127 notecards = 32 pages (4 cards per page)
top 3 leading cancer related deaths
result from proto-oncogene activation and TSG inactivation
minimum amount of DNA alterations needed for a cell to become malignant
process of a normal cell evolving into a highly malignant cell
transcription factor, most frequently mutated gene in cancer, guardian of the genome, regulates at G1- growth arrest and apoptosis, suffers from point mutation which inactivates it -resulting in no DNA repair
inactivated in 50% of all cancers
genes that are like the car brakes, help regulate cell growth, gives loss of function to mutant genes
tumor suppressor genes
cell dividing out of control, mutant form of normal has genes, dominant genes, code for RTK, G proteins, transcription factors, Ras gene, classified as
normal cell division like a gas pedal on a car, but has the potential for a gain-of-function in cancer, these genes are
signaling that effects the same cell
signaling that effects neighboring cells, even of a different type
long distance signaling that is able to signal the whole body, usually through the circulatory
high-affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones, key regulators of normal cellular processes but also to have a critical role in the development and progression of many types of cancer
Receptor tyrosine kinases (RTK)
how does the G-protein coupled receptor work
Binding of an agonist results in a conformation change in the receptor that is transmitted to the bound α subunit, the α subunit exchanges GTP in place of GDP which in turn triggers the dissociation of it from the βγ dimer and from the receptor. The dissociated α subunit interacts with other intracellular proteins to continue the signal transduction cascade
a large protein family of receptors that sense molecules outside the cell and activate inside signal transduction pathways and, ultimately, cellular responses. They are called seven-transmembrane receptors because they pass through the cell membrane seven times, ligands that bind and activate these receptors include light-sensitive compounds, odors, pheromones, hormones, and neurotransmitters, and vary in size from small molecules to peptides to large proteins. They are involved in many diseases, and are also the target of approximately 40% of all modern medicinal drugs
G-protein coupled receptor
general name for a group of more that 100 diseases in which cells in a part of the body begin to grow out of control
Conversion of an impulse or stimulus from one physical or chemical form to another. In cell biology, the process by which a cell responds to an extracellular signal.
Protein that recognizes and responds to a specific signal molecule.
A set of proteins and small-molecule second messengers that interact with each other to relay a signal from the cell membrane to its final destination in the cytoplasm or nucleus.
intracellular signaling pathway
Extracellular signal molecule that is secreted and transported via the bloodstream (in animals) or the sap (in plants) to target tissues on which it exerts a specific effect.
The molecular mechanisms by which cells detect and respond to external stimuli and send messages to other cells.
what do vSNARES do
SNAREs on the vesicle compliment the target tSNAREs
in order to use protein translocators, is the protein folded or unfolded?
how about a nuclear pore?
unfolded to go through the membrane
folded to go through the nucleus
Which of the following is true of lysosomes?
A. The products of digestion in lysosomes leave the
lysosome by transport vesicles.
Proteins destined for regulated secretion:
A. have special surface properties that cause them to
form aggregates that are packaged into secretory vesicles.
Which type of protein binds to improperly folded or improperly assembled proteins in the ER, holding them there until proper folding occurs?
A. Tethering proteins
Vesicle budding is driven by the assembly of a protein coat.
The ER signal sequence on a growing polypeptide chain is recognized by a signal recognition particle (SRP) in the cytosol. This interaction:
A. causes the polypeptide chain to dissociate from
Which of the following is true?
A. A special class of ribosomes embedded in the ER
translates the proteins destined for that organelle.
Which of the following statements is NOT true of mitochondrial proteins that are synthesized in the cytosol?
A. The proteins are unfolded as they are transported
into the mitochondria.
Which proteins bind to nuclear localization signals on newly synthesized proteins?
A. Nuclear pore proteins
The interiors of the ER, Golgi apparatus, endosomes, and lysosomes communicate with each other in which of the following ways?
A. By small vesicles that bud off of one organelle
and fuse with another
Which organelle is essentially a small sac of digestive enzymes that functions in degrading worn-out organelles, as well as macromolecules and particles taken into the cell by endocytosis?
A. An endosome
Which organelle sorts ingested molecules and recycles some of them back to the plasma membrane?
A. An endosome
Which organelle receives proteins and lipids from the endoplasmic reticulum, modifies them, and then dispatches them to other destinations in the cell?
A. A mitochondrion
what signals for proteins to have parts of them embedded in the membrane ER
stop transfer sequence
start transfer sequence
two protein components help guide ER signal sequences to the ER membrane
signal recognition particle (SRP) in the cytosol binds with the ribosome and the signal sequence
SRP receptor embedded in the ER membrane recognizes the SRP
2 kinds of proteins transferred from the cytosol to the ER
water soluble completely translocated
prospective transmembrane partly translocated ( embedded in membrane )
small membrane enclosed organelles that contain several enzymes that produce hydrogen peroxide and have a variety of other functions, derived from the endoplasmic reticulum or replicate by fission- it also transports proteins via translocation
main site of lipid synthesis
how do proteins know to go to the mitochondria
signal sequence at their N-terminus recognized by a chaperone protein that grabs it, unfolds it, the folds back once entered, requires ATP
use a translocator channel- similar to a nuclear pore, but instead of one big pore, it is one in each bi-layer
how are mitochondria and chloroplasts similar to nucleus
double phospholipid bi-layer
own DNA and therefore own proteins
recognize signal sequence- positive charge hydrophobic AA
what brings proteins to the nucleus
importin- nuclear import receptors
take the protein in its 3 prime shape unlike other oraganelles
how do proteins get to where they need to go
signal sequence- nuclear localization signal
positive charged hydrophobic lysine and arginine
binds to the nuclear import receptor to bring it in - requires GTP for energy
nuclear pores are made of
30 proteins complex, act as a gate for proteins to enter and RNA to exit
inner nuclear membrane conatins
membrane most similar to the cell membrane and is continuous with the membrane of the ER
inner layer of nuclear membrane conatins
proteins and binding sites for chromosomes
nuclear lamina for structural support
how many membranes of the nuclear envelope, aka nuclear membrane
double phospholipid bi-layer
inner and outer
The lac operon:
At the E site
A)transfer RNA is released
B)anticodons match with codons
C)peptide bonds are formed between amino acids
An activator must react with its substrate before it can bind to DNA.
Negative control occurs when a repressor is inactivated by an inducer.
In regulation by induction
A)an inducer inactivates the repressor so transcription can proceed
B)an inducer inactivates the repressor so transcription is stopped
C)an inducer activates the repressor so transcription can proceed
D)an inducer activates the repressor so transcription is stopped
In regulation by repression
A)a sugar, such as lactose, acts as an inducer and combines with the repressor to prevent transcription
B)an inducer activates the activator so that it binds to DNA and prevents transcription
C)an amino acid activates the repressor so that the repressor binds to the operator and prevents transcription
D)an amino acid binds to the operator, blocking the repressor, allowing transcription to proceed
Transcription is turned off by
D)all of the above
how does the cell know what proteins go where
1. signal patches made of amino acid residues that are distant to one another in primary form but are close together in tertiary structure
2. sorting signal made of amino acid sequences
no signal= stays in cytosol and functions there
proteins transported to the nucleus are completely synthesized in the cytosol and ______ before import, unlike other organelles
three ways proteins are transported throughout the cell
1. through nuclear pores from cytosol into nucleus
2. across organelle membranes via protein translocators
3. by transport vesicles through plasma membrane to outside of cell
two ways cells can isolate and organize their chemical reactions
aggregate different enzymes
confine different metabolic processes within different membrane enclosed compartments (organelles)
large protein complexes found in the cytosol and nucleus that have protease activity
enzymes that degrade proteins by a process known as proteolysis (hydrolyzes peptide bonds)
regulatory RNA's work by
base pairing with complementary sequences within target mRNA's, leading to mRNA degradation and inhibition of translation
two key aspects of eukaryotic translation are regulated by phosphorylation- same as effects in DNA transcription
1. recognition of the mRNA by ribosome can be inhibited by PO4
2. 5' cap binding proteins can be bound by non-PO4 binding proteins
proteins that block the translation of mRNA because they prevent the attachment of ribosomes by binding to specific nucleotide sequences in the 5' untranslated region (promoter)
translation of mRNA is regulated by regulatory proteins that are needed so ribosomes can translate mRNA are called
three chemical modifications to histones to regulate transcription
1.activator- histone acetyltransferases (nucleosomes loosened)
2.repressor- histone deacetylases
3.repressor- histone methyltransferases
two ways transcription regulators act
1.directly effect the assembly process that require RNA polymerase and transcription factors at the promoter- histone proteins
2.modify the chromatin structure of promoter regions- DNA itself
cell defense mechanism that destroys foreign RNA, man made, double stranded
controls gene expression, single stranded, regulate our own genes, base pairs with specific mRNA
in the absence of lactose, the lac repressor
A)binds to the operator and prevents transcription
B)binds to the CAP site and prevents transcription
C)binds to the CAP site and facilitates transcription
D)binds to the operator and facilitates transcription
The main regulatory gene that acts on the lac operon is a
lac repressor with no lactose and CAP activator with no glucose
repressor binds to the lac operon operator, where it blocks RNA polymerase from transcribing the lac operon
CAP binds to cyclic cAMP before it can bind to DNA, switches on genes to increase intracellular cAMP
In a eukaryote, activating transcription factors may stimulate gene expression by binding to a DNA site called a(n) _____.
You have inserted the gene for human growth factor into the E. coli lactose operon, replacing the structural genes with the gene for human growth factor. What substance must you add to your culture of bacteria to cause them to produce human growth factor for you?
In an inducible operon, the inducer is often the _____ in the pathway being regulated; the inducer binds to the _____, thus rendering it _____.
substrate ... repressor ... inactive
the genetic information contained within the order of nucleotides in mRNA is interpreted to generate the linear sequence of amino acids
which part of the mRNA is used
the protein coding region with nonoverlapping string of codons
ORF- open reading frame
translation starts at what end
5' to the 3'
how many possible codons
3 bases, 4 nucleotides = 43 = 64
61 are translated into AA, the rest are stop codons
provides the genetic information template to be translated
provides the interface between the mRNA and their corresponding AA
enzyme links AA to their corresponding tRNA, one for each of the 20 AA
coordinates recognition between the mRNA and corresponding tRNA and catalyzes the peptide bond formation between tRNA associated AA
does transcription and translation occur at the same time in eukaryotes
one is in the nucleus and the other in the cytoplasm
three binding sites in the ribosome
P- attaches AA
what determines the start of translation
5' end of ORF is methionine (AUG)
base pairing results in structural conformational change which in turn causes some of the bound initiation factors to be
released and new ones bind
in addition to codon-anticodon base pairing, the ribosome has additional proofreading mechanisms to ensure
the correct tRNA is brought into the A site
stop codons are recognized by proteins called
activates hydrolysis of the polypeptide from the tRNA
an mRNA with multiple ribosomes attached is a
Which type of RNA includes the anticodon and brings the
amino acids to the site of protein
Where does translation occur?
Which molecule contains codons?
What form of RNA binds to both the codon and an amino acid?
D)None of the above.
What area of a gene does the RNA polymerase bind to?
RNA is transcribed using the ____ strand of DNA.
Which of the statements below is FALSE?
A)The genetic code is overlapping.
B)The genetic code is universal.
C)Degenerate codons specify the same amino acids
D)The genetic code is triplet in nature.
The first mRNA codon to specify an amino acid in a protein sequence is always _____.
Transfer RNAs bind to messenger RNAs during translation via their _____.
Of the ____ different possible codons, ____ specify amino acids and ____ signal stop.
A)20; 17; 3
B)180; 20; 60
C)64; 61; 3
D)61; 60; 1
An antibiotic interferes with the ability of the ribosome to move. What effect would exposure to this chemical have on a bacterial cell?
A)Protein synthesis will be enhanced.
B)The protein synthesized will be shorter than normal.
C)The protein synthesized will be longer than normal.
D)No proteins will be produced.
What sequence on the template strand of DNA corresponds to the first amino acid inserted into a protein?
Which of the following is an example of the degeneracy of the genetic code?
A)A given amino acid has more than one codon.
B)Each codon specifies more than one amino acid.
C)The first base specifies the amino acid.
D)The genetic code is not degenerate
During translation, the _____ site within the ribosome holds the growing amino acid chain while the ____ site holds the next amino acid to be added to the chain.
Translation terminates when _____.
A)the A site is empty
B)a stop codon is present in the A site
C)a release factor is present in the P site
D)translation reaches the end of the mRNA
what dictates which genes are expressed, where, and when
we rarely use any more of _____ % of our genes at any given time
all cells have the same DNA and therefore the same
but they are not all expressed- gives specificity to muscle, nerve, skeletal cells
all cells require
what events does gene expression control
when and how often a gene is transcribed
how mRNA is spliced
which mRNA is transported
how quickly mRNA is degraded
which mRNA is translated
how quickly protein is degraded
what stage is the most regulated
initiation of transcription
slight continuous level of expression of a gene
transcription activator proteins bind to the DNA and RNA polymerase near the promoter which brings in the RNA polymerase to the promoter
cooperative binding resulting from recruitment
an indirect mechanism because of the domino effect
two proteins acting in one complex, need both of them to be active, one end binds to the DNA binding site, the other end binds to the RNA polymerase
set of three genes plus other things in E. coli involved in the transport and breakdown of lactose into glucose
what is the lac operon composed of
3 genes- lacZ, lacY, lacA
what is the lac operon regulated by
availability of lactose and glucose
how does a cell use lactose as energy
produces beta-galactosidase to break down lactose into glucose
lac promoter directs transcription of all 3 genes as a single mRNA molecule called
what does lacZ do
produces enzyme beta-galactosidase to break down lactose into galactose and glucose
what does lacY do
produces the protein lactose permease that transports lactose into the cell
what does lacA do
produces the enzyme thiogalactosidase transacetylase to break down the toxic thiogalactosidase that was brought into the cell with lactose
when lactose is present and glucose is not then the genes are
regulation in the expression of the lac operon is upstream and controlled by
if or not there is an activator
lac repressor which is encoded by a gene
gene that encodes the lac repressor that binds to the lac promoter region and prevents transcription when there is no lactose
lacI gene and allolactose
when glucose is present but there is no lactose, then
A)cyclic AMP is high, the catabolite activator protein (CAP) binds to the activator binding site, and transcription of lactose is turned on
B)cyclic AMP is low, CAP binds to the site activator binding site, and transcription of lactose is turned on
C)cyclic AMP is high, CAP does not bind to the activator binding site, and transcription of lactose is turned on
D)cyclic AMP is low, CAP does not bind to the activator binding site, and transcription is turned off
lac repressor binds to operator region and prevents RNA polymerase from binding
when glucose is absent but lactose is present, then
an allosteric effect on CAP binding site
cyclic cAMP binds to CAP which then binds to the CAP site on mRNA and RNA polymerase then attaches to the promoter site so transcription can occur
when both glucose and lactose are present
A)cyclic AMP is high so transcription occurs
B)the lac repressor binds with the lactose and transcription occurs
C)RNA polymerase is able to bind to the operator so transcription occurs
D)transcription is at a minimal level
a basal level of transcription occurs
protein exerts its effects from a distance away from the promoter region
works by changing the structure of the mRNA so it bends around in a loop,
can activate or repress
enhancer site for binding of an activator protein