5. Proteins Flashcards
(19 cards)
What are the parts in the structure of an amino acid?
- alpha carbon
- Hydrogen
- Carboxyl group (COOH)
- Amino group (NH2)
- R group
Charged amino acid:
- amino group gains a hydrogen and carboxyl group loses a hydrogen
- NH3, COO-
How do you tell if an amino acid is hydrophobic or hydrophillic?
Look at the R-group
- if it contains N or O, it’s hydrophillic
Where do non-polar amino acids tend to be located in a folded protein?
In the interior
Glycine is a special amino acid. It is where the R group is just Hydrogen. What does this tell us about the flexibility of a protein with glycine?
- glycine is symmetric
- the R group is small and so has free-er rotation
- increases the flexibility of the resulting protein
Proline is a special amino acid where the R group links back to the amino group. What does this tell us about the flexibility of a protein with proline?
- restricts the rotation of the C-N bond for the amino acid
- creates a kink in the polypeptide chain
- resulting protein is less flexible in this area
What makes cysteine a special amino acid?
It can react to from a S-S disulfide bond (strong)
- can connect different parts of the same proteins or connect different proteins
What kind of bonds are between amino acids?
peptide bonds
- electrons in this bond are more attracted to O than N
- has some characteristics of a double bond (shorter, not free to rotate)
What bonds compose of the secondary structure of proteins?
hydrogen bonds between the carbonyl group and amide groups of different peptide bonds in the same protein
What forms does the secondary structure take on?
- the alpha helix
- the beta sheet
At what stages of folding does the protein have function?
tertiary structures and quaternary structures
what are denatured proteins
proteins which have lost their original shape and can no longer perform their function
- possibly due to heat, radiation, acids
What is the use of chaperone proteins?
- protects denatured or slow folding proteins until they can obtain their shape
- binds to hydrophobic groups and nonpolar R groups to protect them, until the polypeptide can find its correct shape
How do:
- peptide bonds
- hydrogen bonds
- ionic bonds
- disulfide bridges
- noncovalent interactions (etc. van der waals forces and the hydrophobic effect)
define a protein’s 4 levels of structure?
primary structure:
- polypeptide chain
- formed of peptide bonds
secondary structure
- alpha helix or beta sheets
- hydrogen bonds between peptide bonds
tertiary structure
- 3-D form
- hydrogen bonds, ionic bonds (basic amino acid and an acidic amino acid), disulfide bridges
quartenary
- multiple tertiary structures joined by disulfide bridges
noncovalent interactions maintain interactions with different parts of the protein
What are the differences in initiation of translation between prokaryotes and eukaryotes?
Eukaryotes:
- initiation factors bind to the 5’ cap and scan downwards until AUG (start codon) is reached
Prokaryotes:
- initation factors bind to the Shine-Dagarno sequence (usually close to the art codon)
Explain the steps of initiation, elongation, and termination for translation
initiation:
- in eukaryotes, initation factors bind to the 5’ cap.
- initation factors recuit the smaller ribosome subunit which attaches to the RNA and begins scanning until start codon, AUG is reached
- in prokaryotes, initation factors bind to the shine-dagarno sequence
- smaller ribosome subunit only attaches once AUG is found
- large ribosome subunit is recuited
elongation:
- tRNA enters through the A site of the subunit, charged with the poly peptide that matches (by the anticodon)
- tRNA shifts, and a peptide bond forms at the P-site
- uncharged tRNA then leaves through the E site
- one amino acid is added per codon (3 nucleic bases)
- energy for reactionrs provided by elongation factors
termination:
- one of the stop codons is encountered, and this recuits a termination factor to the A site (no associated amino acid)
- protein chain is formed, and the ribosome releases the mRNA
What are some examples of posttranslational modification?
many proteins are inactive when produced and need to be activated via methods like:
- cleavage
- phosphorylation (adding phosphates)
If a protein needs to be located in the chloroplast or mitochondria, where might we find its signal sequence?
on the amino end
Where are the signal sequences for a protein located, if it needs to be in the following locations
a) cytoplasm
b) chloroplast/mitochondria
c) nucleus
a) no signal sequence
b) amino end
c) internal signal sequence
what is the point of the SRP, signal recognition particle?
it directs the protein (along with the ribosome) to the ER
- attaches to an SRP receptor on the surface
- protein signal sequence indicates where in the ER it should go (usually amino terminal)
after being fully processed in the ER, the protein might be:
- embedded in the ER membrane
- in the lumen of the endomembrane system
- secreted out of the cell
