2-Proteins Flashcards
(28 cards)
What is the size of a typical protein?
- Typical protein ~20-40K Da
- Average aa in a protein ~110 Da
What are the main 2 shapes of proteins?
- Globular: dominant; enzymes are globular
2. Structural: elongated (fibrous); collegen, elastin, keratin
Where do charges arise from in proteins?
- amino terminal +
- carbonyl terminal -
- side chains of aa (D, E, H, K, R) at ph7
- covalent modification (phosphorylation)
- metal ions
What is a zwitterion?
It’s a neutral molecule that carries two distinct ionizable groups, (a positive and a negative electrical charge).
What is pKa?
The pH oat which an amino acid is half protonated and half unprotonated. Determines the charge state of the amino acid.
what is the pKa of the amino acids with ionizable chains?
Asp 3, Glu 4, His 6, Cys 8,
Tyr 11, Lys 11, Arg 12.5
Why aren’t proteins good buffers?
pKa values of most aa side chains are not useful for physiological buffering. Only histidine and amino groups have a pKa in the righ range, but they are too sparse in serum proteins.
*Blood buffering: by carbonic acid and bicarbonate
What are peripheral proteins?
Those are proteins associated with membrane proteins. No direct contact with plasma membrane.
What are integral proteins?
Proteins embedded in the membrane either directly or indirectly via a lipid anchor.
What are some characteristics of transmembrane proteins?
- Single and multiple pass structures
- External domain: glycosyation & disulfide bonds (cysteines oxidized)
- Transmembrane segment: highly hydrophobic alpha helix
- Internal domain: reduced sulfhydryl groups (cysteines reduced), phosphorylation, no complex carbohydrate.
What are the 2 major types of protein glycosylation?
N-linked: sugar is linked to the side chain N of asparagine
O-linked: sugar is linked to the OH group of serine or threonine.
What is glycosylation?
Modification of proteins that include the addition of carbohydrate chains. Most common in proteins that are secreted or exposed to the environment.
What is Leri-Weill dyschondrosteosis disease?
- Disorder of bone growth, shortening of bones of the arms and legs
- Due to improper localization because of a mutation in SHOX transcription factor.
What are some protein destinations within the cell?
- ER
- Nucleus (reversible)
- mitochondrion
- cytoplasm (“default”)
- peroxisome
Explain how proteins destined for secretion enter the ER:
- Signal peptide is immediately degraded
- S-S bonds formed
- Initial N-linked carbohydrate attachment
- Chaperons assist in folding
- They go to Golgi for packaging
- Secretory granules are released
How do proteins destined for mitochondiral matrix get there?
- Signals (MSF) and many proteins (Tom 37/40/70) get proteins through the first membrane
- Another machinery including chaperone proteins (Tim 17/23/44) allow crossing into 2nd membrane
What allows proteins to go to the proper locations?
- Targeting sequences, essentially molecular mailing addresses for proteins.
- Two types of nuclear localization signals, monopartite and bipartite
- Nuclear localization signal has to be in the surface because it is hydrophilic (has basic aa)
Where can proteins be extracted from?
Tissues and from recombinant systems (yeast, bacteria, insect cells in culture, mammalian cells in culture)
What are some protein isolation methods?
- Ion exchange chromatography (based on charge)
- Gel filtration chromatography (based on size)
- Absorption chromatography (based on hydrophobicity)
- Affinity chromatography (based on interaction with other molecules)
What is the relationship between protein structure and function?
- Same function in different species -> related sequences
- Similar function -> similar sequences
- 3ry structure may be more conserved than 1ry
- Similar function proteins with little structural similarity ma be due to convergent evolution
What are the structural and sequence similaritiesbetween myoglobin and Hb?
- Alpha chain of these two have many identical & similar aa’s in other positions (~30% homology)
- Structures are almost indistinguishable
- Along with leghemoglobin, they have origins in a single gene that underwent duplication
What are paralog proteins?
These are proteins that share evolutionary history and that evolved to have very different functions.
What is Hb’s structure? What is wrong with sickle cell anemia Hb?
- Hb is a tetramer : 2 alpha and 2 beta chains.
- In sickle cell anemia, HbS, the E (charged) at position 6 in beta chain is changed to a V (hydrophobic).
- This causes Hb aggregation due to hydrophobic interactions with F85 and V88 on 2nd beta chain
- Aggregation forms fibers and sickle shape in cell
Based on what does electrophoresis separate proteins?
Size, charge, or both
