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Cell Biology > Lecture 10 Slides > Flashcards

Lecture 10 Slides Flashcards

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AP® Biology flashcards Biology 101 flashcards
0
Q

Lysosomes and vacuoles

A

Digestive organelles
Lysosomes digest proteins in organelles
Vacuoles we associate with plants

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1
Q

Proteozomes

A

Cytosolic proteins

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2
Q

How do I know if my gene is expressed? Where can I test for its expression?

A 
Stages are 
DNA replication
transcription
MRNA
Translation
protein

You can test post transcription or post translation

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3
Q

Suppose you are looking for a specific protein? What test can you use to see if you’ve found it?

A

Western blotting

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4
Q

Why can’t you use PCR with mRNA?

A

It is not a template for DNA

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5
Q

What can you use to test for mRNA?

A

Microarray
Northern blotting
RTPCR?

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6
Q

PCR

A 
Polymerase chain reaction
Amplification
DNA is copied 
Denaturion 95 degrees
Annealing 55-65 degrees
Extension 72degrees
Repeat
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7
Q

RTPCR

A

Reverse transcriptase PCR
Detects RNA expression
Create cDNA, has no introns
Use RNA and enzyme to create cDNA, on which you can use PCR

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8
Q

Glyceraldehydethreephosphate (GAPDH)

A

Housekeeping gene used as reference, control

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9
Q

What is most important regulatory step

A

Transcription controls

BY DNA regulatory proteins

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10
Q

Which subunits do DNA subunits usually have

A
  1. Binds DNA

2. Activator/repressor domain

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11
Q

How does protein subunit bind dna

A

Usually via h bonding to bases, ionic bonds with backbone

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12
Q

How do protein subunits activate or suppress

A

Bind RNA polymerase II or other proteins (how modular transcription)

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13
Q

How does binding happen between protein subunits

A

Alpha helices with major groups in DNA

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14
Q

Why’s codon is at start site

A

ATG

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15
Q

Upstream regulatory element(URE)

A

A short sequence of 6-12 bps “cis”

16
Q

Homeodomain

A

Part of protein that binds to specific regulatory regions of target genes.

17
Q

Homeobox

A

DNA sequence found within genes that are involved in the regulatory patterns of anatomical development in animals, fungi, and plants

18
Q

Benefit of having regulatory sequences and multiple conning sequences on genome

A

Reduces number of monomers you have to make

19
Q

How do I know what DNA my transcription factor binds to?

A 
Chromatin immunoprecipitation(CHIP seq)
DNA sequencing

Primary tissue treated with formaldehyde to covalently cross link DNA and proteins

Protein specific antibodies are added to immunoprecipitates to target protein
Proteins are then unlinked and DNA is purified

DNA fragments are amplified and fluorescently tagged

A library is constructed

Fragments are sequenced

Sequences are aligned to a reference of genome and then can be visualized

20
Q

How many proteins does a promoter bind to

A

Hundreds

21
Q

How is regulation of prokaryotic transcription simple

A

Most controls are at or near promoter

Just one polymerase bacterium

22
Q

What is a repressor? How does it work?

A

A protein that blocks RNAP from binding to promoter

23
Q

What does repressor usually bind to

A

Operator sequence

24
Q

What is activator? How does it work?

A

A protein that helps recruit RNAP to active site

25
Q

How is regulation of eukaryotic dna complex

A

Eukaryotic DNA is flexible
UREs can be 50+ kb from +1
Many proteins are involved and interact together

26
Q

TATA box

A

DNA sequence that indicates where a genetic sequence can be read and decoded. Type of promoter sequence. Says where transcription begins.

27
Q

Example of how many proteins are involved in eukaryotic transcription

A

RnaII binds to TATA. A mediator binds around RNAII. If DNA is flexible and bent, two activators at UREs far away can recruit RNAII/mediator to promoter. Somewhere closer, URE can have a repressor on it so as not to express its sequence.

28
Q

Three abilities of eukaryotic repressors

A

Can compete for activator binding site
Can inhibit activator interaction with RNAPII
inhibit RNAPII directly as well

29
Q

Three ways to get rid of bound repressors

A 
Conformational change
Phosphorylation
Ubi ligase (plants and animals)
30
Q

Epi genetics

A

Heritable changes in gene expression that does not involve changes to the underlying DNA sequence; a change to phenotype without a change to genotype.

31
Q

How can epigenetic mechanisms work

A

In cis -affect only one chromosomal copy

In trans - two self propagating mechanisms that work, affecting both chromosomal copies of a gene.

32
Q

Epigenetic mechanisms that act in cis

A

DNA methylation

Histone modification

33
Q

Epigenetic mechanisms that act in trans

A

Positive feedback loop by transcription regulator

Protein aggregation state

34
Q

What do transcription activators recruit? 4

A

Histone acetyl transferase (HATs)
Histone kinases
Histone chaperones
Chromatin remodeling complexes

35
Q

What do transcription repressors recruit?

A

Histone deacetylase
Histone methyl transferase
Chromatin remodeling complexes to create more heterochromatin and prevent gene expression

Cell Biology (35 decks)

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