Biochem Exam 4 (Nucleotides + DNA metabolism)

What are the two types of nitrogenous bases in nucleic acids?

pyrimidine, purine

How are pyrimidine's numbered?

clockwise

How are purines numbered?

counter clockwise in the big ring, clockwise in the small ring

What are the purines?

adenine, guanine

What specific organic structures does adenine have?

amino group

How many rings do purines have?

2

What specific organic structures does guanine have?

keto group, amino group

How many rings do pyrimidines have?

1

What are the pyrimidines?

cytosine, thymine(DNA), Uracil (RNA)

What organic groups does cytosine have?

keto, amino

What organic groups does uracil have?

2 keto groups

What organic groups does thymine have?

2 keto groups, methyl group

Do nucleosides have bases, pentose, or phosphoric acid?

yes, yes, no

Do nucleotides have bases, pentose, or phosphoric acid?

yes, yes, yes

What is pentose in nucleotides?

central structure for which nucleotide will attach

What type of bond is formed between pentose and nucleotide?

B N-glycosidic bond

Where is the base connected to the pentose in a nucleotide?

connected to the 1' hydroxyl of the sugar

How are phosphates linked for nucleotides?

phosphodiester bond

What is NTP?

nucleotide triphosphate

What are the nucleotides in DNA?

adenine, guanine, cytosine, thymine

What are the nucleotides found in RNA?

adenine, cytosine, guanine, uracil

What function do the major nucleotides dATP, dGTP, dCTP, and (d) TTP do?

DNA structure

What function do the major nucleotides ATP, GTP, CTP, and UTP do?

RNA structure

What function do the major nucleotides ATP and GTP do?

energy carriers

What function do the major nucleotides cyclic AMP and cyclic GMP do?

second messengers/sigaling molecules

What function do the major nucleotides NAD/NADH, NADP/NADPH, FAD/FADH2, CoA do?

coenzymes/cofactors, electron carriers

What function does the minor nucleotide 5' diphospho-3' diphospho-guanosine (ppGpp) do?

protects mRNA

What function does the minor nucleotide 5-methyl cytidine (5-Me-C) do?

regulates gene expression

What function does the minor nucleotide 5-hydroxymethyl cytidine (5-HO-Me-C) do?

regulates gene expression

What function does the minor nucleotide methyl guanosine (Me-G) do?

tRNA structure and function

What function does the minor nucleotide Pseudouridine (Psi) do?

tRNA structure and function

What function does the minor nucleotide Thiouridine do?

tRNA structure and function

What function does the minor nucleotide Inosine (I) do?

tRNA structure and function

How are two nucleotides covalently linked together and what type of reaction mechanism is this?

5' phosphate of one nucleotide forms a phosphodiester bond with the 3' hydroxyl group of another; condensation

What is the polarity of a nucleic acid strand?

5' end to 3' end

What is an oligonucleotide?

2 to ~100 nt

What is a polynucleotide?

> ~100 nt

What are chargaff's 4 rules?

DNA base composition varies between species, species DNA base composition from various tissue is the same, species DNA base composition doesn't change with age, nutritional state or environment, A+G = T+C

How many strands is a DNA molecule, how are they, and how do they run?

2; complementary; antiparallel

How are strands in a DNA molecule held together?

H bonds

What is the form of a DNA molecule?

right handed a-helical structure

What does A pair with in DNA?

T

What does G pair with in DNA?

C

How many H bonds are formed between A-T?

2

How many H bonds are formed between G-C?

3

What must the distance between 2 base pairs be for an H bond to form?

equal or less than 3 Angstroms

What is the B-form of DNA and where is this seen?

when in aqueous solution; in vivo

What is the A form of DNA and where is this seen?

when water content is < 75%; in vitro

What is the Z form of DNA and where is this seen and involved in?

a left-handed helix; in vivo; regulation of gene expression

How is the A form of DNA different from the B form?

shrunk down, same number but shorter

What is Palindrome in nucleic acid structure?

repeats of each other in the 5'-3' direction

What is mirror repeat in nucleic acid structure?

reading 5'-3' the same sequence appears on the same DNA strand but as a mirror image of that

What do Palidrome structures lead to in DNA and RNA for structure and what does it depend on respectively?

hairpin and cruciform DNA; single or double strand

What does a mirror repeat form?

hairpin structure

What does lowering of ionic strength of double-stranded DNA solution cause?

denaturation and strand separation

Is DNA denaturation reversible?

yes

When ionic strength of double stranded DNA is readjusted to original, what can this cause?

renaturation to original structure

As temperature increases, how does this affect denaturation % for DNA and how?

increase, H bonds melt

Does the temp required to melt DNA from different species differ?

yes

How does renaturation occur for DNA denatured by high temps?

bring temp back to physiological temp

What are applications of DNA denaturation?

research, clinical, forensic

How does the DNA/RNA mutation of deamination effect the structure of the molecule?

H bond is lost

How does the DNA/RNA mutation of depurination effect the structure of the molecule?

N-glycosydic bond susceptible to hydrolysis, creates hole in the DNA sequence

How mutations that come from UV rays effect the chemical structure of DNA?

forming dimers between Ts

What could a Ts dimer caused by UV light do to DNA?

cause kink or bulge in DNA molecule

What are some different pharmacological agents that are synthetic nucleotides or nucleosides?

ddNTP, AZT, ddI, ddC

What does DideoxyNTP (ddNTP) do and what is it used to treat?

removal of 3' hydroxyl group from deoxyribose so molecule can't form phosphodiester bond, chain terminator; viral infection

What does Azidothymidine (AZT) do and what is it?

no hydroxyl on 3' so no bonds are formed; competitive inhibitor of the viral enzymes that synthesize DNA

What is the basic chemistry of all the synthetic nucleotide or nucleoside analytical/pharmacological agents?

no OH group on 3'

What are the distinguishing features of rRNA?

large size (28S, 18S, 5S); very stable, secondary structure

What is the cellular location and function of rRNA?

ribosomes; structural component, protein synthesis

What are distinguishing features about mRNA?

varying size, number, and stability

Where is mRNA located and what is the function?

nucleus, cytoplasm, mitochondria; carrier of genetic message

What are distinguishing factors of tRNA?

at least 23 types/cell, many minor bases, unique structure

What is the location of tRNA and its function?

cytoplasm, mitochondria; protein synthesis

What are distinguishing factors of small nuclear RNA?

varying size, number, and stability

What is the location and function of small nuclear RNA?

ribosomes, nucleus, cytoplasm; structural component, protein synthesis, gene regulation

What are distinguishable factors for microRNA?

20-30 nt long; varying stability

What is the location and function of microRNA?

nucleus, cytoplasm; gene regulation

How could RNA acquire a double stranded structure?

hydrogen bonding in regions of complementarity

What do complementarity breaks cause in double-stranded RNA?

loops and bulges

What is a RNA double-stranded loop?

two strands separate from each other

What does a double-stranded RNA structure provide and what is its function?

structural stability, regulatory function

What does de novo purine biosynthesis depend on?

pentose phosphate pathway

What is the enzyme that is important for converting Ribose 5-Phosphate into purines?

PRPP synthetase

What is the product of purine nucleotide synthesis and what does this act as?

Inosine monophosphate (IMP); parent compound for other purine nucleotides

What enzyme is necessary for purine nucleotide synthesis from IMP?

ribonucleotide reductase

What is ribonucleotide reductase?

control enzyme, control DNA synthesis; takes a ribose containing nucleotide and converts it into a deoxyribose containing nucleotide

What does Ribonucleotide reductase convert ADP into?

ADP --> dADP --> dATP

What are the starting materials for pyrimidine synthesis?

aspartate + carbamoyl phosphate

After the pyrimidine ring is formed, what enzyme is used to convert it to UMP?

PRPP

Once UMP is formed from the pyrimidine ring, what can UMP be converted to?

CMP

For deoxythymidine phosphate biosynthesis, what are CDP and UDP converted to respectively and what enzyme is used?

CDP--> dCDP, UDP--> dUDP; ribonucleotide reductase

For deoxythymidine phosphate biosynthesis, what are dCDP and dUDP converted to and using what enzyme?

dCDP --> dCTP, dUDP --> DUTP; nucleoside diphosphate kinase

For deoxythymidine phosphate biosynthesis, what are dCTP converted into and using what enzyme?

dCTP --> dUTP; deaminase

For deoxythymidine phosphate biosynthesis, what is dUTP converted to and using what enzyme?

dUTP --> dUMP; dUTPase

For deoxythymidine phosphate biosynthesis, what is dUMP converted to and using what enzyme?

dUMP --> dTMP; thymidylate synthase

How are ribonucleotide reductases activated and inactivated for conversion of ribonucleotides converted to deoxyribonucleotide?

ATP; dATP

What drug blocks the ribonucleotide reductase reaction and what type of drug is this?

hydroxyurea - anticancer

What does folic acid deficiency affect?

dTTP (TTP) synthesis