BIOCHEMISTRY- Molecular Flashcards
In in which form does the DNA exist in order to fit in the nucleus?
Condensed, chromatin form
How many times does the negatively charged DNA loops around the positively charged histone octamer?
Twice
What does the negatively charged DNA loops around the positively charged histone octamer form?
Nucleosome bead
From which amino acids does the histones are rich?
Lysine and arginine
Which histone is the only one that isn´t in the nucleosome core?
H1
How are the main compounds that manage the stabilization of the chromatin fiber?
H1 binds to the nucleosome and to Linker DNA
In which phase does the DNA condenses to form chromosomes?
In mitosis
In which phase does the histones and DNA synthesis?
During S phase
What is the difference between Chromatin and HeteroChromatin?
HeteroChromatin= Highly Condensed
Is the Heterochromatin active?
No, it´s transcriptonally inactive, sterically inaccessible
What´s the difference between Heterochromatin and Euchromatin?
Euchromatin is less condensed, transcriptionally active, sterically accessible
What happens to the transcription when the DNA is Methylated at CpG islands?
Represses transcription
Which template strand is methylated in DNA reparation?
Cytosine and adenine
What does the DNA methylation allows?
Allows mismatch repair enzymes to distinguish between old and new strands in prokaryotes
So… what´s the difference when the histones are methylated in comparison to DNA methylation?
Usually reversibly represses DNA transcription, but can activate it in some cases
Usually reversibly represses DNA transcription, but can activate it in some cases
Relaxes DNA coiling, allowing for transcription
Which nucleotides form the Purines?
Adenine and Guanine
How many rings does the purines have?
2 rings
Which is the mnemonic for PURines?
PURe As Gold
Which nucleotides form the pyrimidines?
Cytosine, Thymine, Uridine
How many rings does the pyrimidines have?
1
This nucleotide has a methyl…
Thymine
What happens when the cytosine has a deamination?
It makes Uracil
Which nucleotide is found in the RNA and not in the DNA?
Uracil
This nucleotide is present in the DNA instead of the Uracil, which is present in the RNA…
Thymine
Which are the three aminoacids necessary for the purine synthesis?
Glycine
Aspartate
Glutamine
Which bond is stronger between GC bond or AT bond?
GC bond is stronger
What kind of bond does each nucleotide has with another nucleotide?
Hydrogen bond
How many H bonds does G-C have?
3
How many H bonds does A-T have?
2
What is the conformation of the nucleoside?
Base + Deoxyribose
Which are the components for the Nucleotides?
Base + deoxyribose + phosphate
In every nucleotide what kind of bond do they have between each other?
3´- 5´phosphodiester bond
In the novo purines synthesis, what is the process to form one?
Start with sugar+ phosphate
Then add the base
What is the process to synthesis from novo a pyrimidine?
Make a temporary base
Add sugar + phosphate
Modify base
Which one it´s an example of a temporary base?
Orotic acid
This enzyme it´s responsible for the conversion from ribonucleotide to deoxyribonucleotide…
Ribonucleotide reductase
Which ones are the two metabolic pathways that the Carbamoyl phosphate is involved?
De novo pyrimidine synthesis
Urea cycle
In the nucleotide synthesis, which enzyme does the Leflunomide inhibits?
Dihydroorate dehydrogenase
What does Leflunomide inhibits the synthesis for?
Orotic Acid
This two medicines inhibits the effect of inositol monophosphate (IMP) dehydrogenase in order to form GMP
Mycophenolate
Ribavirin
In the conversion from UDP to dUDP which enzyme is inhibited with Hydroxyurea?
Ribonucleotide reductase
Which medicine is the 6- Mercaptopurine (6-MP) prodrug?
Azathioprine
This medicine and its prodrug inhibit de novo purine synthesis…
6- Mercaptopurine (6-MP) and Azathioprine
The 5 –Fluorouracil (5-FU) inhibits the formation of deoxythymidine monophosphate (dTMP) from deoxyuridine monophosphate (dUMP) by inhibiting which enzyme?
Thymidilate synthase
This medicines are the responsible for inhibition of the dihydrofolate reductase in the synthesis of Tetrahydrofolate (THF)
Metrotrexate
Trimetroprim
Pyrimethamine
If there is an excess of adenosine deaminase deficiency what will happen?
There would be an excess of ATP and dATP
What would happen to the ribonucleotide reductase if there is an excess of ATP and dATP?
Inhibition of ribonucleotide reductase with imbalance of the nucleotide
What happens to the DNA if there is an excess of ATP and dATP?
Prevents DNA synthesis by imbalance of the nucleotide because of the ribonucleotide reductase inhibition
If the DNA synthesis its stop what happens to the lymphocyte count?
The lymphocyte count decreases
Which is one of the main causes of the autosomal recessive Severe Combined Immunodeficiency (SCID)?
Adenosine deaminase deficiency
In the Lesh-Nyhan syndrome which enzyme is absent?
Hypoxanthine –guanine phosphoribosyltransferesa (HGPRT)
If there is an absence of the HGPRT enzyme what happens to the purines?
Defective purine salvage
What is the effect of the HGPRT enzyme?
Converts Hypoxanthine to Inosinic acid (IMP)
Converts Guanine to Guanylic acid (GMP)
Which are the main findings on the Lesch- Nyhan syndrome?
Hyperuricemia Gout Pissed off (agression, self mutilation) Retardation (Intellectual disability) DysTonia
What is the treatment for Lesch-Nyhan?
Allopurinol or febuxostat (2nd Line)
True or False… each codon specifies 3 aminoacids
False, each codon specifies only 1 aminoacid
True or False… Most aminoacids are coded by multiple codons
True
Which aminoacids are enconded by only one codon?
Methionine and Tryptophan
This aminoacid is encoded just by the codon UGG
Tryptophan
AUG is the codon that alone encondes…
Methionine
In humans, which is the exception in the genetic code that isn´t conserved throughout evolution?
Mitochondria
In the DNA replication, what is the name of the fragments that are discontinuous in the synthesis?
Okazaki fragments
What is the difference in the origin of DNA replication between Prokaryotes and eukaryotes?
Prokaryotes single
Eukaryotes multiple
Why is so important the replication fork?
It´s the Y-shapped region along DNA template where leading and lagging strands are synthesized
Its purpose is to Unwind DNA template at replication fork
Helicase
Prevent strands from reannealing
Single stranded binding proteins
What is the main purpose for the DNA topoisomerases?
Is to create a single or double stranded break in the helix to add or remove supercoils
This medicine inhibits DNA gyrase (procaryotic topoisomerase II)
Fluoroquinolones
Makes RNA primer on which DNA polymerase III can initate replication
Primase
TRUE OR FALSE… DNA Polymerase III is only present in eukaryotic
False, DNA polymerase III is only present in prokaryotic
In which side does DNA polymerase elongates leading strand by adding deoxynucleotides?
In the 3´ end
Which is the way of synthesis for DNA polymerase?
has 5´ ——::-3´ synthesis
Its purpose is to proofreads each added nucleotide in the 3´—–::- 5´ activity
Exonuclease
Its function is to degrade RNA primer and replace it with DNA, just for procaryotic
DNA Polymerase I
Has same functions as DNA polymerase III but also excercises RNA primer with 5´ ——::-3´ exonuclease
DNA Polymerase I
What is the function of DNA ligase?
IT SEALS. Catalyzes the formation of phosphodiester bond within a strand of double-stranded DNA
Joins the Okazaki fragments
DNA ligase
An RNA-dependent DNA polymerase that adds DNA to the 3´ ends of chromosomes to avoid loss of genetic material with every duplication
Telomerase
What are two types of mutations for the silent, missense and nonsense severity mutations?
Transition and Transversion
What happens in the transition mutation?
Purine to purine (A to G) or pyrimidine to pyrimidine (C to T)
Which is the diferrence with the transversion mutation in comparission with the transition?
In the transversion its a change from a purine to pyrimidine or pyrimidine to purine
What is the main point in the silent mutation?
Nucleotide substitution but codes for same aminoacid
In this kind of mutation the nucleotide substitution resulting in changed aminoacid
Missense
In the sickle cell disease, which kind of mutation can we find?
Missense
In this kind of mutation we find a nucleotide substitution resulting in early stop codon
Nonsense
This is the worst type of mutation beacause there is a deletion or insertion of a number of nucleotidesnot divisible by 3, resulting in misreading of all nucleotides downstream, usually resulting in a truncated, nonfunctional protein
Frameshift
This is an example of a Frameshift mutation
Duchenne muscular dystrophy
From the less severe mutation to the worst which would be the order
Silent, missense, nonsense, frameshift
Who are the responsable of the release of the oligonucleotide- containing damage bases on the single strand DNA repair?
Specific endonuclease
They´re responsable for filling and reasealing the gap that the endonuclase caused on the DNA repair
DNA polymerase and ligase respectively
On this disease there is a prevention in the repairing of pyrimidine dimers because of ultraviolet light exposure
Defective in xeroderma pigmentosum
What is the main function for the Base specific glycosylase?
Recognizes altered base and creates AP site (apurinic/apyrimidinic)
So… in the base excision repair, who manage to remove one or more nucleotides and cleaves the 5´ end
AP endonuclease
In the base excision repair who cleaves the 3´ end?
Lyase
What is the importance of the base excision repair?
Important in repair of spontaneous/toxic deamination
What happens in the mismatch repair?
Newly synthesized strand is recognized, mismatched nucleotides are removed and the gap is filled and resealed
In which disease can we see the mismatch repair?
Defective in hereditary nonpolyposis colorectal cancer (HNPCC)
Are the nucleotide excision repair, base excision repair and the mismatch repair; a single or double strand DNA repair?
Single strand DNA repair
This is an example of double strand repair
Nonhomologus end joining
On this disease we can find a mutation of the nonhomologous end joining repair
Ataxia Telangiectasia
Which way is synthesized the DNA?
5´—/- 3´
Which end bears the triphosphate (energy spurce for the bond)?
5´
Which one is the way in the protein synthesis?
N- Terminus to C-terminus
Which way is synthesized the RNA?
The same as DNA 5´—/- 3´
Which way does the mRNA is readen?
5´—/- 3´
Who is the the target in the 3´ hydroxyl attack?
The triphosphate bond
In the protein synthesis, which one are commonly the start codons for the mRNA?
AUG (rarely GUG)
Who are the main stop codons that are present on the mRNA?
UGA
UAA
UAG
In the regulation of gene expression, this is the site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus
Promoter
From which codons is the promoter rich?
AT with TATA and CAAT boxes
What would happen to the gene transcription if there is a mutation of the promoter?
Commonly results in dramatic decrease if gene transcription
What is the importance of the enhancer in the Regulation of gene expression
Stretch of DNA that alters gene expression by binding transcription factors
This is the site where negative regulators (repressors) bind in the Regulation of gene expression
Silencer
In the eukaryotes how many RNA polymerase exist?
3
This RNA polymerase does the most numerous RNA
RNA polymerase I
Which is the most numerous RNA?
rRNA
Its function is to make the largest RNA
RNA polymerase II
This is the largest RNA type
mRNA
From the three types of RNA polymerase this one has the function to make the smallest RNA
RNA polymerase III
Its the smalles RNA
tRNA
In the DNA, is the site where the RNA polymerase II opens the DNA
Promoter site
What does the a-amanitin, found in Amanita phalloides (death cap mushrooms) inhibits?
Inhibits RNA polymerase II
If ingested, what are the clinical manifestations of the Amanita phalloides (death cap mushrooms)?
Severe hepatotoxicity
In the prokaryotes, who makes all 3 kinds of RNA?
1 RNA polymerase
What is the name of the initial transcript in the RNA processing in Eukaryotes
Heterogeneous nuclear RNA (hnRNA)
What is the result of the modified hnRNA?
mRNA
What happens in the process in the nucleus following transcription?
Capping of the 5´end DNA (addition of the 7-methylguanosine cap)
Polyadenylation of 3´ end
Splicing of introns
Where is the site where the mRNA is transcripted?
in the nucleus
What happens next to the recently form mRNA?
Is transported out of the nucleus into the cytosol, where it is translated
Where does the mRNA cuality control occurs?
cytoplasmatic P bodies
What does the cytoplasmatic P bodies contain?
exonucleases, decapping enzymes and microRNAs
True or false… the Poly-A polymrase requires a template
false… the Poly-A polymrase DOESN´T requires a template
Which is the polyadenilation signal?
AAUAAA
What are the components for the spliceosome?
Primary transcript
Small nuclear ribonucleoproteins (snRNPs)
Other proteins
After the spliceosome is form, what happens next?
Lariat-shaped looped intermediate is generated
After the lariat is released, what does it removes and what does it join?
remove intron and join 2 exons
What are the anti Smith antibodies?
Antibodies to spliceosomal snRNPs
For which disease does the Antibodies to spliceosomal snRNPs or anti Smith antibodies, are highly specific for?
SLE
Which kind of disease does the Anti-U1 RNP antibodies are highly associated?
With mixed connective tissue disease
Who contains the actual genetic information coding for proteins… The exons or the introns?
Exons
What is the purpose for the introns?
Intervening noncoding segments of DNA
Where does the introns are intervening in the Cell?
Introns stay in the nucleus
Does exons stay in the nucleus
NO
This disease is an example of an abnormal splicing
B-thalassemia
How many nucleotides does the tRNA have?
70-90 nucleotides
In the tRNA what is the anticodon end?
Is opposite 3´ aminoacyl end
This nucleotides are at the 3´end in the tRNAs both eukaryotic and prokaryotic
CCA
Who is covalently bound to the 3´ end of the tRNA?
The aminoacids
In the T-arm tRNA structure what does it contains?
Thymine
pseudouridine
cytosine
Why are the components of the T-arm in the tRNA so necessary?
For the tRNA ribosome binding
In the tRNA structure what does the D-arm contains?
Dihydrouracil residues
Why does the dyhidrouracil residues of the D-arm in the tRNA are so necessary?
For the recognition by the correct aminocyl-tRNA synthetase
Where is the Acceptor stem in the tRNA structure?
The 3´ CCA is the aminoacid acceptor site
If the aminoacid and tRNA bond is incorrect, what does the aminoacyk tRNA synthetase causes?
Bond is hydrolyzed
What kind of bond does the aminoacid and tRNA can have?
peptide bond
Which are the three steps for the protein synthesis?
Initiation
Elongation
Termination
What happens to the GTP in the phase of initiation in the protein synthesis?
Hydrolyzes
In the Charging phase of the tRNA, what does the Aminoacyl-tRNA synthetase uses for the matchmaker ?
Uses ATP
During this phase of the protein synthesis the initiation factors help assemble the 40S ribosomal subunit with the initiator tRNA and are realeased when the mRNA and the Ribosomal 60 S subunit asemble with the complex
Initiation
Who assembles with the 40S ribosomal subunit in the initiation phase of the protein synthesis?
initiator tRNA
When does the 40S ribosomal subunit and initiator tRNA are released from the complex during the initiation phase of the protein synthesis
When the mRNA and the Ribosomal 60 S subunit asemble with the complex
What relationship does the GTP and the tRNA have?
The GTP works during the translocation
During the elongation phase where does the Aminoacyl-tRNA binds?
to A site
Who catalyzes the peptide bond formation and transfers growing polypeptide to amino acid in A site in the elongation phase
rRNA (ribozyme)
How many nucleotides does the ribosome advances in the elongation phase?
3 nucleotides
Which way does the ribosome advances in the elongation phase?
toward 3´ end of the mRNA
What is the translocation?
When the peptidyl tRNA moves to the P site
In which phase of the protein synthesis does the translocation happens?
During the Elongation
In this phase the completed polypeptide is released from ribosome during the protein synthesis
Termination
In the posttranslational modifications what is the trimming?
Its the removal of N- or C-terminal propeptides from zymogen to generate mature protein
Which one is an example of a protein who suffered trimming posttranslational modification?
trypsinogen to trypsin
Which ones are covalent alterations?
phosphorylation, glycosylation, hydroxylation, methylation, acetylation and ubiquitination
This kind of proteins are involved in facilitating and/or maintaining protein folding
Chaperone protein
Give an example of a Chaperone protein
In yeast, some are heat shock proteins (Hsp60) that are expressed at high temperatures to prevent protein denaturing/ misfolding
