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Genen en Cellen > Genen > Flashcards

Genen Flashcards

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
Q

Lagging strand

A

 DNA synthesized 5’3’ as Okazaki fragments

 Okazaki fragments consist of RNA primers plus DNA

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26
Q

Both leading and lagging strand

A

 RNA primers are removed by DNA polymerase and replaced with DNA
 DNA ligase joins adjacent DNA fragments

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27
Q

3 mechanisme voor accuratie

A
  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
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28
Q

Wat zijn telomeren

A

 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

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29
Q

Waarom is er telomerase

A

 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

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30
Q

Wat is het gevaar bij tolmoeren?

A

 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

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31
Q

Waaruit bestaan chromosomen?

A 
	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
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32
Q

Wat zijn de 3 niveaus van DNA compaction

A 
1.	DNA wrapping 
	DNA wrapped around histones to form nucleosome
2.	30-nm fiber
	Asymmetric, 3D zigzag of nucleosomes
3.	Radial loop domains
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33
Q

DNA Wrapping

A

DNA wrapped around histones to form nucleosome

Shortens length of DNA molecule 7-fold

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34
Q

30-nm fiber

A

Current model: asymmetric, 3D zigzag of nucleosomes

Shortens length another 7-fold

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35
Q

Radial loop domains

A

Interaction between 30-nm fibers and nuclear matrix

Each chromosome located in discrete territory

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36
Q

Euchromatin

A

Relatively open DNA-protein structure

Contain active genes

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37
Q

Heterochromatin

A
  • Highly compact DNA-protein structure
  • Hardly any genes
  • Composed of ‘junk’ DNA
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38
Q

Wat gebeurd er met chromosomen als cellen gaan splitsen

A

When cells prepare to divide, chromosomes become even more compacted (visible)
Metaphase chromosomes highly compacted
Then in non-active heterochromatin form

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39
Q

Minimum requirement voor neurospora crassa

A 
Carbon source (sugar), inorganic salts, and biotin
Neurospora can synthesize everything else it needs from those molecules
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40
Q

Waarvoor kunnen genes coderen?

A 
	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)
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41
Q

Transcriptie

A

 Produces a transcript (RNA copy) of a gene

 A messenger RNA (mRNA) specifies the amino acid sequence of a polypeptide

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42
Q

Translatie

A

 Process of synthesizing specific polypeptide on a ribosome using the mRNA template

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43
Q

Verschil van de genetische informatiestroom tussen eukaryote en prokyote cellen

A

 Eukaryotes also have an intermediate step called RNA processing, during which pre-mRNA is processed into active mRNA

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44
Q

Waar vind transcriptie en translatie plaats in de eukaryote cel?

A

Transcriptie in nucleus. Na pre-mRNA wordt er mRNA gemaakt, dit verlaat de nucleus en wordt getransleert in de ribosomen

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45
Q

Promotor van transcriptie:

A

Signals the beginning of transcription

46
Q

Regulatory sequence of transcription

A

Site for binding of regulatory proteins. The role of regulatory proteins is to influence the rate of transcription

47
Q

Transcribed region

A

Part of this region contains the information that specifies an amino acid sequence

48
Q

Terminator of transcription

A

Signals the end of transcription

49
Q

Wat zijn de 3 stages van transcriptie

A

Initiation
Elongation
TErmination

50
Q

Initation van transcriptie

A

 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
Q

Elongation van transcriptie

A

 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
Q

Termination van transcriptie

A

 RNA polymerase reaches termination sequence

 Causes both the polymerase and newly-made RNA transcript to dissociate from DNA

53
Q

Richting van RNA synthesis

A

synthesis of RNA transcript is 5’ to 3’ and DNA template strand reads 3’ to 5’

54
Q

gene order and orientation in bacterial genome/chromosome

A

 genes (templates for RNA) can be found on both DNA strands

 no overlap (in general)

55
Q

gene order and orientation in eukaryote genome/chromosome

A

 Also genes on both strands
 A lot of non-coding DNA between genes
 Genes have introns and exons

56
Q

Operon

A
  • Eén promoter (controle gebied)
  • Eén RNA molecuul
  • Meerdere eiwitten
    Alleen bij bacterieen
57
Q

3 vormen van RNA polymerase bij eukaryote transcriptie

A

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
Q

Verschil tussen prokaryote en eukaryote transcriptie

A

 Basic features identical to prokaryotes

 However, each step has more proteins

59
Q

RNA processing in eukaryote cellen

A

 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
Q

Spliceosome

A

removes introns precisely

Composed of snRNPs (small nuclear RNA + proteins)

61
Q

Introns

A

transcribed but not translated

62
Q

Exons

A

coding sequence found in mature mRNA

63
Q

Alternative splicing

A

splicing can occur more than one way to produce different products

64
Q

Capping

A

 Modified guanosine attached to 5’ end

 Needed for mRNA to exit nucleus and bind ribosome

65
Q

Poly A tail

A

 100-200 adenine nucleotides added to 3’ end
 Increases stability and lifespan in cytosol
 Not encoded in gene sequence

66
Q

Genetic code

A

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
Q

Degenerate code

A

more than one codon can specify the same amino acid

68
Q

Start en stop codon

A

AUG: Start codon

UAA, UAG, UGA : Stop codons

69
Q

Anti codon

A

Anticodon – 3 RNA nucleotide part of tRNA molecule

70
Q

tRNA role in translation

A

 anticodon
 Allows baseparing of tRNA with mRNA codon
 tRNA carries the encoded amino acid

71
Q

The wobble base ad tRNAs

A

 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
Q

The open reading frame

A

 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
Q

Wat is er nodig bij translatie

A 
	mRNA
	tRNA
	ribosomes
	rRNA molecules
	*   ribosomal proteins
	*   translation factors
	energie
74
Q

Wat is tRNA

A

 Different tRNA molecules encoded by different genes
 tRNASer carries serine
 Common features
* Cloverleaf structure
* Anticodon
* 3’ acceptor stem for amino acid binding

75
Q

Aminoacyl-tRNA synthetase

A

 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
Q

Verschil van ribosomen prokyote en eukaryote cellen

A

 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
Q

Waaruit bestaan ribosomen

A

 Composed of large and small subunits

78
Q

Welke sites zijn er voor tRNAbinding en polypeptide synthesis

A

Discrete sites for tRNA binding and polypeptide synthesis
 P site – Peptidyl site
 A site – Aminoacyl site
 E site – Exit site

79
Q

Wat zijn de stages van translatie

A

Intiatie
Elongatie
Terminatie

80
Q

Initiation van translatie

A

 mRNA, the first tRNA and ribosomal subunits assemble
 Requires help of ribosomal initiation factors
 Also requires input of energy (GTP hydrolysis)

81
Q

Initiation van translatie bij bacterieen

A

 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
Q

Verschil tussen intiation bij bacterieen en eukaryote cellen

A

 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
Q

Wat is elongation bij translatie

A
  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
Q

Termination bij translatie

A

 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
Q

Welke 3 mutaties hebben effect op translatie?

A

 Nucleotide Substitutions
 Insertions of bases
 Deletions of bases

86
Q

Wat is de frame shift locatie

A

 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
Q

Verschil tussen coding en noncoding RNA

A 
	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
Q

Hoe wordt telomerase gereguleerd?

A

RNA molecule guides Telomerase complex naar uiteinde chromosoom
En functioneert als template, wanneer target is gevonden

89
Q

Waarmee kan ncRNA baseparen en wat beinvloed het dan?

A

ncRNAs kan baseparen met DNA of RNA

Beïnvloedt DNA replication, transcription, and translation

90
Q

Hoe en waarin binden ncRNAs?

A

 ncRNAs binden aan Eiwitten
 Stem-loop structuren in ncRNAs kunnen receptor zijn voor kleine molecule
 Co-regulators

91
Q

Wat zijn de functies van ncRNAs?

A 
	Scaffold
	Guide
	Stabilisatie complex
	Ribozyme
	Blocker
	Decoy
92
Q

Scaffold

A

basis voor complex met eiwitten  Ribosoom

93
Q

Guide

A

brengt complex op specifieke plek in genoom

 Telomerase

94
Q

Stabilisatie comples

A

Ribosoom

95
Q

Ribozyme

A

RNA molecuul heeft catalytische activiteit

 self-splicing van tRNA

96
Q

Blocker

A

regulatoire functie op mRNA niveau

97
Q

decoy

A

Bindt aan ander ncRNA (baseparing) en blokkert dan zijn functies.

98
Q

Wat zijn microRNAs

A

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
Q

Waarvoor worden microRNAs gebruikt?

A

Important mechanism of mRNA silencing

 A.k.a. RNA interference (RNAi)

100
Q

Hoe werkt microRNA?

A 
	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
Q

Wat is gene regulation en waarom is het er?

A

 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
Q

Constitutive genes

A

are unregulated and have essentially constant levels of expression and presence

103
Q

Hoe werkt prokaryote gene regulation en een voorbeeld

A

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
Q

In welke stappen vindt gene regulation plaats bij prokayrote cellen?

A

 Transcription initiation
 Translation
 Post-translation; activation/degradation of proteins

105
Q

In welke stappen vindt gene regulation plaats bij eukaryote cellen?

A 
	Transcriptional regulation common
	RNA processing
	Translation
	Post-translation
Later stages are more influential
106
Q

Hoe werkt eukaryote gene regulation en een voorbeeld

A 
	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
Q

Hoe werkt transcriptie regulatie bij prokayrote cellen?

A

 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
Q

Wat zijn 2 transcriptie regulatoren?

A

 Repressors; negatieve invloed

 Activators; positieve invloed

109
Q

Waar bind repression?

A

Binds often on or downstream of promoter

110
Q

Waar bind activator?

A

Binds on or upstream of promoter

111
Q

Hoe gaat transcriptional regulatie?

A

 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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