b11 final Flashcards
what is polycistronic mRNA?
mRNA with one promoter for many genes
what is monocistronic mRNA?
mRNA with one promoter for one gene
what increases the RNA pol’s affinity for promoter sequences?
sigma factor
what does the RNA polymerase holoenzyme consist of?
RNA polymerase (5 subunits) + sigma factor
What are the two types of transcription termination sequences in prokaryotes?
- stem-loop hairpins (RNA) : intrinsic causes RNA polymerase to pause
- rho factor (protein): protein mediated, there is a binding sequence for the protein (ex. the protein is the rho factor)
what allows 1 gene to be used for production of multiple different sequences of proteins (splice isoforms) ?
Alternative splicing
what is a primary transcript/pre-RNA/precursor-mRNA?
initial RNA molecule synthesized from the template DNA
what are splicing isoforms?
different versions of mRNA that result from alternative splicing (so we have one mRNA transcript and we can cut it into different parts and this produces many parts from one single gene)
which RNA polymerase makes all eukaryotic pre- mRNA?
RNA pol II
what is the equivalent of the prokaryotic sigma factor in eukaryotes?
general transcription factors (GTFs)
what is assembled at the TATA box?
preinitiaiton complex (PIC) that contains general transcription factors (GTFs) and RNA polymerase
which general transcription factor uses ATP hydrolysis to open the DNA double helix at the transcription start point, to expose single-stranded template?
TFIIH (kinase and helicase)
*remember H form helicase
what are the roles of the general transcription factor TFIIH? (there are 2)
- uses ATP hydrolysis to open the DNA double helix aka exposes single-stranded template
- phosphorylates RNA polymerase II tail (C-terminal domain, CTD) aka signals that RNA Pol II can being elongation
what is the name for RNA sequences that do not encode protein but play important regulatory roles?
Untranslated regions:
1. 5’ UTR: methylated guanosine cap
2. 3’ UTR: Poly(A) tail
what are the three types of processing that need to occur in eukaryotic pre-mRNA?
- 5’ cap
- splicing/alternative splicing
- 3’ poly(A) tail
what is the function of the 5’ cap?
- prevents digestion by exonucleases
- plays a role in transport of nucleus
- plays a role in initiation of mRNA translation to protein
- indicator that mRNA is completed
What is polyadenylation?
addition of a string of A (adenine) nucleotides at the 3’ end of the mRNA
how many origins of replication (ori) do bacterial chromosomes have?
1
points where a pair of replicating segments come together are called what?
replication forks
A transcription factor that is activated in response to DNA damage and can prevent cell cycle progression and/or promote apoptosis
p53
Transmembrane protein that is activated by dimerization upon growth factor binding
EGFR
A transcription factor that can activate genes involved in progression from G1 phase to S phase in the cell cycle
E2F
A non-receptor tyrosine kinase that was originally discovered as a viral oncogene
Src
Many signaling pathways converge to regulate phosphorylation of this protein, which controls the R point
Rb
Form complexes with Cdks to promote/regulate events of the cell cycle
cyclins
polypeptides are linear sequences of what?
amino acids
amino acids are linked together by what kind of bond?
peptide bonds
amino acids are joined by the ______ end of one amino acid and the ______ end of another
carboxyl, amino
the amino terminus of an animo acid is also called
N-terminus
the carboxyl terminus of an amino acid is also called
C-terminus
what promotes protein folding?
non-covalent interaction (no sharing of electrons but rather opposite charges are attracted to each other)
what are the structural units of proteins called?
protein DOMAINS
can 1 polypeptide contain more than one domain?
yes
the ribosome moves what direction along the mRNA?
5’ to 3’
what are Shine-Dalgarno sequences?
- a sequence of nucleotides in bacterial (prokaryotic) mRNA that is located upstream from the AUG codon, helps align the ribosome so translation can begin
In prokaryotes, which subunit are initiation factors attached to?
small subunit of ribosome
in prokaryotic translation what do initiation factors do? (3)
- Attachment to mRNA
- Attachment of first AA-tRNA
- Preventing premature attachment of large subunit
what is a kozak sequence
A Kozak sequence is a specific nucleotide sequence found in eukaryotic mRNA that is important for the initiation of translation. It helps the ribosome recognize the start codon where translation begins.
what is a polyribosome or polysome?
multiple ribosomes associated with an mRNA
What happens to the CTD of RNA polymerase to cause proteins involved in capping, splicing, and cleavage/polyadenylation to bind to it?
it is phosphorylated
Helps loosen DNA/histone interactions to transcribe through nucleosomes
transcription elongation factors (Spt4, Spt5, and Elf1)
which is usually longer: introns or exons?
introns
what Initiates transcription elongation by phosphorylating RNA polymerase II
TFIIH
what Binds to the TATA Box
TFIID (with TBP)
Unwinds DNA at the site where transcription will begin
TFIIH
Coordinates recruitment of different processing enzymes in close proximity to the growing strand of new RNA
CTD
Creates a 5’-5’ triphosphate bridge to a GMP at the 5’ end of the RNA
capping enzyme, Guanyl transferase
Adds a string of adenine nucleotides to create the poly(A) tail
poly(A) polymerase
Methylates the 5’ cap
RNA methyltransferase
Binds the RNA consensus sequences for polyadenylation
CPSF
After transcription begins, this component stays bound to the promoter to assemble the next pre-initiation complex
TFIID (with TBP)
what synthesizes pre-mRNA in the 5’ to 3’ direction
RNA pol II
stem cells that produce a related group of cells (ex. Hematopoietic stem cells that create red and white blood cells)
multipotent stem cells
These stem cells can produce only one cell type but have the property of self- renewal that distinguishes them from non-stem cells.
unipotent stem cells
what is one feature that distinguishes stem cells from non stem cells?
self renewal
what is the phenomenon that states that cells can change phenotypically without also changing genotypically
genomic equivalence: each somatic cell contains the same DNA
detects mRNA through base-pairing with a labeled nucleic acid probe complementary to a specific sequence in the RNA of interest
in situ hybridization
what is the ultimate proof of genomic equivalence?
An entire mammal can be cloned from the DNA in an adult somatic cell
what differential gene expression technique is used to separate proteins by charge and mass?
two-dimensional gel electrophoresis
complete set of RNA transcripts produced by the genome at any given time
Transcriptome
refers to the continuous and consistent expression of a gene
Constitutive expression
protein binds to DNA with what kind of bond
non covalent bonds
can be supplied (expressed) from any chromosome meaning they are usually RNA or proteins.
trans regulatory elements
are usually sequences (ex. Binding sites) encoded on the same chromosome they affect
cis regulatory elements
is a large, multi-protein complex that plays a crucial role in the regulation of gene transcription in eukaryotic cells.
mediator complex
sequences of DNA where RNA polymerase can be recruited to initiate transcription
promoters
sequences of DNA that impact how much gene product is made from a promoter
enhancers
what is an example of reporter gene expression
GFP: green fluorescent protein
DNA regulatory element that can prevent promoter use and inhibit transcription.
Required to restrict gene expression to the proper cells/times
silencers
bind enhancer DNA elements
activators
bind silencer DNA elements
repressors
use introduction/alteration of DNA sequences to create a therapeutic benefit
gene therapies
what are hematopoietic stem cells?
one that make red and white blood cells
How many FDA approved uses for stem cell therapy? and what are they?
leukaemia and sickle cell disease
what does Cord blood have the do with stem cells?
cord blood is an FDA approved source of hematopoietic stem cells to treat diseases of the blood/immune system (ex. leukaemia and sickle cell anemia)
are abundant sites for protein degradation and are found in the cytoplasm and nucleus
Proteasomes
what are two signals for degradation of proteins in the proteasome.
- polyubiquitin chains
- misfolded regions
are enzymes that adds ubiquitin to proteins or things
ubiquitin ligases
_________are transmembrane proteins that help cell adhere to the extracellular matrix (ECM)
Integrins
Anoikis: a term for apoptosis that occurs in response to loss adhesion (death due to lack of integrin signaling)
Anoikis
define cancer
a group of diseases of abnormal, uncontrolled cell division
define transformation
process in which a normal cell becomes a cancerous cell
abnormal growth with invasion
maligant
abnormal growth without invasion.
benign
small intracellular molecules that are formed or released in response to an extracellular signal
second messengers (the first messengers being the extracellular signal)
who assess a tumor and provides information about tissue of origin, diagnosis, prognosis and treatment options
a pathologist
a branch of anatomy that studies the microscopic structure of tissues
histology
how large is the tumor and has it spread to other tissues?
stage
how abnormal do the cells look and how fast are they growing?
grade
abnormal number of chromosomes
aneuploidy
in frame fusion of the coding regions of these genes caused by a reciprocal translation between Chromosome 9 and 22
Bcr-Abl
most impactful discovery of molecular mechanisms of cancer
Philadelphia chromosomes
what is a drug that can get rid of CML (in the early stages) by targeting Bcr-Abl
Gleevec
what is easier to have: loss of function or gain of function?
loss of function
the majority of tumors are ________ growths arising from a single normal cell of origin
monoclonal
cause expansion of unique subpopulation of cells
driver mutations
hyper or hypophosphorylation of Rb prevents transcription of cyclin that initiated S phase
hypophosphorylation
hyper or hypophosphorylation of Rb at the R point allows initiation of S phase (DNA replicaiton)
hyperphosphorylation
what is the most commonly mutated gene in cancer
p53 tumor suppressor
what are two examples of tumor suppressors
p53 and Rb
tumor suppressors that are tetramers
p53
cancers caused by the accumulations of mutations that were not inherited from an individuals parents
sporadic cancers
an agent that causes cancer
carcinogen
what is the greatest risk factor for cancer?
age
What are the limitations to scaffold-mediated signaling?
no amplification
Explain the roles of Pl3K and PTEN in regulating Akt
PI3K activates Akt: promotes cell growth, survival, and proliferation
PTEN counteracts PI3K, dephosphorylates it PI#K –> PI2K
- reduces activation of Akt
- acts as a tumor suppressor because its activity helps regulate cell growth and prevent uncontrolled cell proliferation
Rb recruits HDAD and this does what?
HAD removes acetyl groups and this promotes a more closed conformation of chromatin
what is contact inhibition? and do cancer cells exhibit it?
contact inhibition is something present in normal cells. cells grow until they come into contact then they stop growing.
cancer cells do not exhibit contact inhibition because they keep growing on top of each other
NHEJ, HR or both?
This pathway involves Ku protein binding the ends of DNA created by double-strand breaks
NHEJ
NHEJ, HR or both?
This pathway is more active in M phase than in G1
HR (G1 NJEH is more active)
NHEJ, HR or both?
This pathway can result in translocations
both
NHEJ, HR or both?
This pathway acts quickly to repair any double-strand breaks without the need for homology in DNA sequences
NHEJ
NHEJ, HR or both?
This pathway can cause loss-of-heterozygosity
HR
NHEJ, HR or both?
in combination with CRISPR/Cas9, this pathway is used by researchers to insert specific changes into the genome
HR because of specific changes
NHEJ, HR or both?
In combination with CRISPR/Cas9, this pathway is used by researchers to disrupt gene function by repair that includes random insertions and deletions
NHEJ: random
NHEJ, HR or both?
This pathway is involved in crossing over during meiosis
HR
a gene that encodes a protein which is easily detectable and measurable, used to study gene expression, cellular processes, or protein localization.
reporter gene
what are two examples of reporter genes
GFP (green fluorescent proteins)
and
lac Z gene (beta galactosidase)
delete various segments of the DNA and measure transcription (i.e using reporter gene) to determine which specific sequences are required for transcription.
deletion mapping
what marks completed spice
Exon junction complexes (EJC)
Maternal contributions proteins and RNA that are stored in the egg until they are needed to orchestrate early development (and determine the fate of particular cells)
