Midterm 1 Flashcards
What are proteins made of?
Amino Acids
What are nucleic acids made of?
Nucleotides
What are polysaccharides made of?
Carbohydrates
What are lipids made of?
Fatty acids
What are the four main types of macromolecules?
Proteins, Nucleic Acids, Polysaccharides, and Lipids
All macromolecules are built from monomers except for?
Lipids
What is an oligosaccharide?
A small chain of monosaccharides?
What is a fat made of?
A fat is a triglycerol: made of 3 fatty acid tails, and one glycerol
What is the difference between a phospholipid and a fat?
Phospholipids have 2 fatty acid tails and fats have 3 fatty acid tails.
A fatty acid is composed of….
Hydrocarbon chains (hydrophobic) and a carboxyl group (hydrophilic)
Fats, steroids, and phospholipids are all examples of…
Lipids
Describe the structure of a steroid
4 hydrocarbon rings with a hydroxyl group attached to one of the rings
What are the 3 types of proteins?
Enzymes, structural, and regulatory
How do amino acids hook together?
Peptide bonds
What is an amino acid formed of?
An amino group, alpha carbon, hydrogen ion, carboxyl group and a side chain (R group)
What gives an amino acid its determining characteristics?
The R group
What is a peptide?
A short chain of amino acids
What is a protein?
A folded polypeptide
Describe the four levels of structures
1) Primary: linear strain
2) Secondary: alpha helix
3) Tertiary: folded alpha helices
4) Quaternary: group of tertiary structures
What is the function of Ribonuclease A?
Digest RNA
What is a molecular chaperone?
A protein that binds to another to protect it by changing it’s shape
Why are cells compartmentalized?
Separate functions, prevents random movement through membrane, protect from outer activities
What are some membrane functions?
Provide selective barrier, help with cell to cell interactions
What are membranes composed of?
Lipids, Carbs, Proteins
_____ makes up most of membrane lipids
Phospholipids
Up to __% of the membrane can be composed of cholesterol.
50
Lipids are easily able to switch places side by side but in order to flip they require help from membrane proteins containing _____.
Flippase
Why do holes in the lipid bilayer seal almost immediately?
Because hydrophobic tails become exposed so lipids move together to prevent water touching the tails
How do carbs attach to the membrane?
Binding covalently to lipids or proteins
All carbs are either ___ or ___ linked
Nitrogen, Oxygen
Carbs never face ___ the cytoplasm
Into
What does asymmetric mean in terms of the membrane?
Something can be attached to one side of the membrane but not the other
What is the difference between integral and peripheral proteins?
Integral proteins are embedded in the membrane, and peripheral are blinded to the outside/inside layer of the membrane
How are peripheral proteins attached to the membrane?
to integral proteins via electrostatic bonds
What is a GPI anchored protein?
A protein that is bound to a lipid
What are the four features of the fluid mosaic model?
asymmetric, embedded, mosaic, and quasifluid
What are the 3 types of membrane lipids?
Glycolipids, Phospholipids and Cholesterol
Are peripheral proteins hydrophilic, hydrophobic or amphipathic?
Hydrophilic
What is a sphingolipid?
Long chain hydrocarbons come together in membrane, pack tightly and become gel like, like a lipid raft
What is a lipid raft?
Tightly packed lipids/cholesterol in a patch on the membrane outer leaflet where GTI proteins can attach
The ____ is central to the microtubules
Mitochondria
What is metabolism?
collection of all biochemical reactions
The ___ pathway takes complex structures and breaks them into smaller components so the molecules can be reused. Produces energy
Catabolic
The _____ pathway takes simple components and builds more complex ones by using energy
Anabolic
What are a few functions of the mitochondria?
Synthesizing amino acids, calcium transport
What is the function of Drp1
binds/hydrolyzes GTP, involved in splitting mitochondria in half
What is the crust and where is it located?
in the inner membrane, increases SA
What is the inter membrane?
located between the inner and outer membrane
What is a porin?
A major protein channel in the mitochondrial membrane allowing ATP transfer when open. Located in outer mitochondrial membrane
Does the inner membrane contain more protein or more lipids?
3-4 protein: 1 lipid
___ is the loss of electrons and ___ is the gain of electrons
oxidation, reduction
What is glycolysis?
the pathway of glucose oxidation
What is produced by glycolysis?
pyruvate, 2 ATP, 2 NADH
NADH accepts _ é and _ H+
2, 1
What is NADH?
A co-factor
Pyretic Acid + Co A + NAD ->
Co A + 2 C chain + NADH + CO2
What is pyruvate broken down into?
acetyl group, 2e, 2 H+, CO2
What do you get as products in the TCA cycle?
CO2, NADH, FADH2, GTP, Oxaloacetic acid
Cells cannot use electrons as energy, it must be converted into ?
ATP
____ reacts with acetyl Co A to start the TCA cycle again
Oxaloacetic acid
How many times does the TCA cycle occur for every molecule of glucose?
2
What is oxidative phosphorylation?
The formation of ATP driven by the transfer of é to oxygen
What is the electrochemical gradient?
change in voltage/concentration across the membrane
What is chemiosmosis?
the production of ATP using the energy of H+ gradients across membrane to phosphorylate ADP
2,4-dinitrophenol inhibits chemiosmosis by?
Uncoupling é transport and ATP synthesis
What are the four main organelles that are part of the endomembrane system?
Golgi, ER, Endo/Lysosomes
What is the function of the endomembrane system?
Involved in synthesizing membranes and moving stuff around
Which side of the ER membrane contains ribosomes?
Cytosolic side
What are the functions of the sER?
Synthesis of steroid hormones, detoxification, and sequestering calcium
Where are the proteins synthesized?
Ribosomes
What is cell fractionation?
A technique used to show that free ribosomes make different kinds of proteins than membrane bound ribosomes
What experiment was used to examine the secretion pathway?
Pulse Chase Experiment
What is a yeast sec mutant?
yeast with degenerative genes which synthesize secretory proteins but won’t secrete the proteins
Yeast sec will secrete proteins at room temp but will stop secreting proteins when the temp is ____.
increased
What happens when mRNA is translated?
protein is created
Proteins can accumulate in which 5 places which can block the secretion pathway?
2x Vesicles, Cytosol, ER, Golgi
What does a signal recognition particle do?
binds to signal sequence on ribosome causing translation to stop and elongation of polypeptide to occur
How does the cell know if a protein should be inserted into the membrane?
Amino end of protein has signal sequence telling it would be inserted into the membrane
What side of the ER membrane has the signal sequence receptor on it?
Cytosolic side
What is a translocon?
a group of integral membrane proteins and SPP complex that forms a channel
How does con translational translocation mechanism work?
Protein is synthesized by hydrophobic amino acids as it goes through the membrane. Stop sequence forms, hydrophobic part secreted into membrane
What are the names of the 2 leaflets of membrane?
cytosolic, exoplasmic
Why are lipids difficult to synthesize in the cytosol?
because of the hydrophobic tails
What is the function of flippase?
flippase flips lipids from one leaflet of membrane to the other because integral membrane proteins only produce lipids into one leaflet of the membrane so in order for both layers to grow, the material from one leaflet must be flipped to the other side
How are lipids transferred through the cell?
Proteins bin to them covering hydrophobic bits
What is an O-linked protein?
A protein that attaches to serine/theronine
What is an N-linked protein?
a protein that attaches to asparagine
Where does O-linkage occur?
Golgi
Where does N-linkage occur?
ER/Golgi/ERGIC
What is the function of Dolichol Phosphate?
moves sugar around membrane
How many sugars can a dolichol carry at once?
7
What does oligosaccharyltransferase do?
transfers sugar/dolichol chain into an asparagine covalent linkage
What is the point of quality control?
allows cell to select/destroy misfiled protein
What are the names of the 2 ER proteins responsible for quality control?
Calnexin and Calreticium
What is the function of calnexin?
Cuts off glucose and tries to fold it correctly
What is the function of calreticium?
binds to protein by glucose, cuts glucose off and protein is released
What does the enzyme UGGT do?
detects if proteins are folded correctly by checking if hydrophobic regions are exposed to lumen. Then it cuts off the mannose of proteins until it can no longer fold and a proteasome will destroy it.
What is the function of a proteasome?
protein machine that destroys other proteins
What are proteolytic enzymes?
enzymes that destroy proteins
What is ubiquitin?
a signal for the protein to be destroyed, threads protein into proteasome channel
What attaches ubiquity to the protein?
ubiquitin ligase
What happens to a cell containing too many misfiled proteins?
It will die (apoptosis)
What is the function BiP?
Once cell realizes a protein is misfiled. BiP tries to refold the protein
What is the function of the translation factor ELF2 Alpha?
turns of protein translation so bad proteins aren’t made
What is apoptosis?
programmed cell death
What is the endoplasmic reticulum Golgi Intermediate Compartment(ERGIC)?
Space between the ER/Golgi
What are 3 regions of the Golgi complex called?
cis/medial/trans cisternae
The __ cistern is closest to the ER while the __ cisternal is closest to the plasma membrane.
Cis, Trans
Where are proteins usually modified?
Golgi, Integral Membrane Proteins
What are the 2 ways that stuff moves through the Golgi?
Vesicular transport, Cisternal Maturation model
What is the difference between vesicular transport and the cisternal maturation model?
CMM: retrograde, no vesicles
VT: vesicles, anterograde
How do vesicles break off of the organelle?
protein on surface coating of vesicles forces membrane to curve which causes the vesicle to snap off of the organelle.
What do COP2 coated vesicles do?
Move via anterograde to ERGIC/Golgi from ER or form cis to trans
What do COP1 coated vesicles do?
Move via retrograde from ERGIC/Golgi to ER or from trans to cis
What do clathrin coated vesicles do?
Move from trans Golgi network to endo/lysosomes and from PM to cytoplasmic compartments
How are ER proteins secreted?
Vesicles bud off of ER
What are the functions of a coated vesicle?
help shape vesicle, help select which proteins need to be moved
What does Sar1 do?
regulatory protein, responsible for formation of COP2 vesicles
How does COP2 get rid of its coat?
when the vesicle finds its desired location, GTP is hydrolyzed to GDP making the coat fall off
What is retention?
“if a protein is supposed to be in the ER than it stays in the ER” keeping what is meant to stay
What does ARF1 do?
regulatory protein responsible for formation of COP1 vesicles
What is retrieval?
retrieving a vesicle that took the wrong proteins to the wrong place, COP1 takes them back
What kind of protein recognizes if there is an incorrect protein in a vesicle?
Transmembrane proteins
What is the KDEL sequence at the end of a protein?
Lys-asp-glu-leu
What is the function of a lysosome?
destroys parts of cell that are no longer needed
How many enzymes do lysosomes contain?
50 works best in low pH
How do enzymes not destroy the lysosome?
lumen inside of membrane is very glycosylated which protects the membrane
How do lysosomes know when to destroy cell part?
Autophagosome surrounds organelle, lysosome binds to autophagosome and destroys the organelle
How are lysosomal enzymes taken to the lysosome?
coated vesicles from ER take them there
How do particles in vesicle get to target membrane?
vesicle membrane bind
What is tethering?
fibrous proteins tether vesicle to target
What do rabs do?
bind to GTP, help with tethering
What is docking?
fibrous proteins pull vesicle tighter and eventually fuse
The proteins on membrane and vesicles that determine where they go are called?
t/v-SNAREs
What are the 2 types of t SNAREs
syntaxin, SNAP 25
What is the name of a v-SNARE
synaptobrevin
What do SNAREs do?
bring vesicle closer to membrane via helical complex
What is the function of the NSF?
binds to SNARE complex and break it apart allowing t/v membranes to form together making a pore
What is a ligand?
anything taken into cell by endocytosis
There is a concentration of _____ that forms on a coated pit
LDL: Low density lipoprotein cholesterol
Describe the composition of clathrin?
3 heavy chains, 3 light chains, in Triskelion shape
The cytosolic membrane of a vesicle has one layer of ___ and one layer of ___ ___
clathrin, adapter proteins
What kind of structure does an adapter protein have?
quaternary
What is GTPyS
a kind of nonhydrolyzable GTP
What does Dynamin do?
hydrolyzes GTP causing conformational change in neck region of clathrin
What do house keeping receptors do?
bind to things cell needs
What do signalling receptors do?
bind to info containing molecules
What is endocytosis?
movement from outside cell to inside cell
Why would a cell want to degrade signal proteins?
to prevent over stimulation
Where does postranslational uptake of proteins occur?
nucleus, mitochondria, peroxisomes, and chloroplast
Name the 4 mitochondrial compartments?
Inner/outer membane, Inter membrane space, matrix
What is required to transfer a protein into mitochondria?
a transfer sequence telling the mitochondria to take in the protein
Describe the function of chaperone proteins?
affect the folding of other proteins, no structural info, recognize unfolded proteins, help them find their tertiary structure, require energy
Why are mitochondrial DNA synthesized in the nucleus?
Because they have encoded DNA
The ___ doesn’t make any mitochondrial proteins so it gets its proteins from the _____
mitochondria, nucleus
Hsp 60 and Hsp 70 are examples of….
Chaperone proteins
Hsp 7 interacts with proteins made in ____ to assist in _____
cytosol, folding
What makes protein unfold in the matrix?
Hsp60/70, requires energy, chaperone hydrolyzes ATP, folds protein, pulls into matrix
What are amino acids made of?
A carboxyl group, amino group and side (r) chain
Carbs only attach to the _____ leaflet
exoplasmic
What kind of proteins are Myristate and Farnesyl?
GPI anchored proteins
____ is involved in membrane fluidity
Cholesterol
___ _____ move as a unit
Lipid rafts
Where are F1 particles located?
the inner mitochondrial membrane
Where does glycolysis take place?
The mitochondria/cytosol?
What is the purpose of the proton motive force in the case of this class?
Drives synthesis of ATP by chemiosmosis
What is 2,4-dinitophenol?
Passage ways in membrane for H+ to travel across
What does the F1 Complex (ATPsynthase) do?
changes ATP to ADP + Pi
Which unit of the binding change mechanism is the rotating unit?
Gamma
The beta subunits of the binding change mechanism are always in different conformations which are:
tight, loose, open
Microbodies, Peroxisomes, Glyoxysomes are all similar to…
the mitochondria
