protein and amino acid metabolism Flashcards
how are proteins made
from amino acids forming polypeptides and then polypeptides forming proteins
amino acids are joined together by what bond and when
by a polypeptide bond
Amino acids are joined together during translation
- Peptidyl transferase,
Main enzymatic function of the ribosome
60S (large) subunit of the eukaryotic ribosome
what does tRNA do
tRNAs bring amino acids, which reacts with the other tRNA held within the ribosome
The carboxyl group reacts with the amino group on the new amino acid
Condensation reaction:
-OH- lost from Carboxyl
-H+ lost from the Amino
peptide bonds form between what
carboxyl and amino group
what is the primary structure
chain of amino acids. Its unfavourable as massive and not energy sufficient
name the smallest and larges proteins
Smallest protein: TAL in Fruit Flies (11aa)
Largest protein: Titin in humans (34,350 aa)
explain secondary structure
Hydrogen bonds between the N-H and the C=O
α-helix:
- Right-handed coiled strand
- Hydrogen bonds form intra-strand, bonding the C=O to the N-H 4 amino acids below it
β-sheet:
- Inter-strand, with the C=O bonding to a N-H group on an adjacent strand
- Parallel or anti-parallel depending on the alignment of the strands (Anti-parallel is more stable)
are antiparallel strands in secondary structure more or less stable
more stable
explain the tertiary structure
The most stable, lowest energy conformation
Held in place by interactions between the R-groups:
- Disulphide bridges
- Ionic bonds
- Hydrogen bonds
- Van der Waals interactions
what is Levinthal’s Paradox
How does the polypeptide find the most energetically favourable conformation for its tertiary structure?
Is every random conformation tested?
If, 100 amino acid protein
Each residue can assume 3 possible positions, Total time it would take: 1.6x10 to the power of 27 years
The enormous difference between the calculated protein folding time and actual protein folding times
Average protein folding is in the scale of milliseconds
Dependent on a number of factors, including size.
Partially correct intermediates are retained
- Each correct conformation of an amino acid is maintained, reducing the number of possible positions over time.
Protein holding is more complex than this
- Protein intermediates are short lived
Energy
- Intermediated can only be scored by the amount of free energy they have, and connect be observed on a residue-by-residue basis
- Some intermediates are called kinetic traps – the conformation has a favourable energy but is not on the path to the final protein conformation
Why is knowing the biochemistry behind protein folding important?
In this respect the knowledge how the linear sequence of amino acids is translated into spatial information is the “missing link”.
There is a tremendous interest in the over-expression of recombinant proteins for industrial, biotechnological, and research applications.
Incorrect folding or misfolding of proteins is often related to protein aggregation and fibrillogenesis, which is connected to a number of serious diseases, such as BSE (Mad Cow Disease), or Huntington’s and Alzheimer diseases.
How do you figure out how proteins fold?
You figure out how they denature.
what is denaturation
Denaturation is an unfolding process and not a disruption of the peptide bonds
what does the The Levinthal Paradox disprove about the molten globule
U ↔ N
Unfolded state can convert to Native State
and native state can reversibly change to unfolded state
what is α-lactalbumin
milk protein
give an example of how The Levinthal Paradox disproves
U ↔ N
as in, α-lactalbumin:
Denaturing the protein with 6M Guanidine Hydrochloride produces the unfolded state
At pH 4 the protein is still denatured, but has a similar structure to that of the native protein – suggesting an intermediate state
U ↔ M ↔ N
M = Molten Globule
what happens to amino acids (molten globule) in water
Many amino acids have hydrophobic groups, and thus in water the unfolded protein is very unstable
To avoid water, the hydrophobic groups come together as a cluster
known as Hydrophobic collapse
This is myoglobin
whats hydrophobic collapse
when the hydrophobic groups come together as a cluster to avoid water
explain quaternary structure
Not all proteins have a quaternary structure
Oligomeric proteins = made up of multiple proteins held together by non-covalent interactions (lactate dehydrogenase is a good ex of this)
there is:
- Homo-oligomers – formed of identical subunits
- Hetero-oligomers – formed of non-identical subunits (ex lactate dehydrogenase)
what advantages do oligomeric proteins have
Easier to repair than tertiary structure protein as if a subunit stops working then it can be substituted out and protein will still work
