Week 6 Textbook Flashcards
what is a codon
it is 3 nucleotides in rna that = specific amnio acids
- some nucleotide codons = stop codon
AUG = start
what are reading frames
3 different reading frames
can sequence into different AA depending on the reading frame that is used during translation
what is the purpose of tRNA
rna molecule that serves as an adaptor that reads a codon in mRNA and serves as the source of the amnio acid added to the growing polypeptide chain
- forms in the shape of a cloverleaf and then forms a compact L shape held together by H bonds
the anti codon attaches at the bottom at the amnio acid matching the anticodon is attached to 3’ end of the tRNA
what is an anticodon
3 nucleotides that bind throught base pairing to the complementary codon in an mRNA molecule
there is another end on the tRNA that is unpaired - this area at the 3’ end of the molecule is where the AA that matches the codon in covalently attached to tRNA
what is the function of the enzyme amnioacyl-tRNA synthetases
they covalently couple each amnio acid to the appropriate set of tRNA molecules
each synthetase enzyme recognizes its designated amnio acid and the anticodon area on the tRNA
what is the process called when each synthetase couples a particular amnio acid to the proper tRNA
charging
what is the ribosome and its subunits
ribsome = large complex made from small proteins = rRNA= ribosomal RNAs which form the structural and catalytic core of the ribosomes
the ribosome translates the mRNA into polypeptide chains
the small ribosomal subunt matches the tRNA to the codons of the mRNA
the large subunit catalyzes the formation of the peptide bonds that covalently link the amnio acids together in the polypeptide chain
- starts its synthesis on the 5’ end
after the polypeptide chain is made the 2 subunits of the ribosome separate
where does the tRNA enter the ribsome to grow the amnio acid peptide chain
enters to the A site by base pairing with the complementary codon on the mRNA molecule
- the amnio acid is linked to the polypeptide chain - this is held into place by the tRNA at the P site.
when the ribsomal unit shifts forward to reveal more mRNA- the tRNA moves to the E site before being ejected
- process continues until the mRNA = stop codon
the P site in the middle holds the polypeptide chain and then gives the chain to the tRNA that enters thru the A site and the middle goes to E site to leave and the A now becomes the P
what gives the ribosome its overall shape
ribosomal RNAs that are compact into the core
the ribosomal proteins are located on the surface - to help fold and stabilize the RNA core
what are ribozymes
RNA molecules that possess catalytic acitivity
what is the initiator tRNA and why is it so significant
it sets the reading frame for the entire message - one error in the nucleotide = messed up codon - nonfunctional protein
- also has a major impact on the overall rate at which proteins are synthesized
- begins with AUG = methionine
- all newly made proteins have AUG at the beginning on the N-terminal end - but it is usually removed later by a specific protease
what are translation initiation factors
proteins that promotes the proper association of ribosomes with mRNA and is required for the initiation of protein synthesis
how does the initiator tRNA start the translation process
enters into the P site (middle) of the SMALL ribosomal subunit - along with the translation initiation factors
- only a charge initator tRNA molecule is capable of binding tightly to the P site in the absence of the large ribosomal subunit
- then binds to the 5’ end of the mRNA molecule which has the 5’ gap of guanine
- the small ribosomal subunit scans the mRNA for the AUG start codon - once found, the large ribsomal subunit binds to complete the factory and start protein synthesis
- the incoming tRNA is placed in the A site
T/F bacterial mRNA’s do not have a 5’ cap
true, they dont
they cant tell the ribosome where to being searching for the AUG but htey have 6 nucleotide long specific ribosome-binding seq
a bacterial ribosome can readily bind directly to a start codon that is on the inside of the mRNA - this is necessary bc the mRNAs of bacteria are usually polycistronic (encode several different proteins on the same molecule)
UAA, UAG, UGA are ____
stop codons
the tRNAs do not specify an amnio acid for these codons but the ribosome understands to stop translation
what are release factors in the stop codons
releases factors bind to any stop codon that reaches the A site inside the ribosome - this alters the acitivity of the peptidyl transferase in the ribsosome - causing it to catalyze the addition of a water molecule instead of an AA
- this rxn frees the carboxyl end of the polypeptide chain from its attachment to the tRNA molecule
- then the ribosome breaks into its 2 parts and releases the mRNA which can be reassembled on another mRNA molecule for more protein synthesis
t/f multiple ribosomes will bind to a part of the mRNA
true
if it is being translated successfully a new ribosome will hop onto its 5’ end almost as the preceding ribosome has translated enough of the nucleotide to move out of the way
= polyribosomes /polysomes = large cytosolic assemblies that are made up of many ribosomes spaced closely tg
= boosts efficiency of the protein synthesis process
t/f some of the most effective antibiotics speed up the protein synthesis in bacteria
false - they inhibit it by either messing up the process, blocking channels
- these can be taken in high doses without being toxic to humans
- these compounds likely arose during evolution as a weapon deployed by microbes that used them to gain competitive advantage in the ecological niches they shared
why is the process of proteolysis and protease enzymes important
the proteins have different lifespans
proteolysis = breaks down proteins into its AA
they degrade the short peptides and finally to individual amnio acids = protease
they hydrolyze the peptide bonds - they do this to break down the proteins that have a short lifespan and to recognize and quickly remove the proteins that are damaged and misfolded
what are proteasomes
proteins are broken down by large machines called proteasomes
they are in the cytosol and the nucleus
each end of the cylinder has large protein complexes - act as stoppers that bind the protein subunits that need degration and then using ATP they unfold the proteins and thread them into the proteasome cylinder which uses protease to chop them into short peptides
- the protease is found in the inner part of this complex so that it doesn’t go and degrade important proteins
what is ubiquitin
this is how proteasomes select which proteins in the cell should be degraded
- they are marked for destruction by the covalent attachment of a small protein called ubiquitin
- these proteins are feed into the proteasomes
- proteins that are short lived have sequences that targets the protein for ubiquitylation as well as damaged or misfolded proteins
what are chaperone proteins
after peptide chains are made from ribosomes - they have to be folded - they don’t do this spont - they use chaperone proteins
- uses noncovalent interactions
covalently attaches phosphate group by phosphorylation
what are the post-translational modifications that are needed by proteins
needed to come fully functional
phosphorylation
T/F some codons code for more than one amnio acid
false
- none of the codons code for more than one AA but multiple codons can code for THE SAME amnio acid
what is the function of the lysosome
degradation of cellular components that are no longer needed
what are the 2 types of vacuole in plant cells
degration
storage
what is the difference between cytoplasm and cytosol
cytoplasm is the contents of the cell outside the nucleus
- including organelles
the cytosol is just the aqueous part of the cytoplasm, not including organelles
what does the lumen mean
it is the inside of any organelle
what are some of the functions that occur at the membrane(s) of the cell
- compartmentalization = creating boundaries
- interactions between cells
- transport solutes in
- respond to external signals
- semi permeable membrane for fluids and molecules like h20
- acts as a scaffold for biochemical activities like ATP production
what does the fluid mosaic model mean
that is has different proteins inside, embedded
what are some characteristics of the lipid bilayer
most energetically favored when the hydrophobic parts are inside and the hydrophilic parts are on the outside of the 2 part leaflet
lipid bilayers are ___
amphipathic
what is a phospholipid
it is a lipid that has different groups attached to the hydrophilic head
- has a glycerol + phosphate + (choice of group)
what is the structure of cholestrol
structure with a hydrophobic end - labelled with an OH molecule
and the hydrophobic part is labelled with the hydrocarbon tail
what is the structure of a glycolipid
2 hydrocarbon chains/tails attached to more carbon chains but with a molecule of hydrophilic like OH
forms phosphoglycerides
what is the difference between a saturated and an unsaturated phospholipid
kink = unsaturated = double bond
saturated = straight chains
what are liposomes
artificial lipid bilayers used to study the properties + function, membrane proteins and the best ways to insert drugs into the cell
its in the form of a circle bc it is in the most energetically favourable position with all the hydrophobic tails facing inward
cell membranes are ___
fluid
they can be deformed without breaking or releasing contents inside
proven by using laser tweezers to manipulate the membrane
what are the ways that phospholipids can move
rotation = rotating in its place (singular)
lateral diffusion = squeezing together and spacing out
flexions = the 2 hydrophobic tails attached to the head moving further apart or closer together (singular)
flip-flop = rarely move from one side of the leaf let to the other bc it has to undero unfavourable processes (philic goes into phobic zone temporarily0
what determines the cell membranes fluidity
important for its function
membrane proteins like transport, enzymatic, signalling
what is membrane fluidity affected by
- temperature (low temp = less fluid)
- composition
+saturation vs unsaturation, double bonds increase fluidity at low temps bc of tight packing)
+phospholipid tail length
- short tails = increase fluidity at lower temp = less tail to tail interaction
+ lipid composition - having cholestrol added, makes the membrane less permeable and stiffens the membrane
what does cholestrol do to the membrane
decreases mobility of the tails - stiffen and rigid membrane
- less permeable to polar molecules like water
- fills in space
CHOLESTROL IS VERY HYDROPHOBIC
what is scramblase
moves phospholipds
rapid flipfloping of RANDOM PL from one leaflet to the other
- if there is an imbalance in PL in one leaflet, scramblase will randomly move enough PL to the other leaflet
t/f phospholipids can be synthesized (added) to any leaflet side
false
cytosolic side of the ER
not on the lumen side (inside the ER)
the ER is where new membranes are made
the enzymes like scramblase is made in the ER
t/f in the golgi the phospholipid distribution is asymmetric
true
what does flippase do
it is an enzyme in the golgi membrane that flip flops a very SPECIFIC PL from the lumen side to the cytosolic side = phosphatidylserine
- some can bind cytosolic proteins to the cytosolic side but usually it is the extracellular side
how are glycoproteins and glycolipids added to the outside of the membranr
they start formed by adding sugar groups to lipids and proteins that are already attached facing the luminal side of the golgi
they end up on the noncytosolic side (EXC fluid) but transport vesicles fusing to the PM
- they maintain the same orientation
they protect the membrane from harsh environments
what are integral membrane proteins and peripheral
the ones embedded inside = integral
the ones only on the EXC or lumen side = peripheral
what are the three kinds of integral membrane proteins
- transmembrane - embedded inside bilayer
- monolayer associated - embedded on one side of the leaflet
- lipid-linked - attached to a lipid which is inserted into lipid bilayer
what is the one kind of peripheral proteins
protein attached
- proteins do not interest themselves inside the membranse - they are either bound to other proteins/lipds or face on side held together by noncovalent bonds
how do u extract integral proteins
using detergents
- destroying the bilayer
how to do extract peripheral proteins
gentle extraction methods like buffers
keeping the layer intact
what are the 3 kinds of transmembrane proteins
single alpha-helix (single pass that had an hydrophobic and hydrophilic area
mutliple alpha-helices, that sit adjacent to each other = philic/phobic
beta-barrel rolled sheet
explain the structure of the alpha helix in the membrane
the spiral has the R groups of the protein (the ones that give it identity) on the outside of the chain which interact with the inside of the membrane = hydrophobic and the hydrophilic parts are hanging on the outside of the membrane
what can be formed with multiple alpha-helices
forms a circle/pore which can transport water soluable molecules
= amphipathic by having the philic/phobic areas arranged accordingly = CHANNEL
whats an example of beta-barrel proteins being used
in bacteria
porin proteins form water filled aqueous channels that have inside hydrophilic and the surrounding hydrophobic parts (touch the adjacent PL)
what are examples of multiple alpha-helices
NA+ and K+ pumps
K+ leak channels
enzymes
what are examples of single alpha-helices
integrins = anchors
receptor kinases (signal binds to outside receptor and passes a signal to the inside
how are the structures of proteins identified
- x-ray crystallography which identifies its 3D structure
- hydrophobicity plots - scans AA to see how hydrophobic they are
how do you use hydrophobicity plots
the y axis tells you the index which is how hydrophilic and hydrophobic it is (closer to the top = + = hydrophobic) (closer to the bottom = - = more hydrophilic)
the x axis is the N terminus to the C terminus and spans the amino acid numbers
when theres a peak in the hydrophobic side it means that there is a alpha-helix domain somewhere there
why are some proteins anchored on the cytosolic face by an amphipathic alpha-helix
involved in curving the membrane
- vesicle budding at the ER
what side of the leaflet do proteins anchored with GPI end up?
top leaflet
synthesis in the ER lumen and ends up on the cell surface (the EXC fluid)
proteins with other lipid anchors end up on the bottom leaflet
how do the detergents work to break the PLB
the detergent is amphipathic
it can form detergent micelles which are clusters that attack the transmembrane proteins
to remove the detergent you need to add the phospholipds that were broken off and remove the micelles to artificially incorporate the protein in the bilayer = to study its properties while isolated
what is FRAP
fluorescence recovery after photobleaching
the protein gets fused to GFP which is the green fluorescent protein
- the membrane proteins gets bleached by laser beam so you get an area that is white, then the labelled proteins diffuse randomly throughout the membrane to fix it - shows how the PM is mobile
depending on the type of membrane they do this to, the amount of recovery differs - if its the ER membrane - mostly recoverd, but if its the nuclear membrane - not recovered
