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BIOL 200 > Unit 3 > Flashcards

Unit 3 Flashcards

1
Q

Nuclear envelope

A

outer nuclear membrane is continuous with the inner membrane via nuclear pore. The perinuclear space in between is continuous with the ER lumen. Surface is studded with ribosomes. Cytoplasm and nucleoplasm are connected with nuclear pores

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2
Q

Nuclear lamina

A

made up of lamins and is located beneath the inner membrane and provides support to the nuclear envelope. The nuclear lamina is where interphase chromatin is attached. Proteins in the inner membrane can also be anchored to the nuclear lamina

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3
Q

What happens to the nuclear lamina during mitosis?

A

1) nuclear lamins are phosphorylated by attaching a phosphate group
2) the phosphorylation causes a slight conformation change in the lamins and destabilizes the lamin
3) nuclear lamina breaks down and causes the nuclear envelope to break down

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4
Q

How does the nuclear envelope reform?

A

1) phosphate groups are removed from the lamins and the nuclear lamina reforms
2) since nuclear lamina is attached to the chromosome and nuclear envelope, mitosis ends with al the components of the nucleus separated away from the cytoplasm

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5
Q

Ribosomes

A

made from protein and rRNA. Ribosomal proteins are made in the cytosol. Once they’re synthesized, they’re imported into the nucleus and assembled with the rRNA molecules in the nucleolus

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6
Q

rDNA (nucleolus organizer regions, the regions where the nucleolus forms)

A

regions in the human genome that have rRNA genes on theme and codes for rRNA. Structural proteins in the nucleolus interacts with rDNA to collect these regions in a single area of the nucleus

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7
Q

Nuclear pores

A

controls macromolecule transport in the nucleus. Transport method depends on the size of molecule:

1) very small molecules (approx. 9 nm) can diffuse (free diffusion) without help, such as H2O, ions, ATP, GTP.
2) molecules above the free diffusion limit needs an input of energy. Uses GDP in active transport

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8
Q

What goes in and out of the nucleus?

A 
in:
histone proteins
polymerases
transcription factors
ribosomal proteins

out:
ribosomal subunits
mRNA protein complexes
fully processed and spliced transcripts

All these proteins have a code in their primary sequence that are specifically targeted

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9
Q

How is a protein sent? (Or how does protein targeting work?)

A

1) protein must have a destination-specific code
2) there must be a specific receptor that recognizes the signal seq for destination

Differences in the final destination of the protein depends on its primary amino acid sequence

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10
Q

Where are proteins synthesized?

A

it occurs in the cytosol on free (unattached) ribosomes

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11
Q

Consensus sequences

A

they are the most common amino acid sequences that are used for a specific type of protein targeting. If one lines up the amino acid sequences of a number of proteins that are targeted to a particular organelle, they’ll all contain this sequence or similar

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12
Q

Consensus sequence (or NLS) of proteins destined for the nucleus and where is it often found?

A

-Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val-
also called KKKRK

it’s often found near the N-terminus of the molecule and it must be on the surface of the protein so nuclear import machinery can access/identify the protein for import. This tells us that proteins are imported into the nucleus after translation, in a folded state

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13
Q

Nuclear import steps

A

1) a Nuclear Localization Signal (NLS) is recognized (usually KKKRK), which should be on the surface found near the N-terminus
2) NLS region binds to soluble cytosolic Nuclear Import Receptor protein (NIR) and forms a protein-receptor complex
3) protein receptor complex binds to cytosolic fibril of nuclear pore and a GTP reaction results in a change of configuration of the pore, allowing the protein complex to go through the pore and in the nucleus
4) Once in the nucleus, NIR dissociates from the nuclear protein and returns to the cytosol
5) NLS remains a part of the nuclear protein

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14
Q

Nuclear export steps

A

1) proteins contains nuclear export signal that binds with a receptor, which then binds to the nuclear pore
2) after transport, nuclear export receptor and protein dissociate

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15
Q

Interphase chromatin (30 nm fibre)

A

made up of DNA and histones and packed DNA in the interphase cell. During gene expression, regions of the packed DNA will loosen by shifting/removing some of the packing proteins. Most common form of chromatin

Interphase chromatins can either arrange to euchromatin or heterochromatin

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16
Q

Non-histone chromatin-associated proteins

A

different types of proteins that interact with DNA and/or other histones that regulate organization of chromosomes, gene expression, and control folding chromatin patterns

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17
Q

Histones

A

basic proteins that strongly interact with DNA

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18
Q

Types of histones

A

core histones - H2A, H2B, H3, and H4 interact strongly with each other and with DNA to form the nucleosome

H1 - binds outside of the nucleosome and helps pack the nucleosome together to tightly pack the DNA

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19
Q

What is a core histone octamer and how is it formed?

A

eight protein complex found at the center of a nucleosome core particle. It comprises of 2 copies of 4 polypeptides that form primarily due to hydrophobic interactions between these polypeptides

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20
Q

What makes up a nucleosome?

A

nucleosome core particle: DNA + core histones

linker DNA: DNA between each nucleosome core

therefore, a nucleosome is made up of the nucleosome core particle and linker DNA

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21
Q

Beads-on-a-string (11 nm fibre)

A

can only be produced experimentally by removing the H1 histone and not really seen in a live cell

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22
Q

Chromatin (30 nm fibre)

A

11 nm is condensed through interaction with histone H1, which binds to the outside of the nucleosome and brings adjacent nucleosomes together. Looks like a loose spiral

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23
Q

Upper levels of chromatin packing

A

only during mitosis. 30 nm is further packed during interphase by non-histone scaffolding proteins and help make large chromosomal loops of DNA with genes exposed at the end of the loops

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24
Q

Transcriptional control

A

determines when and how often genes are transcribed

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25
Q

Where does transcription and translation occur?

A

transcription occurs in the nucleus, translation occurs in the cytosol

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26
Q

Euchromatin

A

chromatin that’s transcriptionally active and “loosened” to allow access to DNA

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27
Q

Types of heterochromatin

A

constitutive heterochromatin - always condensed and is found structural areas like centrosomes and telomeres. No genes are located in areas with constitutive heterochromatin

facultative heterochromatin - not always condensed and their genes are temporarily shut down by restricting access to DNA

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28
Q

How are some DNA expressed?

A

active DNA are regularly transitioned between different states of condensation (ie. euchchromatin heterochromatin) to allow/restrict genes, which are controlled by histone modifying enzymes and chromatin remodeling complexes

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29
Q

Histone modifying enzymes

A

chemically alter the histones of the nucleosome core. Acetylation, methylation, and phosphorylation add functional groups to the short tails of the 8 core histones. These 3 are covalent modifications

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30
Q

Chromatin remodeling complexes

A

histone tail modifications serve as docking sites for chromatin-remodeling complexes. They can “shift” the DNA around the nucleosome through energy release of ATP hydrolysis. The exposed genes can now be transcribed

NOTE: chromatin remodeling and transcription are physically linked

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31
Q

Transcription factors

A

enhance or inhibit the ability or rate to transcription. It controls when and how transcription occurs. Their presence mean chromatin-modifying complexes are also present, which allows the RNA polymerase to access the DNA without completely dissociating the histone complexes

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32
Q

Combinatorial control

A

the binding of different combinations of transcription regulators in different tissues during different times, which allow us to continue to function properly

33
Q

General properties of transcript processing

A

1) all transcripts are processed (mRNA, rRNA, tRNA) in the nucleus before they’re transported into the cytoplasm
2) processing is carried out by proteins and RNA that bind and modify transcripts
3) all processing signals are encoded into the primary sequence of RNA transcripts themselves

4) processing involves modifications:
- addition of sequences
- cleavage of transcript into several pieces
- removal of some sequences
- splicing
- folding

34
Q

Small nuclear RiboNucleoProteins (snRNPs)

A

protein-RNA complexes that contain a small RNA molecule that’s complementary to the recognition sequences in the RNA transcript

35
Q

Spliceosome

A

when small nuclear RiboNucleoProteins (snRNPs) come together to form a large complex

36
Q

Lariat loop

A

formed when the left boundary of the intron is cut and the intron end is bounded to the 3’ hydroxyl of one of the nucleotides near the “right” end of the intron

37
Q

Advantages to introns and exons

Alternative splicing

A

splicing of pre-mRNA in different ways can produce different mRNA and result in diverse products using the same gene. This is an advantage in having introns and exons

38
Q

Why do we have a nucleus?

A

it separates transcription from translation, which controls which genes get expressed and when. It is a sort of “quality control” for the cell. Without a nucleus, mutation that occur will immediately be made into a protein. It also protects the genetic material

39
Q

Nucleolus

A

a specialized region where rRNA is made. It’s function is to synthesize RNA and assemble ribosomal subunits from rRNA and ribosomal proteins

40
Q

Ribosomal proteins

A

1) ribosomal proteins are synthesized in the cytoplasm, imported into the nucleus, and enter the nucleolus
2) ribosomal subunits are assembled from ribosomal proteins and ribosomal RNAs
3) after proper assembly, each ribosomal subunit (large and small) is exported to the cytoplasm and assembled together during translation in the cytoplasm

41
Q

Nuclear Pore Complex (NPC)

A

transport gate at the nuclear envelope and is bi-directional. Transported molecules do not have to unfold to cross the NPC

42
Q

Nucleoporins

A

make up the nuclear pore complex and form a tangled mesh work that fills the centre of the NPC, preventing the passage of large molecules

43
Q

What is imported in and out of the nucleus?

A 
In:
Histones
RNA polymerase
Spliceosomes
Ribosomal and transcription proteins
Proteins involved in replication
Lamins that make up the laminate
DNA replication
Gene regulation

Out:
mRNA
tRNA
Ribosomal subunits

NOTE: only fully processed and spliced transcripts are allowed out the nucleus

44
Q

What are the two mechanisms for proteins to undergo nuclear transport?

A

1) free diffusion - ions smaller then 9nm. Not selective and doesn’t require energy
2) active transport - molecules from 9 - 39 nm. It’s selective and proteins need to have an AA seq called NLS. A receptor binds to the NLS so the protein can be transported. Requires energy via the hydrolysis of GTP

45
Q

What happens to proteins with no targeting signals?

A

since protein synthesis occurs in the cytoplasm, they just end up in the cytosol

46
Q

Nuclear localization signal (NLS)

A

-Lys-Lys-Lys-Arg-Lys
This seq can be anywhere in the AA seq of the protein, but it HAS to be exposed so the nuclear import receptor can bind to it. NLS is not cleaved after the protein is imported into the nucleus

47
Q

Nuclear Import Receptor (NIR)

A

they are soluble proteins in the cytosol that recognize NLS

48
Q

Mechanism of nuclear import of proteins (5)

A

1) NIR binds to the NLS and targets the protein to the NPC
2) receptor-cargo complex binds to the NPC cytoplasmic fibrils
3) receptor-cargo complexes cross the NPC
4) in the nuc, the receptor separates from the protein releasing the protein into the nuc
5) NIR returns to the cytoplasm through the NPC

49
Q

Mechanism of nuclear export

A

1) nuclear export signal (NES) in the AA rich in Leu is exposed
2) nuclear export receptor (NER) recognizes it
3) GTP (energy) is used and GTPase is used to cleave the GTP

50
Q

Do mRNAs have a NES?

A

no. This is because mRNAs do not have amino acids, but have nucleotides. So they do not have an NES, which is an amino acid. Instead, a protein containing the NES is bound to the mRNA and is what is recognized if the mRNA needs to leave the nucleus

51
Q

How do the dispersed nuclear proteins return to the nucleus after cell division?

A

within the primary sequence, the dispersed nuclear proteins contain a NLS. In the cytosol, receptors bind the NLS, which allows proteins to be moved through the nuclear pore using the energy generated by hydrolysis of GTP

52
Q

is the NLS necessary and sufficient to direct a protein to a particular destination? What experiments would you perform to test this?

A

(in the cell, yes) in other situations, we can only find out by doing a:

Lost of function (LOF) experiment - delete/mutate the thing and observe. This tests if the component is necessary

Gain of function (GOF) experiment - add a component not normally present and observe. Tests if the component is sufficient

53
Q

How is the nucleus functionally organized?

A

interphase nucleus has “chromatin territories”, meaning the interphase chromosomes are spatially organized. Specific regions of the chromosomes are attached to the nuclear lamina

54
Q

Chromosomes vs. Chromatin

A

chromatin is the material that makes up the chromosomes in the nuc

55
Q

Why is DNA a double helix?

A

sugar phosphate backbone is hydrophilic, so it faces the aqueous solution

the bases projecting towards centre, stacked on top of the other, forms a hydrophobic core away from aqueous solution

allows bases to form H-bonds with each other

56
Q

Naked DNA (2 nm)

A

2 anti-parallel polynucleotide chains form an alpha helix and H-bonds form between the bases

57
Q

What kinds of interactions/bonds allow DNA to wrap around the histone octamer?

A

hydrogen bonds and ionic bonds. The phosphate group in the DNA is responsible for forming non-covalent bonds with histones

58
Q

How can we experimentally separate DNA from the histones?

A

first, remove the H1 histones to get beads-on-a-string. Nuclease can digest linker DNA, where we are left with nucleosomes. Then use salt washes to dissociate ionic bonds between the wrapped DNA and the octameric histone core resulting in naked DNA, which we can then use for gel electrophoresis

59
Q

Histone H1

A

“linker histone” that binds linker DNA and pulls nucleosomes together into the 30 nm fiber in a twisted array

60
Q

How are the loops of 30 nm chromatin formed?

A

they are formed by non-histone chromatin proteins that form a scaffold

61
Q

Do histones in the nucleosomes bind tightly to the DNA?

A

no. If this occurs, the DNA will not be able to move, meaning the DNA would be unstable since it would be inaccessible for transcription and replication

62
Q

What are chromatin condensation states controlled by? aka heterochromatin euchromatin

A

1) histone modifying enzymes
2) chromatin remodeling complexes
3) binding of transcriptional regulators

63
Q

Acetylation and deacetylation

A

acetylation of histone tails promotes gene transcription by loosening chromatin and deacetylation condenses the chromatin to stop transcription

64
Q

Transcription regulators

A

(an example of one can) further destabilize nucleosomes and facilitate binding of other transcription-related proteins

65
Q

Quick review: what are the 2 major parts of a transcription unit (gene) and what do they consist of?

A

1) regulatory region
Promoter - regulatory region of DNA near the transcriptional start site. It binds general transcription factors and RNA pol
Enhancers/silencers - bind activators and repressors to control transcription. May be far away from the actual gene

2) transcribed region
Transcribed by the RNA pol moving along the DNA template in 3’ to 5’ direction. New ribonucleotides are added to the 3’ end of the growing RNA molecule which is growing in the 5’ to 3’ direction. RNA is the product of transcription

66
Q

Open reading frame

A

the code for translation

67
Q

Quick review: how do genes produce proteins (ie briefly describe what happens during transcription and translation)

A

transcription - DNA is always read 3’ to 5’ and RNA is always synthesized 5’ to 3’

translation - mRNA is read 5’ to 3’. Protein is synthesized from N to C

Scientific convention is to write all DNA/RNA sequences 5’ to 3’

68
Q

Brief summary of transcription units and DNA

A

transcription can occur in both directions on chromosomes, but genes are always read 3’ to 5’

the promoter region determines which strand of DNA is the template

“template/coding strands” and “upstream/downstream” are used relative to the gene being discussed

69
Q

How do DNA-binding proteins (transcription factors) specifically recognize the correct binding site on DNA? aka how is the promoter recognized by general transcription factors

A

they make specific non-covalent interactions with the sides of the base-pairs in the major or minor groove of that sequence

70
Q

Does the assembly and stability of the general transcriptional machinery depend on the binding of other regulators?

A

yes. It is an interplay between all of the regulatory seqs and proteins that bind it that will determine where (which tissue), when, and how often a gene is transcribed

aka:
general transcription factors - bind to the promoter and help recruit and position RNA pol

activators and repressors - bind up/downstream regulatory regions and turn on/off transcriptions

71
Q

Post-transcriptional control of gene expression

A

in the nucleus, all RNA molecules are processed while they are being synthesized. RNA processing must be completed before export from the nucleus

72
Q

How is RNA processed?

A

they have a signal that is encoded within the RNA primary seq

73
Q

mRNA processing events (mRNA processing control decreases chances of mutations)

A

1) 5’ cap is added to pre-mRNA shortly after initiation of RNA synthesis. It consists of a guanine with an added methyl group
2) 3’ polyA tail - a signal for cleavage is encoded in the pre-mRNA’s primary nucleotide seq (endonuclease cleaves it). Following the cleavage, multiple adenines are added (via polyA polymerase)
3) RNA splicing, where exons are expressed and introns are removed

74
Q

Purpose of mRNA processing events

A

1) the 5’ cap helps stabilize the transcript (protect from nuclease degradation). It also helps bind to protein for export from nucleus, and aids in ribosome recognition and binding to initiate translation in the cytoplasm
2) 3’ polyA tail helps stabilize the transcript and helps with translation termination
3) RNA splicing results in a continuous open reading frame for translation and it can give alternative transcripts to allow for variation in the final mRNA product

75
Q

What is the process of removing non-coding introns from pre-mRNA

A

1) special recognition sequences (signals) on the pre-mRNA are located at the intron-exon junctions and within the intron
2) these special recognition seqs are recognized by snRNPs
3) snRNPs are at the core of spliceosomes and the spliceosomes cleaves the RNA and links the exons together

76
Q

How does the spliceosome “know” where to catalyze the splicing reaction?

A

there is complementary base pairing between snRNA and mRNA

77
Q

snRNP process

A

1) RNA in the snRNP recognizes intron/exon junctions and base pairs
2) other proteins and snRNPs join to form the spliceosome
3) 5’ (left) end of intron is cut and forms a lariat. The lariat is the intron. 3’ (right) end of intron is cut and intron is released
4) the exons are linked together

78
Q

When does the assembly of spliceosome begin and when does the actual splicing occur?

A

the assembly of the spliceosome begins during transcription and splicing occurs after transcription is finished

79
Q

How is alternative splicing controlled?

A

it is controlled by proteins that can activate, silence, or enhance splicing by binding the pre-mRNA. The secondary structure of pre-mRNA can also help by bringing together specific splice donor and acceptor sites or by masking a specific donor or acceptor site

BIOL 200 (7 decks)

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