Moyzis Flashcards
Name the purines
Adenine and Guanine
About what mass of AA is used for protein synthesis in a day? For other molecules?
400 g/day; 30 g/day
Which nitrogenous bases have two rings?
Purine
Name the pyrimidines
Cytosine, Uracil, Thymine
Which nitrogenous bases have a single ring?
Pyrimidine
Which is more stable ribose or 2-deoxyribose?
2-deoxyribose
What are nucleosides?
Pentose sugar plus base
What is responsible for the negative charge associated with DNA?
Phosphate groups
How do we name nucleotides?
Ribonucleoside 5’-mono/di/triphosphate
E.g. Adenosine 5’-triphosphate
Nucleotides are?
Composed of a nitrogenous base, a pentose monosaccharide, and one/2/3 phosphate groups
T or F: Donated atoms of a nitrogenous base are added to a preformed ribose 5’-phosphate
T
Purine rings contain atoms donated from?
Formate, Glutamine (Amide groups), Aspartate, Glycine, and Carbon dioxide
What is the first step of purine synthesis?
Ribose 5-phosphate is made into 5-Phosphoribosyl-1-pyrophosphate (PRPP)
PRPP enzyme?
PRPP synthetase. Needs magnesium ion and ATP
How is PRPP synthetase regulated?
Positive: Inorganic phosphate
Negative: Purine ribonucleotides (end product inhibition)
What is PRPP made into?
5’-Phosphoribosylamine; made by Glutamine phosphoribosyl pryrophosphate amidotranferase; consumes Glutamine and Water Releasing Glutamate and Pyrophosphate. In presence of magnesium
What step is the commit step for purine synthesis?
PRPP to 5’-Phosphoribosylamine
What is the parent purine nucleotide?
Inosine monophosphate (takes 4 ATP to make)
How many ATP are required to make IMP?
4 ATP
What is the mechanism of sulfonamides?
Block synthesis of folic acid. Since purine synthesis requries THF (a folic acid derivative) as a coenzyme, the sulfa drugs inhibit this pathway. Doesnt harm human cells since we just eat folate
T or F: Humans can synthesize folic acid
F
What is the mechanism of methotrexate?
Structural analog to folic acid used in cancer. Interferes with nucleotide synthesis. Hurts healthy cells too like bone marrow, hair follicles, GI tract
What energy source is needed to make AMP?
GTP
What energy source is needed to make GMP?
ATP
What inhibits IMP to AMP pathway?
AMP levels
What inhibits IMP to GMP pathways?
GMP levels
What is mycophenolic acid?
A potent reversible inhibitor of IMP dehydrogenase which prevents GMP production (promising in graft rejection prevention). Deprives rapidly producing cells of a key nucleic acid
What is the function of base-specific nucleoside monophosphate kinases?
Converts AMP and ATP to ADP and back. Balances M,D,T forms
What does adenylate kinase do?
Balances AMP, ADP, and ATP levels
What are nucleoside diphosphate kinases?
Converts between di and tri forms only
What is the source of phosphate in the nucleoside phosphate conversions?
ATP almost exclusively due to high levels
T or F: The pyrimidine ring is made before being attached to the ribose 5-phosphate
T; this is distinct to the piecewise method for purines
What are the sources for the pyrimidine ring?
Glutamine, carbon dioxide, and aspartic acid
What is the first step of pyrimidine synthesis?
Formation of carbamoyl phosphate from Glutamine, HCO3-, and 2 ATP via Carabmoyl phosphate synthetase II to produce carabmoyl phosphate, glutamate, 2 ADP and 1 Pi
What enzyme makes carbamoyl phosphate?
Carbamoyl phosphate synthetase
What regulates carabmoyl phosphate synthetase?
Negative: UTP
Positive: ATP and PRPP
Carbamoyl phosphate is converted to what first ring form?
Dihydroorotate
T or F: The first three steps of pyrmidine synthesis is catalyzed by three different domains on the same polypeptide
T
T or F: Enzymes in pyrimidine synthesis are from mitochondria genes
T
Dihydroorotate is made into?
Orotate
Orotate is made into?
OMP via PRPP
OMP is made into?
UMP (Uridine 5’-monophosphate)
T or F: Dihydroorotate is made into OMP and OMP to UMP by the same protein with different domains
T
What is orotic aciduria?
Orotic acid in urine due to genetic defect in the last two steps
How is UTP made into CTP?
Via CTP synthestase and ATP, with glutamine to glutamate as the source of nitrogen
What is the source of nitrogen for UTP to CTP?
Glutamine
What is the parent molecule for pyrimidines?
UMP
How is 2’-deoxyribonucleotide formed?
Via ribonucleotide reductase
What is the structure of ribonucleotide reductase?
Two identical B1, Two identical B2 subunits which are specific for ADP, GDP, CDP, and UDP
Describe the allosteric activity of Ribonucleotide reductase
Binding of dATP inhibits enzyme and prevents reduction of any NDPs effectively preventing DNA syntehsis
What controls the substrate specificity of ribonucleotide reductase?
Binding of NTPs to a substrate site
What is adenosine deaminase deficiency?
Excess dATP which prevents DNA synthesis
How is dTMP made?
From dUMP via thymidylate synthetase
What is the mechanism of 5-fluorouracil?
Thymine analog that inhibits thymidylate synthase as an antitumor agent. 5-fluorouracil to 5-FdUMP which is permanent bound.
What is the “suicide” inhibitor?
5-fluorouracil
dUMP is made to dTMP by the oxidation of what molecule?
THF (tetrahydrofolate) to dihydrofolate (DHF)
How is DHF reduced?
Via dihydrofolate reductase to THF
T or F: Methotrexate inhibits both purine synthesis as well as dUMP to dTMP
T
How does methotrexate inhibit pyrimidine synthesis?
Methotrexate inhibits dihydrofolate reductase (DHF to THF) which prevents dUMP to dTMP
How are purine nucleotides degraded?
In the small intestine into uric acid
What is gout?
Excess uric acid in the blood
How are pyrimidine nucleotides degraded?
Opened and degraded to beta-alanine and beta-aminoisobutyrate which are precursors for acetyl-CoA and succinyl-CoA respectively
How is uric acid produced?
Amino is removed from AMP to IMP. IMP and GMP are converted to inosine and guanosine. Inosine and guanosine are converted to bases. Guanine is deamined to xanthine. Hypoxanthine is oxidized to xanthine.
Xanthine is oxidized to uric acid
What is guanine deaminated to?
Xanthine
What is inosine converted to?
Hypoxanthine
What does allopurinol do?
Prevents conversion of xanthine to uric acid
T or F: Adenine deaminase deficiency has been treated successfully by gene therapy
T
What enzyme does allopurinol inhibit?
Xanthine oxidase
What two enzymes are responsible for purine salvage?
Adenine Phosphoribosyltransferase (APRT) and hypo-xanthine-guanine phosphoribosyltransferase (HPRT)
What cofactors do APRT and HPRT need?
PRPP (taken to pyrophosphate)
T or F: Purine salvage is irreversible
T
HPRT takes hypoxanthine to?
IMP
HPRT takes guanine to?
GMP
APRT takes adenine to?
AMP
What is Lesch-Nyhan syndrome?
X-chromosome linked recessive disorder leading to complete deficency of HPRT leading to increased PRPP and decreased IMP and GMP. Uric acid is highly produced leading to severe gout and self-mutiliation
What is another name for epinephrine?
Adrenalin
Name three catecholamines
Dopamine, norephinephrine, epinephrine
The catecholamines do?
Degredation of glycogen and increase blood pressure and heart output
What is serotonin?
5-hydroxytryptamine and plays role in pain, affective disoreders, regulation of sleep, temperature, and blood pressure
The catecholamines are derived from what ?
Tyrosine
What AA can be made into tyrosine?
Phenylalanine
Tyrosine is hydroxylated to?
DOPA
DOPA is decarboxylated to?
Dopamine
Dopamine can be hydroxylated to?
Norepinephrine
What are MAOs?
Oxidatively demainate catecholamines (monoamine oxidases)
What are MAO inhibitors?
Block MAO enzyme raising NT levels (used in anti-depression meds)
What NT is given to Parkinson’s patients?
L-dopa
What is methylphenidate?
Blocks reuptake by dopamine transporters leading to synapse stimulus
What AA is the progenitor to serotonin?
Tryptophan
How is Tryptophan made into serotonin?
Hydroxylated and then decarboxylated
Low levels of serotonin is associated with?
depression
How to paxil and prozac work?
Block serotonin transporters and increase synaptic serotonin levels
T or F: Phenylalanine and Tryptophan are essential AA
TRUE (crazy)
Nucleotides are composed of?
Nitrogenous base, pentose monosaccharide, and 1/2/3 phosphate groups
How do T and U differ in structure?
T has a methyl group
What is a nucleoside?
Pentose and base
What are the five nucleoside names?
Adenosine, guanosine, cytidine, uridine, thymidine
What inhibits PRPP synthetase?
AMP, GMP, and IMP
What is the committed step in purine biosynthesis?
PRPP synthetase taking Ribose 5-phosphate to PRPP
What is another name for PRPP synthetase?
Glutamine phosphoribosyl pryophosphate amidotransferase
What controls the rate of reaction for production of PRPP?
PRPP levels (far below Km so small changes give proportional change in rate of reaction)
How many ATP are required to take PRPP to IMP?
4
What folic acid analog is required in two steps of purine synthesis?
N10-formyltetrahydrofolate
What does trimethoprim do?
Folate analog that selective inhibits bacterial dihydrofolate reducatase
T or F: AMP and GMP production are self-inhibiting (feedback)
T
T or F: MPA is uncompetitive inhibitor
T
T or F: Interconversions of phosphate lengths for nucleotides are all powered by ATP
T
Which are more specific: Base-specific nucleoside monophosphate kinases or nucleoside diphosphate kinase
First one, however second one only works on DP nucleosides
What is the source of ribose 5-phosphate in pyrimidine synthesis?
PRPP
What two AA are needed for both purine and pyrimidine synthesis?
Glutamine and aspartic acid
What is the regulated step of pyrimidine synthesis?
Synthesis of carbamoyl phosphate from glutamine and CO2 via carbamoyl phosphate synthetase (CPS) II.
What regulates CPS II?
Negative: UTP
Positive: ATP and PRPP
T of F: CPS requires biotin cofactors
F
Carbamoyl phosphate is made into?
Carbamoylasparate by asparate transcarbamoylase
Where is orate enzyme located?
Inner mitochondrial membrane
What three enzymes are on the same multicatalytic polypeptide in pyrimidine synthesis?
CPS II, aspartate transcarbamoylase, dihydroorotase
Orotate is made into?
OMP by orotate phosphoribosyl transferase converting PRPP to PP
OMP is made into?
UMP by OMP decarboxylase losing CO2
T or F: OMP decarboxylase and Orotate phosphoribosyl transferase are on the same protein
T
UTP is made to CTP by?
CTP synthetase
What provides the nitrogen in the UTP to CTP step?
Glutamine
2’-deoxyribonucleotides are produced from what two things?
Ribonucleodtide diphosphates and ribonucleotide reductase (enzyme)
What happens when dATP binds to allosteric sites on ribonucleotide reductase?
Stops overall catalytic activity (adenosine deaminase deficiency leads to toxicity)
dUMP is converted to what by what enzyme?
dTMP by thymidylate synthetase
What donates methyl group for dUMP to dTMP?
THF which is oxidized to DHF
T or F: Methotrexate affects both purine and dUMP to dTMP synthesis
T
T or F: Dietary DNA is used to a large extent in synthesis of cellular DNA
F
Dietary purines are converted to…
Uric acid by intestinal mucosal cells
Dietary pyrimidines are made into…?
Opened and degraded into soluble products releasing ammonia and CO2
The rate limiting enzyme in DOPA production is?
tyrosine hydroxylase
What inactivates catecholamines besides MAOs?
COMTs catechol-O-methyl-transferase
Approximate size of genome of human? Percent coding proteins? Repetitive? Gene number?
3000 Mb, 1.5 percent, >50 percent, ~25,000
Average exon, size, polypeptide for a gene?
9, 122 bp, 500 AA
RNA and DNA are degraded to what and where?
Oligonucleotides in the small gut
What happens to oglionucleotides in the gut?
Absorption into intestinal mucosal cells to be degraded into free bases
Hyperuricemia is associated with what degredation pathway?
Purine degradation leading to uric acid
What does idiopathic mean?
No known cause
What is alternative splicing?
mRNA is spliced into different processed forms introns/exons
T or F: Human exons are comparitively short
T
T or F: Human introns are short comparitively
F; they are long
T or F: Larger genes are more likely to be mutated
T (doesn’t mean deadly, in fact most small genes are deadly if mutated)
T or F: Human genes have many copies
T
What percentage of genes have known function?
Only 50 percent!
Describe what is meant about genes within genes?
Sense and Anti-sense strands have different genes on them in the same gene (exons)
Deletion/mutation in NF1 causes?
Neurofibromatosis
50% of the genome is repetitive, what makes this up?
Tandem repeats at centromeres and telomeres as well as Interspersed repeats (Alu and L1)
Tandem repeats are often found near what on the chromosome?
Centromere (very heterochromatic)
What is the sequence of human telomere?
TTAGGG
Telomerase solves what problem in regards to DNA replication?
End replication problem
What happens to the telomere with age?
Shortens
What is dyskeratosis congenita?
Mutation in RNA portion of telomerase
What is the size and count of Alu?
300 bp, more than a million copies
What is the size and count of L1?
7kb, more than 100,000 copies (many truncated)
T or F: Alu and L1 are retroposons
T (move through reverse transcriptase mechanism)
Describe the chain reaction of L1?
Brings its own promoter and codes for endonuclease and reverse transcriptase so they are coded in again and again
T or F: L1 genes are used to fill DSB
T
T or F: L1 Reverse Tx can be used to make copies of any gene
T (pseduogene)
T or F: Movement of transposons is a major source of new mutation in humans
T
What is VJ rejoining?
A major source of diversity in antibodies due to transposon recombinase
What is genomic imprinting?
Maternal or Paternal allele is silenced by methylation
T or F: Methylation is reset in the germline
T
T or F: Due to X-silencing, female cells are mosaics
T
The maternal equivalent of Prader-Willi syndrome is?
Angelman syndrome
What is the out of africa hypothesis?
Modern humans evolved out of Africa 50kyrs ago and migrated throughout world
What is the mutation rate and how is it used anthropologically?
3 x 10^-9 mutations/bp/generation, molecular clock
SNPs tell us?
Each SNP tells us age of DNA
Allele variation tells us?
Spelling of the gene are genetic markers
A bottleneck leads to what?
Low genetic diversity
Humans are not very genetically diverse because of a ?
Genetic bottleneck
Humans in Africa are roughly how old? Europe? Asia? America?
100 kyrs, 40kyrs, 50-70 kyrs, 15-30 kyrs
Roughly how many years per generation?
20 yrs
Which population has the greatest genetic diversity?
African populations, then Asian and European, then Americans
T or F: Human genome has remnants of other species like neanderthals ?
T (meaning they mated while migrating)
T or F: SNPs have distinct geographic bias
T
DRD4 7R is associated with what?
Blunted response to dopamine and is associated with ADHD (highly prevalent in the Americas, not common in Asia for example)
Where is lactase gene most likely found?
Populations that ate milk (europe and Middle East)
What is sickle cell disease?
Common in areas where malaria is common
What is heterozygote advantage?
Individuals with one of each allele has an advantage (sickle cell)
What is the disease gene? Do we have it?
We do not have genes for disease, we have altered genes that lead to disease
What is the genome wide association study approach?
Use of genome level examination to tell us that a functional variation must exist without telling us function. Then we can study these to see what they are
