Topic 6: Making proteins Flashcards
Which mechanism do amino acids use to form dipeptide bond?
Is this reaction favourable and why?
Condensation polymerization
Very thermodynamically unfavourable because these amino acids are surrounded by water
Hydrolysis is more favored in aqueous environment
Identify and describe functions of RNA types and proteins used in protein synthesis process
- Messenger RNA (mRNA): template for protein synthesis
- Transfer RNA (tRNA): has anticodon at 1 end and complementary amino acid at the other end –> match correct aa to the template
- Ribosomal RNA (rRNA): a complex containing proteins to form machinery for catalyzing peptide bond formation between amino acids and making protein
- aa-tRNA: binds to tRNA to help tRNA bind to correct amino acid
How does a specific protein help tRNA to do its functions?
aa-tRNA synthetase recognizes the amino acid, anticodon and other parts of tRNA –> helps tRNA to bind correctly
Helps to overcome the unfavorable reaction to activate amino acid
- Amino acid and ATP bind to aa-tRNA.
- ATP is hydrolyzed to AMP. Pyrophosphate is then hydrolyzed to release energy used to join the amino acid with the the AMP.
- AMP is then replaced by the tRNA which bind to amino acid using the previous energy.
- Aminoacyl tRNA is released from the enzyme.
What is ribosome made of/why is it called riboproteins?
Made up of RNA and proteins
Identify and describe the steps in protein synthesis
- Initiation:
+ Small subunit of ribosome binds mRNA and Met-tRNA (special Met-tRNA in prokaryotes)
+ mRNA has extra bit of sequence at the start to help recognizing the start codon
+ Large subunit binds - Elongation:
+ aa-tRNA are guided by anticodon/codon matching and come in A-site.
+ Activated amino acids are placed close together –> easy for bond formation catalyze
+ Peptidyl transferase in ribosome catalyzes peptide bond formation using energy stored in the aa-tRNA bond.
+ tRNA continue to go in, amino acids are bind together, then tRNA are released. - Termination:
+ Stop codon is reached, no tRNA matches, but release factor binds
+ Peptidyl transferase adds water instead of amino acid
–> release the polypeptide
+ The ribosome disassembles, can be reused
Compare and contrast prokaryotic and eukaryotic translation
Overall the same in steps but different in regulation
- Initiation:
+ Prokaryote: special tRNA and special Met
+ Eukaryote: special tRNA and normal Met
- Termination:
+ Prokayote: 2-3 release factor
+ Eukaryote: only 1 release factor
Why do we need protein folding?
The amino acid sequence doesn’t do anything until it is folded into the active structure.
Classify different levels of protein structure
- Primary: the amino acid sequence
- Secondary: local structures including
+ EG Alpha helix - spiral structure, always same shape, right-handed
+ Beta sheet - in strands which come together to form sheets, varieties in direction, curving or flat - Tertiary: overall 3D structure after the helix and strands fold
- Quaternary: organization of many subunits
+ very important for some proteins as they need multiple protein chains to come together to be functional
Describe features of secondary structure of proteins
Local features allow formation of structure
- Backbone-backbone hydrogen bonding:
+ across the strand in Beta sheets
+ every 4 residues between above and below strands of Alpha helix
–> patterns and angles define the structure
- Sidechain interactions:
+ Alpha helix: sidechain point outwards
+ Beta sheets: sidechain point above and below
–> interact together to form tertiary structure
What are some bonds and interactions to form tertiary structure from secondary?
How does tertiary structure form from primary structure?
Lots of interactions and bonds between the sidechains and other parts
- H bonds
- ionic/electrostatic and polar interactions (outside of the protein)
- Hydrophobic interaction (inside of proteins where hydrophobic parts cluster together in the middle of the protein) –> force driving protein folding
These bonds - non-covalent bonds - are sensitive to surrounding conditions (pH, solvents, temp)
- Amino acid sequence starts to fold
- Collapse of protein chain due to the hydrophobic effect
- Secondary structure formation follows by backbone hydrogen bonding
- Tertiary structure reinforces by diff. interactions and bonds between sidechains
Are biomolecules including proteins and other ones rigid or dynamic?
NOT rigid, actually moving around, twisting, lengthening and shortening withing certain ranges
In what range of environmental conditions are most biological macromolecules stable?
A narrow range
- 5 degrees Cel to 50
- atmp
- nearly neutral pH
Between being hydrolysed and unfolded, which one can proteins go through more easily and why?
- Proteins can still be hydrolysed but really hard since it has to be done in extreme envi (very acidic or basic with high heat/pressure)
- Much more easy to be unfolded or to lose 3D structure by adding heat and breaking weaker bonds
Demonstrate how 3D protein structure is related to function using the example of the alpha helix in DNA binding proteins.
Alpha helix can fit perfectly into the major groove of DNA (the size as well as the charge - DNA backbone is (-) charged while the alpha helix is (+))
Single strand of protein can fit in the minor groove
–> feature of DNA binding
–> such structure “coevolve” to be able to work together in processes like transcription
Identify and describe some types of mutation and their effects on protein structure and function
- Silent mutation - no change
- Frameshift mutation: different amino acid sequence –> protein unlikely to fold correctly –> without correct structure, function can be affected
- Point mutation:
+ Similar residue (same feature or similar size): minor change in structure or stability –> but no major effect
+ Different residue (diff. charge eg.): affect folding/structure (ins the middle of sequence) and function (near binding site)
