otro Flashcards
Which histone modifications do you know and where do they play a role?
Histone modifications regulate gene expression (epigenetics)
they have central globular domain and flexible amino ends (N-terminal end) where modifications can take place, changing the chromatin structure.
1. acetylation: act expr genetica
2. Fosforilation: reaccion a señales externas
3. Metilation: inhibition arn poli
4. Ubiquitination: labelling target proteins
What does “recycling” of purine bases mean and why does recycling take place? (+1 example)
Recycling saves energy (ATP) because de novo synthesis requires significant amounts of ATP.
Example: Adenine + PRPP (activated ribose) –> Adenylate + PPi
Enzym: Adenin-Phosphoribosyltransferase
What do ribonucleotide reductases (RNR) catalyze and how are these enzymes structured (subunits with
characteristic elements/binding sites)?
Occurs during synthesis of deoxyribonucleotides from ribonucleotides
replaces OH group with H
Ribonucleotid-Reduktase: Ribonucleosiddiphosphat + NADPH —> Desoxyribonukleotid
two subunits: R1 and R2
R1 has an active center and two allosteric control sites
R2 stabiles Tyrosylradikal
Which diseases are associated with the breakdown of adenylate (AMP)?
> Immune defects:
* Gout (hyperuricemia, high urate levels)
Uric acid loses an H+ at physiological pH and becomes urate
(cristalizacion d acido urico ) (gota )
tratamiento con ALLOPURINOL
* Lesch-Nyhan syndrome (congenital gout)
Cause: Mutation in the recycling of purine nucleotides: lack of HPRT (transferase enzyme)
Consequences: Acceleration of de novo purine biosynthesis and overproduction of urate (uric acid salts).
What factors determine the accuracy of DNA replication? What causes the extremely low error rate (1 error in a replication of 109 - 1010bp)?
ÿ Proofreading function during DNA synthesis
ÿ Repair function in case of mismatch: Base mismatches are corrected
What structural features are characteristic of DNA polymerases?
Klenow fragment of DNA polymerase I
They have a polymerase unit “right hand” from the “Finger”, “palm” and “thumb” domains
The finger and thumb domains serve to grasp or hold the DNA at the active center of
the enzyme (“palm of the hand”).
and a domain with 3’5’ exonuclease activity
for proofreading and patching.
+2 metal ions for catalisis
What does primase synthesize during DNA replication and why?
the primer: serves as an attachment point for the
DNA polymerase
Describe briefly the process of DNA replication.
- apertura doble hebra de adn con la topoisomerasa
- Helicase splits double strand – the resulting single strands form leading strand and antiparallel lagging strand.
- single-strand stabilizing proteins support the single strands and prevent them from twisting again
- Primase (RNA polymerase) begins synthesis of the primer
- DNA polymerase III va sintetizqando complementarios de las hebras molde
- Primers are removed and gaps are filled by DNA polymerase I
- DNA ligases link the Okazaki fragments
Name 2 DNA repair systems (brief explanation of the mechanism).
- Single strand repair:
detection and removal of faulty bases, reparain the gap wth polimerasa y ligasa - Mismatch repair system (MMR):
mismatches are detected and corrected
The heterodimer hMutSalfa yhmutLalfa
the exonuclease EXO1
- Mismatch repair system (MMR):
What causes the skin disease “xeroderma pigmentosum”?
extremely sensitive to UV light.
Mutations in genes of various proteins of the nucleotide excision repair system. defecto en las endonucleasas, falta de eliminacion d nucl defectuosos–> mutaciones
What DNA damage do you know?
ÿ DNA-Strangbruch
ÿ “frame shift”
ÿ Raster mutations
ÿ missense mutations
ÿ nonsense mutations
Differences in transcription: mRNA from bacteria vs. eukaryotes
I. Transcription Eukaryotes:
- much more complicated than prokaryotes
- Eukaryotes can precisely regulate the timing and extent of gene expression
1. Nuclear membrane - spatial and temporal separation of transcription and translation
2. Complex regulation of transcription
3. Processing of RNA (splicing, posttranslational & posttranscriptional)
II. Transcription Bacteria:
The bacterial RNA is hardly or not at all changed. Some RNA molecules splice themselves.
What are the general steps in transcription? (+ short description)
= the transcription of a gene into an mRNA (initiation, elongation, termination)
1. iniciacion:
arn poli se une a un promotor
2. elongacion
nucleotides are
attached by RNA polymerase
3. Termination
by factors such as hair loop structure or Rho factor
proceso de iniciacion de la transcripcion
- Binding of the RNA Pol Core enzyme
- Binding of the subunit (sigma factor)
- Recognition of a promoter by Sigma = start of transcription
Difference in promoter (which elements) and initiation of transcription in bacteria versus
eukaryotes
> Prokaryotes: A protein (sigma factor) binds to the Probnow box [2
Eukaryotes: initiation complex
in which the RNA polymerase transcription factors (TF) are required as mediators.
What is a transcription bubble?
A complex of DNA, RNA and RNA polymerase. In the front part of the transcription
bubble, the DNA double helix is unraveled and broken open; in the rear part, the newly synthesized RNA is displaced
from the binding to the template strand and the DNA double helix is regenerated.
RNA-DNA hybrid helix 8 bpe RNA polymerase base pairings con el ribonucleotido q toca y forming the fosfodiester bond
How is transcription typically terminated in bacteria?
Rho factor (ÿ):
The Rho protein (hexamer protein, helicase) binds to a
Region of the RNA with a lot of G and C
stem-loop structure:
formation of a stem-loop structure of the mRNA via GC
pairings., forcing the arn poli to stop
What are rifampicin and actinomycin (explanation of how they work)?
Streptomyces strains.
Rifampicin inhibits transcription initiation in bacteria by blocking the enzyme channel for passage of the RNA-DNA
hybrid. Thus, it blocks RNA elongation after 2-3 nucleotides have been added.
Actinomycin inhibits transcription by binding to the DNA double helix (intercalation).The DNA thus loses its properties as a template for transcription.
What elements can promoters of eukaryotic genes contain?
GC-Box, CAAT-Box, TATA-Box
What are enhancer sequences?
regulatory sequences in the genome to which transcription factors bind and thereby enhance or
suppress transcription
What are tRNAs and how are they structured (shape, characteristics)?
tRNAs provide amino acids during translation. They act as intermediaries between codon and
amino acid transport/incorporation. tRNAs have a cloverleaf structure (3 loops).
The anticodon loop has a base triplet (= 3 bases), the so-called anticodon, which is
complementary to a specific triplet on the mRNA . The amino acid encoded by the anticodon
binds to this triplet
- Binding site for amino acids (3’OH of adenosine)
- Acceptor arm
- D-loop
- Anticodon loop
- Variable loop
- TÿC loop
What does the “wobble” hypothesis say?
predictable steric freedom (“wobble”) with regard to pairing with the 3rd base of the codon
How are AAs activated? By which enzymes and how is their high specificity achieved? What catalyzes
aminoacyl-tRNA synthetase?
Activated amino acids are required for protein synthesis. This is done by aminoacyl-tRNA synthetases. These are
enzymes that break down the ester bond between tRNA and
a specific amino acid.
The products are called aminoacyl-tRNAs
The aminoacylation of a tRNA occurs in 2 steps:
- The carboxyl group of the amino acid reacts with ATP, whereby the separation of
Pyrophosphate forms an aminoacylate . - The free 3’-OH group of the tRNA attacks the aminoacyl adenylate, whereby the aminoacyl-tRNA molecule
is formed by cleavage of AMP and formation of an ester bond .
