Unit 4: Eukaryotic DNA Rep, Genes, Genomes Flashcards
Where are chromosomes located?
nucleus
What is the difference between replicons in prokaryotes and eukaryotes?
Eukaryotes chromosome consist of a number of replicons where prokaryotes have only one single replicon
In eukaryotes, how are duplicated chromosomes distributed to the daughter cells?
during mitosis by means of mitotic spindle.
After mitosis, what are the two pathways of the daughter cell?
daughter cells can continue to divide aka enter G1 or enter G0 which is a resting state
If a daughter cell decides to continue dividing what must happen?
if decision is to divide, cell enters G1 where it needs to grow to the size of parent cell. In G1 everything (macromolecules, proteins, lipids) except DNA is doubled
What must happen for a cell to enter S phase?
There is tight regulation/checkpoint from G1 to S phase. This checkpoint ensures there is no DNA damage and that the cell has grown to its proper size.
How does S phase begin?
S phase begins w/initiation of first replicon in the area of an active gene.
What is the signal transduction pathway?
The process by which a stimulus or cellular state is sensed by and transmitted to pathways w/in the cell. This pathway is found in all eukaryotes
Genes that encode for proteins in the cell cycle are called?
proto-oncogenes
What is an oncogene?
a gene that when mutated may cause cancer
The cell cycle/signal transduction pathway is initiation by what receptor and protein?
Growth Exchange Factor: Epidermal growth factor
Growth factor receptor: epidermal growth factor receptor
What is the function of a growth factor?
to cause dimerization of its receptor and subsequent phosphorylation of the cytoplasmic domain of the receptor
What is the function of the growth factor receptor?
to recruit the exchange factor SOS to the membrane to activate RAS
What is the function of activated RAS?
the function of activated RAS is to recruit RAF to the membrane and become activated
What is the function of RAF?
the function of RAF is to initiate a phosphorylation cascade leading to the phosphorylation of a set of transcription factors that can enter the nucleus and begin the S phase (DNA replication)
What type of protein is epidermal growth factor receptor (EGFR)?
an integral membrane protein w/extracellular domain with a single pass transmembrane region and a cytoplasmic domain with tyrosine kinase activity
What type of growth factor is the epidermal growth factor? What is the role of EGF?
- a peptide hormone that binds to the extracellular domain of EGFR leading to dimerization
- its role is to stabilize the EGFR dimer.
EFGR phosphorylate each other where?
at the tyrosine residues
Phosphorylated tyrosine residues on EFGR serve what function?
serve as binding sites for other adaptor proteins and have docking sites for multiple adaptor proteins.
How is a cell able to control the number of receptors on the surface or accidental triggering of the transduction pathway?
by clathrin mediated endocytosis of the hormone receptor complex to lysosome for destruction thus preventing accidental triggering of the pathway
What protein binds to phosphorylated tyrosine?
Grb2, which is in complex with SOS
What is SOS?
SOS is an guanine exchange factor (GEF) that can exchange GDP with GTP. It activates RAS and continues the transduction signal by removing GDP with GTP. SOS is recruited to the membrane.
What is RAS and how is RAS connected to the membrane?
RAS is part of the signal transduction pathway. It is connected to the membrane by a protonated tail. It is a G protein and active when bound to GTP and inactive when bound to GDP
How does RAS become inactive? and why wouldn’t we want RAS to always be active?
RAS has GTPase activity (RAS-GAP) which turns GTP back to GDP
-Inactivating RAS protein is required as b/c always active leads to RAS oncogene. RAS oncogenic mutations are the most common in tumor and the mutation causes RAS to bind to GTP more tightly than GDP and as a result it does not require a growth factor to trigger activation.
What is the only role of RAS, once it is activated?
once RAS is activated, its only role is to recruit serine/threonine protein kinase called RAF
How is inactive RAF brought to the membrane?
on a scaffolding platform called connector enhancer KSR (CNK) along with KSR which is a kinase suppressor of RAS
What is KSR?
a kinase suppressor of RAS
Activation of RAF, KSR, and CNK lead to what?
dimerization of KSR and RAF which opens up protein complex allowing phosphorylation and the KSR-RAF dimer is released from the scaffold (where the KSR now serves as scaffold for the next steps of the pathways)
What does phosphorylated RAF do?
activates MEK by phosphorylating and triggering the phosphorylation cascade. Then activates ERK, which activates transcription factors which enter the nucleus and initiate transcription of the genes to prepare for passage through G1 and then S phase
How is cell cycle progression controlled?
by a set of serine/threonine protein kinases called cyclin dependent kinases (CDKs).
CDKS are normally inactive until they are activated by cyclins proteins.
How are CDKs regulated?
Become activated by cyclins but also regulated by other kinases
-inhibitor proteins negatively regulate cyclin/CDKs and a set of activator proteins called CAKs positively regulate cyclin/CDKs
What are tumor suppressor proteins?
p53 and Rb, which prevent uncontrolled cell growth and act as guardians of the cell.
Even if the RAS is oncogenic the tumor suppressors can prevent the cell from progressing from G1 to the S phase.
Mutations in tumor suppressors can lead to?
damage of the size cell replication
What is the role of p53?
role of p53 is prevent cell from entering S phase if there is DNA damage. If damage occurs then p53 needs to relay this info to cyclin/cdks to prevent cell from entering S phase.
If damage is irreparable p53 causes apoptosis aka cell death
How does p53 sense that there is DNA damage?
damage to DNA is relayed via the protein kinase system that phosphorylates p53 stabilizing it from degradation causing p53 levels to increase in the cell and serve as a transcription factor for genes like GADD45, p21, and MDM2
What does p21 when activated by p53?
binds to CDK cyclins inhibiting them and arresting cell in G1 phase?
What does GADD45 do?
initiates DNA repair when p53 senses DNA damage
What does MDM2 do?
serves as THE major regulator of p53. Although transcription of MDM2 is increased by p53, the MDM2 will inhibit p53 in a positive feedback loop. It targets p53 for degradation and binds to it preventing it from transcribing
How does MDM2 become inactive?
DNA damage leads to phosphorylation of MDM2 inactivating it and allowing p53 levels to increase
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What is Rb?
tumor suppressor and the MAJOR guardian of the cell as it integrates information about. DNA damage and cell growth/size to control progression into S phase
-Rb binds the activation domains of a set of essential transcription factors, the E2F family, to prevent them from turning on the genes required fro cell cycle progression. When Rb is phosphorylated by Cyclin/CDK complex it releases E2F to permit cell progression
What is the restriction point?
is a critical point during G1 at which a cell becomes committed to division. This is controlled by Rb.
What happens when Rb binds to E2F?
it prevents E2F entry into the nucleus where it would turn on genes required for cell cycle progression.
What needs to happen for cell cycle progression to occur?
Rb must be phosphorylated by cyclin/cdk complex which will cause to release E2F
Name a CKI (inhibitor) and its role
p21, is a CKI and provides the link between p53 and Rb
When are individual replicons actived?
at characteristic times during S phase. Not all get turned on at the same time.
What do regional activation patterns suggest about replicons?
that replicons near one another are activated at the same time.
How do replicons vary in euchromatin regions and heterochromatin regions?
replicons in the euchromatin region replicate first while those in heterochromatin region replicate last.
What happens to the multiple origins of replication on chromosomes?
they ultimate merge during replication.
Replication of origins in s cerevisiae are displayed in what way?
Identified as the ARS (autonomous replicating sequences) and were show to be in short A-T sequences taht have an essential 11-base pair sequence called the A domain
What is the Cdc6 and Cdt1 protein?
-cdc6 and cdt1 are key licensing factors that bind to ORC
Cdc6 protein is an unstable protein that is synthesized only in G1 and binds to the ORC and allows MCM protein to bind.
Cdt1 facilitates MCM loading on origins
When replication is initiated, what happens to Cdc6 and cdt1?
cdc6 and cdt1 are displaced. The degradation of cdc6 prevents reinitiation and return to the origin in the postreplication complex which is just the orc
What is the prereplication complex in yeast?
a protein-DNA complex at the origin in S cerevisiae that is required for DNA replicaiton. The complex contains the ORC, cdc6, and the MCM proteins. and cdt1
What is the postreplication complex in yeast?
a protein-DNA complex in s cerevisiae that consist of the ORC compmlex bound to the origin
The replication fork in eukaryotes has which DNA polymerase?
3 polymerase, alpha, delta, and epsilon
-most nuclear replicases are heterotetramers w/one subunit involved in catalysis while others subunits are involved in priming and processivity
What is the role of DNA polymerase alpha/primase complex
This polymerase/primase initiates the synthesis of new strand both leading and lagging DNA strand. it binds to the complex at the origin and starts synthesizing short 10 base primer followed by 20-30 DNA bases.
-b/c of its ability to prime and extend it iis also a primase
Pol alpha is displaced by pol epsilon and delta
what is the role of dna polymerase epsilon?
elongates the leading strand.
What is the role of DNA polymerase delta?
it elongates the lagging strand
What is the proccesivity of polymerase epsilon?
the proccesivity of pol epsilon is very high due to its interaction with the RFC clamp loader and PCNA clamp
What is the role of the RFC clamp loader and the PCNA clamp?
the role of these two clamps is similar to the e.coli gamma clamp loader and beta2 clamp in prokaryotes.
How is the processivity of pol delta maintained?
by another PCNA clamp, which holds the pol delta to the strand.
True of false: Mammals systems DNA polymerase have 5’-3’ exonuclease activity?
FALSE: it does not have 5-3’ exonuclease activity.
How are okazaki fragments linked in eukaryotes?
in two steps.
As the okazaki fragment is being synthesized, it displaces the RNA primer of the preceding fragment forming a flap.
The flap of the primer is cleaved by FEN1
Once RNA is excised out and replaced by the extending okazaki fragment, the adjacent fragments need to be ligated together by DNA ligase
SHORT: primer is displaced, FEN1 cleaves primase and ligase seals gap with help of AMP
What is the role of FEN1?
In okazaki fragments it cleaves the the primase
What is the role of DNA ligase?
joins okazaki fragments and performs this function w/the help of AMP
What is a gene?
a gene encodes any RNA or polypeptide product other than a regulator
What is a chromosome?
a chromosome is a unit of the genome carrying many genes.
Each chromosome consist of molecule of duplex DNA and an equal mass of proteins and is visible as a morphological entity only during cell division.
Define allele
alternative forms of a gene occupying a given locus on a chromosome
what is the locus?
the position of a chromosome at which the gene for a particular trait resides; it may be occupied by any one of the alleles for the gene
What is genetic recombination?
a process by which separate DNA molecules are joined into a single molecule, due to such process as crossing over or transposition
What is a genome?
a genome is the complete set of sequences in the genetic material of an organism. it includes the sequence of each chromosome plus any DNA in organelles
What is a transcriptome?
transcriptome is the complete set of RNAs present in a cell, tissue, or organism. its complexity is due mostly to mRNAs, but also includes noncoding RNAs
What is a proteome?
the complete set of proteins/polypeptide that is expressed by the entire genome. The term is sometimes used to describe the complement of proteins expressed by a cell at any one time.
What are interactomes?
the complete set of protein complexes and protein-protein interactions present in a cell, tissue, or organism
What are transposons?
a large part of moderately repetitive DNA may be made of of transposons, which are short sequences that can move to new locations in the genome
What is gene conversion?
gene conversion between multiple copies allows the active genes to be maintained during evolution
What are the x-transposed, x-degenerate and amplicons sequences on the y chromosome?
1) x-transposed: regions which is transposed from the x chromosome
2) x-degenerate: are sequences that have a common origin as the x chromosome
3) amplicons: are the sequences repeated on the Y chromosome
Why is redundancy important?
to some degree the organism is protected against the delirious effects of mutations by having redundancy
In any particular cell, most genes are expressed at what level?
low levels. only a small number of genes whose products are specialized for the cell type are highly expressed.
Satellite DNA
DNA that consist of many tandem repeats identical or related of a short basic repeating unit.
AKA
w/in the highly repetitive DNA are short sequences that are repeated several times. These are satellite DNAs
