Theme 1- Module 3 (Proteins) Flashcards
What are some functions of proteins in our bodies?
Transport and signalling
Movement and structure
Enzymes
Defense (i.e. antibodies)
How is the TATA box able to interact with DNA molecules?
A groove in the protein allows for this interaction
Porin proteins have a structurally hydrophilic pore. How does this relate to their function?
They transport water across the cell membrane; their pore should be hydrophilic (compared to the hydrophobic inner membrane) in order for this to occur.
Heamoglobin is globular and has a hydrophobic interior and a hydrophilic exterior. What does this structure allow it to do?
It allows the haemoglobin to be soluble in the aqueous environment of the cytosol
*most soluble cellular proteins have a similar shape
Name two ways protein structures are represented
Space-filling diagram
Ribbon diagram
What are some key features of a space-filling diagram?
Shows actual size and location of each atom
Atoms rep with diff colours
What are some key features of a ribbon diagram?
Lines rep backbone of the polymer
Thicker line = organized reiterated alpha helix
Thinner line = less ordered loop
The genetic info for each protein is encoded in the _____ for each cel
DNA
What are the main steps of making proteins?
1) Transcribe genetic info from DNA into RNA
2a) Prokaryotes —> RNA goes straight to step 3
2b) Eukaryotes —> RNA to mRNA
3) Transported in cytoplasm
4) Ribosomes translates the thing
It is within the _____ that the ribosomal RNA molecules that are an important component of the ribosomes are transcribed
Nucleolus (middle of the nucleus)
Where does transcription occur?
Nucleus
What do nuclear pore complexes used for? Describe using the example of ribsomal RNA
Allows materials to flow in and out of the nucleus
Ex. Ribosomal RNA manufactured in nucleolus; bind to proteins to make the ribosome subunits; exit via nuclear pores
Where is the ribosomal RNA manufactured?
Nucleolus
What can enter the nucleus via the nuclear pores? What can exit?
Enter: building blocks of DNA and RNA, enzymes
Exit: ribosomal subunits + RNA
What do the subunits of the ribosome contain?
RNA and proteins
What’s the difference between free ribosomes and bound ribosomes?
Free ribosomes = remain soluble in the cytoplasm
Bound = attach to the endoplasmic reticulum
What do bound ribosomes produce and what happens to the product?
Polypeptide strands into the lumen or membrane of the ER which will be destined for other parts of the cell or secretion
What do free ribosomes produce and what happens to the product?
Polypeptide strands that will remain in the cytoplasm of the cell or be transported to other organelles
Amino acids linked together are called…?
Polypeptides
What process links amino acids together? What breaks them apart?
Link = condensation (forms water) Break = hydrolysis
What does the transfer RNA (tRNA) do?
Matches the sequence of nucleotides on the mRNA and carries the appropriate amino acid to the next position in the growing polypeptide chain
What is a peptide bond?
The C-N bond that results thru a condensation rxn between a carboxyl group of one amino acid and the amino group of the other
When the amino acids are linked together via peptide bonds, the amino acids are referred to as ______ and the formed polymer is referred to as a polypeptide
Residues
What determines the properties of an amino acid?
It’s R group
If the proteins were synthesized by free ribosomes (located in cytosol), where do they go?
Remain in cytosol or go to various organelles
Examples of proteins that remain in the cytosol?
Enzymes involved in glycolysis
Structural proteins of the cell (actin and tubulin)
How do some proteins know that they are targetted towards specific organelles?
There are special sequences on the protein
True or false: some proteins are flat and linear
False
All proteins take on a three-dimensional, folded shape
In order to function, all proteins require what?
Proper folding
Free proteins become folded and functional in the cytosol. Where do bound proteins become folded and functional?
The ER
What determines function of a protein?
It’s tertiary structure / how it’s folded
Why is an alpha helix a spiral?
Hydrogen bonds between the carbonyl of the carboxyl group of one amino acid residue and the amide of the amino group of another amino acid residue four positions away
The alpha helix is coiled, why is this important in terms of the protein’s properties?
Since it’s coiled, the R-groups stick out
This det how it folds (its tertiary structure) and thus det the properties of the protein
What is the structure of beta-pleated sheets?
Parallel protein strands with hydrogen bonds formed between the carboxyl and amino groups of adjacent strands
Where are the R-groups in the beta-pleated sheets?
Extend above and below
What are the two secondary structures of proteins?
Alpha helix
Beta helix
Why determines whether or not a protein folds into an alpha helix or a beta-pleated sheet?
The interactions between the components of a protein’s backbone
When does protein folding occur?
Spontaneously as the polypeptide leaves the ribosome
What are some cellular mechanisms that assist in protein folding?
Molecular chaperones
Chaperonins
How do molecular chaperones work?
Small, monomeric proteins
Bind to hydrophobic regions of the nascent polypeptide and prevent incorrect folding just long enough for the correct structure to form
How do chaperonins work?
These are large complex polymers
Form isolation chambers where a single protein (in the middle of forming) is sequestered away so it can fold without interference
What are quaternary structures?
The association of diff polypeptide subunits to form the final, functional structure
What is included in the endomembrane system?
Nuclear envelope
ER
Golgi apparatus
Lysosomes
What is the importance of the endomembrane system?
Allows for the cell to compartmentalize diff areas to serve diff functions
Once bound ribosomes produce proteins, where do those proteins go?
Goes through the lumen of the ER for further processing (including protein folding)
How do certain proteins know that they are supposed to go through the ER and not just into the cytosol?
mRNAs that encode proteins destined for the endomembrane system include a special sequence at the beginning
Describe the process in which bound ribosomes synthesize proteins in the ER
Special signal sequence synthesized by the ribosome
SRP binds to the signal sequence of the growing polypeptide and halts translation
SRP binds to SRPR (SRP receptor) on the ER membrane
SRP brings ribosome to transmembrane channel on ER
SRP dissociates
Protein synthesis resumes, polypeptide chain is threaded thru the ER (via the channel)
Inside lumen, signal sequence is removed and it can now be folded
What are vesicles?
Small membrane-bound compartments that bud off of the ER
Contain proteins that have been translated by bound ribosomes
What is glycosylation?
Addition of one or more carb chains to a protein
Where does glycosylation take place?
The lumen of the ER
Golgi apparatus
What kinds of proteins take part in glycosylation?
Most secreted and membrane-bound proteins
What is an advantage of glycosylation?
Helps contribute to protein stablity, folding, and even cell-to-cell recognition
How does the cell proteins from the ER to the golgi apparatus?
Vesicles that pinch off of the ER fuse with the Golgi and deposit their contents into the lumen of the Golgi apparatus
What does the golgi apparatus do?
It modifies and ships ER products in new vesicles
True or false: all proteins from the golgi apparatus will be secreted from the cell
False
Some will stay in the golgi apparatus/ER. Others will go to the cell membrane, or to other organelles
What kinds of proteins are secreted from the cell?
Antibodies
Hormones
Enzymes
What kinds of proteins will be shipped to the cell membrane?
Porins
Receptors
What is the leading hypothesis as to how these proteins are sorted as they leave the Golgi?
Proteins are tagged with specific markers that target them to diff regions of the cell
These tags, when added to proteins, bind to receptors on the internal membrane of the Golgi and form transport vesicles
What happens once the tagged vesicles reach their destination?
Once at the destination, the vesicle fuses with the membrane/organelle. This allows for the release of soluble proteins or the embedding of transmembrane proteins
How is the vesicle able to bind with the membrane?
It also has a phospholipid bilayer
How are vesicles able to travel to their destinations?
Motor proteins attach to transport vesicles and walk from negative to positive along polar microtubules
Microtubules are part of a larger network. What is this network called and what is its purpose?
Cytoskeleton
Dense network of fibers that help maintain and change cell shape
What are microtubules?
Polymerized tubulin proteins that form long fibers which stretch thru the cell and act as roadways
Give two examples of motor proteins
Kinesin
Dynein
True or false: the transport of vesicles to their various destinations does not require energy
False
Where are soluble proteins synthesized and folded?
In cytosol in free ribosomes
Some stay there others are transported afterwards
Proteins destined for membrane bound organelles required for fatty-acid metabolism (i.e. mitochondria, chloroplasts, and peroxisomes) are synthesized where?
Free ribosomes
Are proteins synthesized in free ribosomes folded before transport to the organelles or after transport?
Both
Describe the aquaporin structure
4 protein subunits (monomers) that together form the tetrameric aquaporin channel
Each subunit contains membrane-spanning alpha-helixes that form a central pore; each monomer contains an independent water pore; a central pore in the middle
Is the tetrameric aquaporin channel its tertiary or quaternary structure?
Quaternary
Why is the aquaporin’s structure important for its function?
The independent water pores (in each monomer) allow water to move through in either direction
Centralized pore allows several water molecules to move simultaneously thru
True or false: like the sodium-potassium pumps, aquaporins also undergo changes in shape in order to transport water
False
Each water molec forms specific hydrogen-bonds with hydrophilic amino acid side groups that line the core of the monomer.
This displaces nearby water molecules that pass ahead thru the channel
Describe the structure of prok membrane pores compared to euk pores
Beta sheets form a barrel with hydrophobic exterior and hydrophilic interior
True or false: those beta-sheet barrels are only found in prok membranes
False
Also found in mitochondria and chloroplast membranes
*Further evidence of prokaryotic ancestry
What causes cystic fibrosis?
Genetic mutation that leads to the malfunction (misfolding) of a cystic fibrosis transmembrane conductance regulator (CFTR) ion channel protein. Causes accumulation of thick mucus in the lungs
