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Genen Flashcards

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1
Q

Wat vormt het genoom?

A

DNA

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2
Q

Wat is de invloed van omgevingsfactoren op het genoom?

A

 Omgevingsfactoren kunnen leiden tot mutaties
 schade aan het DNA, verstoring code
 aantasting cel functie  Leidt tot celdood/kanker/veroudering
 Omgevingsfactoren kunnen organisatiegraad van DNA beïnvloeden
 DNA is ingepakt in chromatine eiwitten
 Chromatine complex heeft invloed op gebruik van DNA

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3
Q

Welke criteria moet genetisch materiaal aan voldoen?

A
  1. Informatie  codering
  2. Replicatie  maken copie voor dochtercel
  3. Transmissie  overgeven aan dochtercel
  4. Variatie  evolutie / individu vs soort
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4
Q

Nucleotide

A

monomeren van DNA/RNA

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5
Q

Streng

A

lineaire polymeer van DNA/RNA-nucleotiden

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6
Q

Dubbele helix

A

twee verbonden strengen DNA

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7
Q

Chromosoom

A

complexe structuur van dubbelstrengs DNA en gespecialiseerde eiwitten

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8
Q

Genoom

A

de complete set aan genetisch materiaal van een organisme

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9
Q

Waaruit bestaat DNA?

A

 Phosphate group
 Pentose sugar
 Deoxyribose
 DNA = Deoxyribonucleic Acid
 Nitrogenous base
 Purines – Adenine (A), Guanine (G)
 Pyrimidines – Cytosine (C), Thymine (T)

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10
Q

Nummer systeem van nucleotide

A

 Sugar carbons are 1’ to 5’
 Base attached to 1’ carbon on sugar
 Phosphate attached to 5’ carbon on sugar

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11
Q

Hoe ziet een DNA streng eruit

A 
Phosphate-sugar backbone
•	Basen steken uit 
•	Richting: 5’  3’ (!)
5’ – GATC – 3’
•	zo genoteerd
•	Zo gesynthetiseerd
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12
Q

Hoe ontstaat de dubbele streng van DNA

A 
	A bindt aan T
	C bindt aan G
	H-bruggen
	2 tussen A-T
	3 tussen G-C
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13
Q

Wat is het verschil tussen DNA nucleotide en RNA nucleotide?

A

DNA heeft maar 1 OH groep, RNA heeft er 2. De base Thymine (T) van DNA is bij RNA Uracil (U)

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14
Q

Wat is de chargoff regel?

A
  • amount of adenine similar to thymine
  • amount of cytosine similar to guanine.
  • A pairs with T
  • G pairs with C
  • Afstand steeds hetzelfde
  • Complementaire DNA strengen
  • Antiparallel
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15
Q

Wat bepalen de grooves in de space-filling model

A

 Major groove Proteins bind to affect gene expression

 Minor groove Narrower

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16
Q

Wat is semiconservatief

A

 De twee DNA strengen van dubbele helix smelten uit tot enkelstrengs en dienen als enkelstrengs Template
 Nucleotiden worden ingebouwd volgens AT/GC regel, complementair aan template
 Replicatie resulteert in twee dochter moleculen
 * Dubbel strengs
 * Eén oude en één nieuwe streng

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17
Q

Waar is de replication fork en wat doet die?

A

 Origin of replication provides an opening called a replication bubble that forms two replication forks
 DNA replication proceeds outward from forks
 Bacteria have single origin of replication
 Eukaryotes have multiple origins of replication

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18
Q

DNA Helicase

A

Binds to DNA and travels 5’ to 3’ using ATP to separate strand and move fork forward

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19
Q

DNA topoisomerase

A

Relives additional coiling ahead of replication fork

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20
Q

Single-strand binding protein

A

Keep parental strands open to act as templates

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21
Q

DNApolymerase

A

 Synthetiseert Covalente binding tussen nucleotides

 Tri-phosphate nucleotiden, twee phosphaat eraf  energie

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22
Q

Deoxynucleoside triphosphates

A

 Free nucleotides have three phosphate groups

 Breaking covalent bond to release pyrophosphate (two phosphates) provides energy to connect nucleotides

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23
Q

Features of DNA Polymerase

A
  1. DNA polymerase cannot begin synthesis on a bare template strand
     Requires primer to start
     Enzyme Primase makes the primer (RNA)
     The RNA primer is removed and replaced with DNA later
  2. DNA polymerase only works 5’3’
    5’-Phosphate, 3’-OH
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24
Q

Leading strand

A

 DNA synthesized in as one long molecule
 DNA primase makes a single RNA primer
 5’3’ direction

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25
Lagging strand
 DNA synthesized 5’3’ as Okazaki fragments |  Okazaki fragments consist of RNA primers plus DNA
26
Both leading and lagging strand
 RNA primers are removed by DNA polymerase and replaced with DNA  DNA ligase joins adjacent DNA fragments
27
3 mechanisme voor accuratie
1. Hydrogen bonding between A and T, and G and C is more stable than mismatches 2. Active site of DNA polymerase cannot form covalent bond if pairs mismatched 3. DNA polymerase can proofread to remove mismatched pairs  DNA polymerase track backward and remove mismatch
28
Wat zijn telomeren
 Serie herhaalde nucleotide sequenties (repeats) aan beide eindes van chromosomen (in eukaryoten)  Eigen vorm van DNA replicatie  Telomeer aan 3’-OH kant is enkelstrengs   3’ overhang
29
Waarom is er telomerase
 DNA polymerase III cannot copy the tip of the strand at 3’ end  no RNA primer   every replication round linear chromosomes would become progressively shorter  The enzyme Telomerase attaches many copies of DNA repeat to the ends of chromosomes
30
Wat is het gevaar bij tolmoeren?
 Telomeren geassocieerd met veroudering (senescence)  Worden korter bij doorgaande deling van cellen (bij differentiatie van cel typen en doorgaande deling)  Telomerase is actief in ‘snel-delende’ cellen  stam cellen, embryonale cellen, beenmerg cellen, sperma cellen, etc.  Telomerases verminderen in concentratie als organisme ouder wordt  In 99% van humane tumoren is activiteit van Telomerase verhoogt
31
Waaruit bestaan chromosomen?
```  Typical eukaryotic chromosome may be hundreds of millions of base pairs long  Length would be ~1 meter  must fit in cell 10-100µm  Chromosome (23 pairs)  Discrete unit of genetic material  Chromosomes composed of chromatin  DNA-protein complex ```
32
Wat zijn de 3 niveaus van DNA compaction
``` 1. DNA wrapping  DNA wrapped around histones to form nucleosome 2. 30-nm fiber  Asymmetric, 3D zigzag of nucleosomes 3. Radial loop domains ```
33
DNA Wrapping
DNA wrapped around histones to form nucleosome | Shortens length of DNA molecule 7-fold
34
30-nm fiber
Current model: asymmetric, 3D zigzag of nucleosomes | Shortens length another 7-fold
35
Radial loop domains
Interaction between 30-nm fibers and nuclear matrix | Each chromosome located in discrete territory
36
Euchromatin
Relatively open DNA-protein structure | Contain active genes
37
Heterochromatin
* Highly compact DNA-protein structure * Hardly any genes * Composed of ‘junk’ DNA
38
Wat gebeurd er met chromosomen als cellen gaan splitsen
When cells prepare to divide, chromosomes become even more compacted (visible) Metaphase chromosomes highly compacted Then in non-active heterochromatin form
39
Minimum requirement voor neurospora crassa
``` Carbon source (sugar), inorganic salts, and biotin Neurospora can synthesize everything else it needs from those molecules ```
40
Waarvoor kunnen genes coderen?
```  Not all proteins are Enzymes  * genes encode all proteins  Some genes code for RNA not protein  * ribosomal RNA (rRNA)  * tRNA  * regulatory small RNAs  Some enzymes have multiple subunits  * Hemoglobin (2 alpha 2 beta subunits) ```
41
Transcriptie
 Produces a transcript (RNA copy) of a gene |  A messenger RNA (mRNA) specifies the amino acid sequence of a polypeptide
42
Translatie
 Process of synthesizing specific polypeptide on a ribosome using the mRNA template
43
Verschil van de genetische informatiestroom tussen eukaryote en prokyote cellen
 Eukaryotes also have an intermediate step called RNA processing, during which pre-mRNA is processed into active mRNA
44
Waar vind transcriptie en translatie plaats in de eukaryote cel?
Transcriptie in nucleus. Na pre-mRNA wordt er mRNA gemaakt, dit verlaat de nucleus en wordt getransleert in de ribosomen
45
Promotor van transcriptie:
Signals the beginning of transcription
46
Regulatory sequence of transcription
Site for binding of regulatory proteins. The role of regulatory proteins is to influence the rate of transcription
47
Transcribed region
Part of this region contains the information that specifies an amino acid sequence
48
Terminator of transcription
Signals the end of transcription
49
Wat zijn de 3 stages van transcriptie
Initiation Elongation TErmination
50
Initation van transcriptie
 Recognition step  In bacteria, sigma factor causes RNA polymerase to recognize promoter region  Stage completed when DNA strands separate near promoter to form open complex
51
Elongation van transcriptie
 RNA polymerase synthesizes RNA  Template strand (‘non-coding’ strand) used as template for RNA synthesis  coding strand is not used  RNA molecule synthesized 5’ to 3’  Uracil RNA nucleotide for Thymine DNA nucleotide
52
Termination van transcriptie
 RNA polymerase reaches termination sequence |  Causes both the polymerase and newly-made RNA transcript to dissociate from DNA
53
Richting van RNA synthesis
synthesis of RNA transcript is 5’ to 3’ and DNA template strand reads 3’ to 5’
54
gene order and orientation in bacterial genome/chromosome
 genes (templates for RNA) can be found on both DNA strands |  no overlap (in general)
55
gene order and orientation in eukaryote genome/chromosome
 Also genes on both strands  A lot of non-coding DNA between genes  Genes have introns and exons
56
Operon
- Eén promoter (controle gebied) - Eén RNA molecuul - Meerdere eiwitten Alleen bij bacterieen
57
3 vormen van RNA polymerase bij eukaryote transcriptie
RNA polymerase II – transcribes mRNA RNA polymerase I and III – transcribes nonstructural genes for rRNA and tRNA RNA polymerase II requires 5 General Transcription Factors to initiate transcription pre-initiation complex (fig. 12.7)
58
Verschil tussen prokaryote en eukaryote transcriptie
 Basic features identical to prokaryotes |  However, each step has more proteins
59
RNA processing in eukaryote cellen
 Eukaryotic mRNAs are made in a longer pre-mRNA form that requires processing into mature mRNA  * Introns  * Exons  Splicing – removal of introns  Other modifications – addition of tails and caps  rRNA and tRNA are self-splicing  They are ribozymes – RNAs that can catalyze reactions
60
Spliceosome
removes introns precisely | Composed of snRNPs (small nuclear RNA + proteins)
61
Introns
transcribed but not translated
62
Exons
coding sequence found in mature mRNA
63
Alternative splicing
splicing can occur more than one way to produce different products
64
Capping
 Modified guanosine attached to 5’ end |  Needed for mRNA to exit nucleus and bind ribosome
65
Poly A tail
 100-200 adenine nucleotides added to 3’ end  Increases stability and lifespan in cytosol  Not encoded in gene sequence
66
Genetic code
sequence of bases in an mRNA molecule Read in groups of three nucleotide bases or codons  “open reading frame” (ORF) Most codons specify a particular amino acid Codons also function as Start and Stop codons
67
Degenerate code
more than one codon can specify the same amino acid
68
Start en stop codon
AUG: Start codon | UAA, UAG, UGA : Stop codons
69
Anti codon
Anticodon – 3 RNA nucleotide part of tRNA molecule
70
tRNA role in translation
 anticodon  Allows baseparing of tRNA with mRNA codon  tRNA carries the encoded amino acid
71
The wobble base ad tRNAs
 degenerate code; less important third nucleotide at 3’ end of codon  tRNAs can recognize multiple codons  disregard wobble base  codons – tRNAs not in every organism one on one  also multiple tRNAs for same codon possible
72
The open reading frame
 Start codon defines reading frame  Addition of a nucleotide (U) shifts the reading frame and changes the codons/amino acids encoded  often also premature stop codon
73
Wat is er nodig bij translatie
```  mRNA  tRNA  ribosomes  rRNA molecules  * ribosomal proteins  * translation factors  energie ```
74
Wat is tRNA
 Different tRNA molecules encoded by different genes  tRNASer carries serine  Common features * Cloverleaf structure * Anticodon * 3’ acceptor stem for amino acid binding
75
Aminoacyl-tRNA synthetase
 Catalyzes attachment of amino acids to tRNA  One for each of 20 different amino acids  Reactions result in tRNA with amino acid attached (charged tRNA or aminoacyl tRNA)
76
Verschil van ribosomen prokyote en eukaryote cellen
 Prokaryotes have one kind of ribosome  Eukaryotes have distinct ribosomes in different cellular compartments * In cytoplasm, mitochondria and chloroplasts * Here, we focus on cytosolic ribosomes
77
Waaruit bestaan ribosomen
 Composed of large and small subunits
78
Welke sites zijn er voor tRNAbinding en polypeptide synthesis
Discrete sites for tRNA binding and polypeptide synthesis  P site – Peptidyl site  A site – Aminoacyl site  E site – Exit site
79
Wat zijn de stages van translatie
Intiatie Elongatie Terminatie
80
Initiation van translatie
 mRNA, the first tRNA and ribosomal subunits assemble  Requires help of ribosomal initiation factors  Also requires input of energy (GTP hydrolysis)
81
Initiation van translatie bij bacterieen
 mRNA binds to small ribosomal subunit  facilitated by ribosomal-binding sequence * upstream of start codon in mRNA * Start codon a few nucleotides (~6) downstream  Initiator tRNA recognizes start codon in mRNA  Then large ribosomal subunit added  This places the initiator tRNA in the P site * middle of E/P/A site
82
Verschil tussen intiation bij bacterieen en eukaryote cellen
 1) Instead of a ribosomal-binding sequence, mRNAs have guanosine cap at 5’ end  mRNA is capped after transcription  Recognized by cap-binding proteins  2) Position of start codon more variable  In many cases, first AUG codon used as start codon
83
Wat is elongation bij translatie
1. Aminoacyl tRNA brings a new amino acid to the A site 2. Peptide bond is formed between the amino acid at the A site and the growing polypeptide chain 3. Movement or translocation of the ribosome toward the 3’ end of the mRNA by one codon
84
Termination bij translatie
 When a stop codon is found in the A site, translation ends  3 stop codons – UAA, UAG, UGA  Recognized by release factors  There is no tRNA for stop codons
85
Welke 3 mutaties hebben effect op translatie?
 Nucleotide Substitutions  Insertions of bases  Deletions of bases
86
Wat is de frame shift locatie
 Insertion -Extra base added into gene region  Deletion 0 Base removed from gene region  Both shift the mRNA reading frame wrong amino acids a premature stop codon  shortened protein
87
Verschil tussen coding en noncoding RNA
```  mRNA codeert voor eiwitten  Gen: structural gene • ncRNAs hebben andere funtie  Gen: non-structural gene  Grote variëteit in  Lange en korte ncRNAs  kort heeft regulatoire functie ```
88
Hoe wordt telomerase gereguleerd?
RNA molecule guides Telomerase complex naar uiteinde chromosoom En functioneert als template, wanneer target is gevonden
89
Waarmee kan ncRNA baseparen en wat beinvloed het dan?
ncRNAs kan baseparen met DNA of RNA | Beïnvloedt DNA replication, transcription, and translation
90
Hoe en waarin binden ncRNAs?
 ncRNAs binden aan Eiwitten  Stem-loop structuren in ncRNAs kunnen receptor zijn voor kleine molecule  Co-regulators
91
Wat zijn de functies van ncRNAs?
```  Scaffold  Guide  Stabilisatie complex  Ribozyme  Blocker  Decoy ```
92
Scaffold
basis voor complex met eiwitten  Ribosoom
93
Guide
brengt complex op specifieke plek in genoom |  Telomerase
94
Stabilisatie comples
Ribosoom
95
Ribozyme
RNA molecuul heeft catalytische activiteit |  self-splicing van tRNA
96
Blocker
regulatoire functie op mRNA niveau
97
decoy
Bindt aan ander ncRNA (baseparing) en blokkert dan zijn functies.
98
Wat zijn microRNAs
micro RNAs are small RNA molecules that silence the expression of mRNAs  A.k.a. small or short interfering RNA (siRNA)  siRNAs are man-made and added to cell
99
Waarvoor worden microRNAs gebruikt?
Important mechanism of mRNA silencing |  A.k.a. RNA interference (RNAi)
100
Hoe werkt microRNA?
```  Synthesized as pre-miRNA  Cut by Dicer to release miRNA  Forms RNA-induced silencing complex (RISC)  Upon binding mRNA is silenced by 1. mRNA degradation  dsRNA recognized by nucleases 2. RISC blocks translation  No binding ribosome ```
101
Wat is gene regulation en waarom is het er?
 control of level of gene expression  To ensure that proteins are produced at the correct time and amount  Saves energy by producing only when needed
102
Constitutive genes
are unregulated and have essentially constant levels of expression and presence
103
Hoe werkt prokaryote gene regulation en een voorbeeld
Responds to changes in the environment. Ecoli en lactose  When lactose is available, two proteins are made:  lactose permease – transports lactose into the cell  β-galactosidase – breaks down lactose  When lactose levels drop, the proteins are no longer made
104
In welke stappen vindt gene regulation plaats bij prokayrote cellen?
 Transcription initiation  Translation  Post-translation; activation/degradation of proteins
105
In welke stappen vindt gene regulation plaats bij eukaryote cellen?
```  Transcriptional regulation common  RNA processing  Translation  Post-translation Later stages are more influential ```
106
Hoe werkt eukaryote gene regulation en een voorbeeld
```  Responds to signals from environment  Necessary make different cell types  Cell differentiation  Cell types contain the same genome but different proteomes  because of gene regulation  Different set of proteins Different amounts of a protein Vb: verschillende types hemoglobine afhankelijk van noodzaak van O2 ```
107
Hoe werkt transcriptie regulatie bij prokayrote cellen?
 Door Transcriptie Regulatoren  Binden DNA op of in de buurt van de promoter en leiden tot meer/minder transcriptie van de genen onder controle van die promoter  herkennen een specifieke sequentie  binding site
108
Wat zijn 2 transcriptie regulatoren?
 Repressors; negatieve invloed |  Activators; positieve invloed
109
Waar bind repression?
Binds often on or downstream of promoter
110
Waar bind activator?
Binds on or upstream of promoter
111
Hoe gaat transcriptional regulatie?
 via small effector molecules (or co-regulatoren)  Binden Transcription Regulator geven dan conformationele verandering  Bij Repressors en Activatoren  Resultaat: wel/niet biden aan binding site

Genen en Cellen (2 decks)

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