanine: (Deoxy)Guanosine,
(Deoxy)Guanylate, (DNA)RNA
-Pyrimidines:
-Cytosine: (Deoxy)Cytidine, (Deoxy)Cytidylate, (DNA)RNA
-Thymine: Thymidine/(Deoxythymidine), (Deoxy)Thymidylate, DNA
-Uracil: Uridine, Uridylate, RNA
———
ribothymidine is used to describe its unusual occurrence in RNA
Give structure, name and symbol of:
- Deoxyadenylate
- Deoxyguanylate
- Deoxythymidylate
- Deoxycytidylate
+draw them
-Deoxyadenylate (deoxyadenosine 5’- monophosphate) (A, dA, dAMP)
-Deoxyguanylate (deoxyguanosine 5’- monophosphate) (G, dG, dGMP)
-Deoxythymidylate (Deoxythymidine
5’- monophosphate) (T, dT, dTMP)
–Deoxycytidylate (deoxycytidine 5’- monophosphate) (C, dC, dCMP)
Give structure, name and symbol of (Ribonucleotide):
- adenylate
- guanylate
- uridylate
- cytidylate
+draw them
- adenylate (adenosine 5’- monophosphate) (A,AMP)
- guanylate (guanosine 5’- monophosphate) (G, GMP)
- Uridylate (uridine) (U, UMP)
- Cytidylate (cytidine 5’- monophosphate) (C, CMP)
What is use of epigenetic marker in prokaryotes and eukaryotes?
- Way to mark own DNA so that cells can degrade foreign DNA (prokaryotes)
- Way to mark which genes should be active (eukaryotes)
Where is 5-Methylcytosine common? Where is N^6-Methyladenosine common?
- in eukaryotes, also found in bacteria
- in bacteria, not found in eukaryotes
Draw the structure of 5-Methycytidine, N^6-Methyladenosine, N^2-Methylguanosine, 5- Hydroxymethylcytidine
.
Backbone polynucleotides; stability, directionality,
-Covalent bonds formed via phosphodiester linkages negatively charged backbone -DNA backbone is fairly stable: Hydrolysis accelerated by enzymes (DNAse) -RNA backbone is unstable: In water, RNA lasts for a few years In cells, mRNA is degraded in few hours -directionality: 5’ end is different from 3’ end We read the sequence from 5’ to 3’
Linear polymers do not have?
-branching (verzweigungen) or cross-links (Querverbindungen)
Describe the mechanism of Base-catalyzed RNA Hydrolysis
- RNA hydrolysis occurs when the deprotonated 2’ OH of the ribose, acting as a nucleophile, attacks the adjacent phosphorus in the phosphodiester bond of the sugar-phosphate backbone of the RNA
- > phosphorus is bonded to five oxygen atoms
- ->The phosphorus then detaches from the oxygen connecting it to the adjacent sugar, resulting in ester cleavage of the RNA backbone
- This produces a 2’,3’-cyclic phosphate that can then yield either a 2’- or a 3’-nucleotide when hydrolyzed
Describe the hydrogen-bonding interactions
- Two bases can hydrogen bond to form a base pair
- For monomers, large number of base pairs is possible
- In polynucleotide, only few possibilities exist
- A pairs with T
- C pairs with G
- Purine pairs with pyrimidine
What can you say about the difference between DNA strands?
-Two chains differ in sequence
(sequence is read from 5’ to 3’)
-Two chains are complementary
-Two chains run antiparallel
Give a general description of RNA
- Code Carrier for the Sequence of Proteins
- 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 transfer RNA (tRNA) transfers genetic information from DNA to proteins
What happens with the bodes in DNA Denaturation? How can it be induced?
- Covalent bonds remain intact
- Genetic code remains intact
- Hydrogen bonds are broken
- Two strands separate
- Base stacking is lost
- > UV absorbance increases
- induced by high temperature, or change in pH
- -> denaturation may be reversible : annealing
Describe there thermal DNA Denaturation (Melting)
- DNA exists as double helix at normal temperatures
- Two DNA strands dissociate at elevated temperatures
- Two strands re-anneal when temperature is lowered
- The reversible thermal denaturation and annealing form basis for the polymerase chain reaction (
Name factors affecting DNA Denaturation
- The midpoint of melting (Tm) depends on base composition
- High CG increases Tm
- Tm depends on DNA length
- Longer DNA has higher Tm
- Important for short DNA
- Tm depends on pH and ionic strength
- High salt increases Tm
Why is the Denaturation of large DNA molecules
is not uniform ?
-AT rich regions melt at a lower temperature than GC-rich regions
