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YEAR 2 S1 MOLECULAR > Kourosh L1 > Flashcards

Kourosh L1 Flashcards

1
Q

what is epigenetics

A

study of how heritable changes in GENE EXPRESSION or CELLULAR PHENOTYPE occurs without changes in BASE PAIRING

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2
Q

what is the most important example of epigenetic effect

A

DUTCH FAMINE STUDY

  • showed that children of mothers who survived the famine had:
  • inc risk of schizophrenia
  • overweight
  • cardiovascular disease

shows epigenetics

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3
Q

how are DNA and histone proteins associated together

A

electrostatic interactions

DNA wraps around the histone proteins, whose tails protrude from structure and are modified

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4
Q

what did Conrad Waddington propose epigenetics was about

A

nt the process of cellular decision-making during development. At various points in this dynamic metaphor, the cell can take specific permitted trajectories, leading to different outcomes or cell fate
ie a link between genotype and phenotype

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5
Q

what are histones

A

Proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes

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6
Q

what are nucleosomes

A

Fundamental unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores

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7
Q

what is chromatin

A

the complex of DNA and its intimately associated proteins

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8
Q

describe DNA methylation
what catalyses
where
what does this act as

A
  • adding methyl to DNA
  • catalysed by DNA METHYLTRANSFERASES
  • on position 5 of CYTOSINE nt
  • next to guanine
  • linked by phosphate group to form CpG dinucleotide
  • forms 5-methyl-cytosine

acts as: BINDING SITE for other proteins which “read” the modification and recruit other proteins which modify histones

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9
Q

describe histone modification

A
  • multiple types, catalysed by multiple enzymes
  • eg ACETYLATION and METHYLATION of histones H3 AND H4
  • directly alters DNA-protein interactions to change chromatin structure O alters the ability for a gene to be transcribed and expressed
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10
Q

acetylation of histones is performed by what

A 
HISTONE ACYLTRANSFERASES (HATs)
- adds an an acetyl group to lysine amino acids in this histone tail which causes loosening of chromatin to promote gene activation
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11
Q

how is acetylation of histones reversed

A

by HISTONE DEACETYLASES

- causes chromatin condensation, gene inactivation

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12
Q

describe methylation of histones
what is methylated
what doe sit cause

A

on LYSINE or ARGININE aa

  • in mono, di or tri methylation events
  • METHYLTRANSFERASES
  • gene activation and inactivation
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13
Q

relaxation of chromatin happens why

A
  • replication
  • transcription
  • repair
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14
Q

condensation of chromatin happens why

A
  • inhibit transcription

- cell division

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15
Q

how does chromatin remodelling occur

chromatin remodelling

A
  • change the position of the nucleosome
  • nucleosome sliding:
  • Histone chaperones (Nucleosome Assembly Protein (NAP-1))
  • ATP dependent chromatin remodelers (SWI2, SWF2)

both interact with histones DIRECTLY

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16
Q

how does histone variant exchange occur

what is it controlled by

A
  • change the composition of the nucleosome
  • core histones (2 of eaach: H2A, H2B, H3 AND H4)
    (H2AZ present at ACTIVE GENE PROMOTORS
    H2AX X present where DNA repair occurs)
  • controlled by:
    1) HISTONE CHAPERONES (eg Asf1)
    2) ATP dependent chromatin remodelers (eg SWR complex)
17
Q

how does histone tail modification occur

what is it controlled by

A
  • histone tails are flexible regions that flank both ends of the histone fold- Lysine (K) and Arginine (R) residues are modified on histone tails by:
  • Acetylation +
  • Methylation -
  • Phosphorylation ±
  • Ubiquitination
    • Degradation
18
Q

how does chromatin distribution affect protein exression

A

affects access of proteins to DNA seq

  • Process specific transcription factors (e.g. JAK/STAT transcription factors)
  • General transcription factors (e.g. TFIID)
  • RNA polymerase
19
Q

what is the name of the case study on methods used to detect histone changes

A

Encode Project

  • how proteins and DNA interact
  • which genes are coding etc
20
Q

why do we want to learn about protein-DNA interaction

A
  • interaction= important in normal development and function, and important in disease
    Important mechanism: DIRECT BINDING eg when proteins bind to DNA
21
Q

what does ChIP stand for

A

chromatin imuunoprecipitation

22
Q

what is ChIP

A

a method to investigate protein-

  • DNA interaction in vivo, find WHERE ON THE DNA seq a protein is acting
  • output is is enriched fragments of DNA that were bound by a particular protein
  • The identity of DNA fragments need to be further determined by a second method
  • formaldehyde used to covalently cross link proteins to DNA
  • bind the protein you are looking for to specific ANTIBODIES
  • covalent linking=reversed
  • wash everything else away
  • recovered DNA can be PCR amplified and map to reference genome (ChIP-seq)
    or hybridise to microarray (ChIP-chip)
23
Q

case study 1:amyotrophic lateral sclerosis (ALS)

A
  • rare neurological (motor nerve) disease, involvs neurons for VOLUNTARY muscle control
  • gradual deterioration
  • early symptoms: muscle weakness, stiffness
  • late: all voluntary muscles affected, cannot speak, eat, move, breathe
24
Q

treatment for ALS

A
  • no cure
  • no effective treatment
  • most patients die from resp. failure (3-5 years after first symptoms, 10% survive for 10+ years)
25
Q

what are risk factors for ALS

A

age
gender
ethnicity
military veterans (exposure to lead, pesticides env toxins)

26
Q

what causesALS generally

A
  • GENETICS: familial and sporadic: SOD1 gene

- ENV: - Exposure to toxic or infectious agents, physical trauma, diet, and behavioural/occupational factor

27
Q

what causes ALS to be progressive

A

DECREASE in acylated histone

  • p300 transcriptional co-activator proteins
  • FUS is an RNA-binding protein that regulates transcription, alternative splicing. Aberrations of FUS are causally associated with familial and sporadic ALS/FTLD.
  • Reduction in histone acetyl transferase (HAT) activity OR Increased HDAC activity

YEAR 2 S1 MOLECULAR (7 decks)

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