Exam 2 10/11 Britton Flashcards
What is the cell cycle
Set of 4 phases in which DNA/cellular components duplicate and divide into daughter cells
What are the phases of the eukaryotic cell cycle
- G1
- S phase
- G2
- M phase
Interphase is made up of:
G1, S phase, G2
G1 phase
cell grows and synthesizes all cellular components that are essential for DNA duplication
S phase
DNA synthesis replicates the genetic material
(each chromosome duplicated/2 sister chromatids)
G2 phase
Cell prepares for division in M phase
M phase
Mitosis/cytokinesis - generates 2 identical daughter cells
What are the cell cycle checkpoints?
Regulate cell cycle transition
- G1 checkpoint
- G2 checkpoint
- M checkpoint
G1 checkpoint
determines whether conditions are favorable for cell division to proceed
G2 checkpoint
correct chromosome duplication is assessed
M checkpoint
attachment of each centromere to the spindle fibers is assessed, mitosis only proceeds if this is correct
At each cell cycle checkpoint, cell examines:
internal and external cues and decides whether or not to move forward with division
Cell enters next phase of division if:
Necessary conditions exist
Cell cycle is halted if:
Necessary conditions are not met
Normal cells transition through the cell cycle in a ____ way
Regulated
Cell division, growth, repair of genetic damage is regulated
Errors in checkpoints have _____
Catastrophic consequences - uncontrolled cell division or cell death
Regulation of the cell cycle involves what proteins/enzymes?
- cyclins
- cyclin dependent kinases (CDK)
____ are serine/threonine protein kinase enzymes that phosphorylate specific target proteins
CDKs
____ act as the signal for the cell to pass into the next phase of division
CDKs
CDKs are inactive in the absence of
Cyclins (cyclins bind to CDKs and activate them)
____ are regulatory proteins with no catalytic activity
Cyclins
True or false: Cyclins themselves have catalytic activity
False
After binding to CDKs, what eventually happens to cyclins?
Get degraded by cytoplasmic enzymes, deactivating the CDKs
Cyclin-CDK complexes are unique to:
Each cell cycle phase
Cyclin-CDK complexes activate:
Specific genes to drive cells through the cell cycle
Cyclin A can form a complex with which CDK(s)?
CDK 1 and CDK 2
Which phase of cell cycle is associated with CDK1 and Cyclin A/B complexes?
Mitosis
Cyclin E can form a complex with which CDK?
CDK 2
Which phase of cell cycle is associated with CDK2 and Cyclin A/E complexes?
Entry into S phase
Cyclin D can form complexes with which CDK?
CDK 4 and 6
Entry into G1 phase requires which cyclin/CDK complexes?
CDK4-cyclin D
CDK6-cyclin D
Cyclins and CDKs must undergo _____ during the cell cycle
constant cycle of synthesis and degradation
Before a cell can progress from one phase of the cell cycle to the next:
it must degrade the cyclin that characterizes that phase of the cell cycle
If cyclin is not degraded:
Cell cycle does not continue
Favorable conditions for replication
- growth factor signals
- DNA integrity
- cell size
- protein reserves assessed
What checkpoint is referred to as the restriction point?
G1
What happens at the restriction point?
Cell is committed to division and moves into the S phase
If conditions are not favorable during G1 checkpoint:
cell enters G0 resting state, await further signals when conditions improve
True or false: some cells remain in G0 for lifetime
True - neurons, skeletal muscle cells
Transition from G1 to S phase is ruled by: (2)
- CDK4/6-cyclin D (G1 checkpoint)
- CDK2-cyclin E (entry into S phase)
What is E2F
transcription factor important for cell growth
What happens when E2F is bound to retinoblastoma (Rb) protein?
Production of proteins necessary for G1/S transition is blocked
Rb
Retinoblastoma protein
tumor-suppressor protein/negative regulator of cell cycle
How does E2F get released from Rb?
CDK4/6-CyclinD phosphorylates Rb, releasing E2F
E2F induces ____ progression in association with ____
S-phase; CDK2-cyclin E
Ras protein is a
Proto-oncogene
Ras activates:
G1 checkpoint cyclins
What happens if Ras protein is mutated?
- Becomes constantly active so will constantly activate G1 cyclins, leading to uncontrolled cell cycle into S phase
- causes cancer
____ checkpoint prevents entry into M phase if certain conditions are not met
G2
What happens if DNA is not properly replicated/intact during S phase?
- Cell cycle is paused at G2 checkpoint
- cell will attempt to complete DNA replication or repair the damaged DNA
Forkhead box M1 protein
transcription factor that allows for transition to M phase
activates expression of FoxM1 target genes
In order for FoxM1 to become active, what needs to happen?
Needs to get phosphorylated by CDK2-cyclin A and CDK2-cyclin E
M checkpoint also known as
Spindle checkpoint
What are the mitotic CDK’s?
CDK1-cycin A, CDK1-cyclin B
G1/S phase CDKs are inhibited by
Mitotic CDKs
When mitotic CDKs are high during M phase, what happens?
factors that initiate DNA replication are inhibited
2nd DNA synthesis stopped til mitosis is complete/passes G1 checkpoint
Mitotic CDKs activate:
APC/C
APC/C function
allow chromatids to separate at anaphase and complete mitosis
___ decreases the possibility to aneuploidy
APC/C
Negative regulators of the cell cycle- function
Halt the cell cycle
Cyclins/CDKs are negatively regulated by
Cyclin-dependent kinase inhibitors (CKIs)
Examples of negative regulators of the cell cycle
- INK4 protein inhibitors of CDK4
- CDK-interacting proteins
- E3 ubiquitin enzyme
- tumor suppressor proteins (p53, p21, Rb)
Tumor suppressor proteins act primarily at the
G1 checkpoint
True or false: tumor suppressor proteins are often mutated/damaged in cancer cells that replicated uncontrollably
True
p53 function
halts cell cycle if damaged DNA is detected, recruits enzymes to repair the DNA
Where is p53 found
In almost every cell
p21 function
enforces the halt dictated by p53 by inhibiting the activity of CDK/cyclin complexes
Rb binds to E2F transcription factor to:
block production of proteins needed for G1/S transition
Many anti-cancer drugs act at the level of
Cell cycle signaling pathways
1st and 2nd generation anticancer drugs inhibit
Range of CDKs
3rd gen anticancer drugs
Specific inhibitors of CDK4 and CDK6 (G1 CDKs)
Side effects of anticancer drugs
- neutropenia
- thrombocytopenia
Even though we have many different cell types and organs:
All cells have the same genome
What gives a cell its unique properties?
Different cells express different RNA transcripts and proteins due to gene regulation
Central dogma
DNA to RNA to protein
Genome is ____-specific
Species
Exome
- entire collection of RNA molecules
- different in different tissues
Proteome
Total collection of proteins in a cell
_____ are always transcribed in all cell types
Housekeeping genes
Examples of housekeeping genes
genes needed for DNA polymerases, metabolism proteins
Specialized genes involve those which transcription is:
either on or off in certain cells
Hb only expressed in RBC
Finely tuned genes can ____ in response to external signals
Change expression
The set of genes expressed in a cell determines:
the set of RNAs and functional proteins it contains, giving it unique properties
Many genes are regulated primarily at the level of:
transcription
DNA normally exists as:
Chromatin/chromosomes
How is chromatin formed?
When DNA wraps around histone/non-histone proteins
Euchromatin
lightly packed, transcriptionally active
Heterochromatin
Highly condensed, transcriptionally inactive
What is the first stage of DNA compaction?
Nucleosome
Methods of epigenetic modification
- DNA methylation
- Histone modifications
What adds methyl group to DNA molecule?
DNA methyltransferase enzyme
True or false: DNA methylation occurs anywhere on a DNA molecule
False - on CpG dinucleotide
DNA methylation forms
5-methyl-cytosine
DNA methylation acts as a signal/marker for:
other proteins that read the modification that then recruit other proteins who can modify the histones
Histone proteins found in nucleosome
2 each of:
- H2A
- H2B
- H3
- H4
Nucleosomes are further packed together by
- histone N-terminal tails
- histone H1 molecules
Chromatin blocks access of
Transcription factors to potential DNA binding sites
Changes in chromatin structure play a major role in:
regulating gene expression and DNA replication
Mechanisms of changing chromatin structure
- enzymatic modification of the histone N-terminal tails
- ATP-driven chromatin remodeling complexes (ATP hydrolysis)
Modifications of histone proteins include:
- acetylation
- methylation
- phosphorylation
Histone acetylation is done by
Histone acetyl transferase (HAT)
Histone methylation is done by
Histone methyl transferase (HMT)
Removal of acetyl groups of histones is done by
Histone deacetylase complex transferase (HDAC)
Histone code
pattern of histone modifications; has specific meanings
Methylation function
usually promotes heterochromatin formation to silence DNA transcription and gene expression
ATP driven chromatin remodeling complex is thought to
Push on the DNA and loosen the attachment to the histone core, encourages transcription
Gene regions include
- coding region (introns and exons)
- 5’ UTR
- 3’ UTR
Promoter
region upstream from a gene which is a binding site for transcription factors, RNA polymerase, etc
Regulatory sequences
binding sites on DNA for various transcription factors
Outcomes of transcription factors binding to DNA
Enhance, diminish, silence the transcription of a gene
Where is regulatory sequence located relative to the associated gene?
At a distance
Genetic switch
Transcription can be turned on and off in response to a variety of signals
Components of a genetic switch
- specific DNA sequences
- proteins that bind to these DNA sequences
Other names for transcription factors
- DNA binding proteins
- Gene regulatory proteins
Specific transcription factors recognize:
specific DNA consensus sequences
Transcription factors contain _____ that can read DNA sequences
Structural motifs
Examples of transcription factors structural motifs
- helix-turn-helix proteins
- zinc finger proteins
- leucine zipper proteins
Transcription factors read ___ of DNA helix
outside of
Positive control
transcription factors
When TFs bind to DNA and turn gene transcription on
Negative control
transcription factors
When TFs bind to DNA and turn transcription off
Negative control TFs are known as
Repressors/gene repressor proteins
True or false: TFs can function as activators or repressors or both on different genes
True
True or false: A single type of TF can regulate the expression of different genes
True
TFs can form ____ and ____ proteins
Homomeric; heteromeric
Combinatorial Gene Regulation
Different combinations of TFs can give rise to different cell/tissue types (ex. in development)
____ are critical for development
Transcription factors
Mutations in TF PAX9 results in
Partial/total anadontia
Mutations in TF RUNX2 causes
Supernumerary teeth
TATA box
- Gene promoter
- consensus sequence of TATAA/TAA/T
- -30 upstream to gene transcription start site
Before transcription can begin:
RNA polymerase II requires general transcription factors to assemble at the promoter
Once TFs are recruited:
- recruits RNA Pol II to promoter
- position and help RNA Pol bind to promoter
Initiation of transcription
- DNA is pulled apart (helicase activity)
- RNA Pol phosphorylated
Post transcriptional control of gene expression methods
- attenuation
- RNA processing
- RNA transport
Attenuation
- premature termination of an RNA molecule while being transcribed
- growing RNA chain creates a structure that interacts with RNA Pol to cause it to stop transcription
Pre-mRNA
primary mRNA transcripts in the nucleus
RNA transcript processing involves
- 5’ capping
- 3’ polyadenylation
- splicing
When does RNA processing occur
As soon as transcript is being made
Exon-intron junctions contain
Consensus sequences (where splicing happens)
GU-AG rule
mRNA splicing - GU at 5’, AG at 3’
Spliceosome
complex of small nuclear RNA (snRNA) and ribonucleoproteins
Lariat
Loop structure resulting from cut 5’ end of intron that links to adenine
Intron is removed as a shape of a
Lariat
Splicing makes genes more
Modular - allows new combinations of exons to be created
Alternative splicing gives rise to
Different proteins rising from single mRNA transcript
Example of a gene that undergoes alternative splicing
- Tropomyosin gene
- amelogenin gene (exon 4 inclusion detrimental to enamel matrix formation)
Alternative exon splicing can cause disease such as in:
abnormal processing of the beta globin transcript in beta thalassemia
mutations can give rise to abnormal exon splicing
Alternative splicing can be regulated by
Activator and repressor proteins
Where are RNAs transported from/to
From nucleus to cytoplasm
Where is mRNA processed
In nucleus before leaving for cytoplasm
RNA exits via
Nuclear pore complexes that cover the nuclear membrane
The amelogenin gene is composed of ____ exons
7
(inclusion of 4 deleterious to enamel production)