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
how many amino acids are there and what 2 groups can they eb divided into
20
divided into essential and non essential
explain essential and non essential amino acids
Essential
Cannot be produced by the body
Non-essential
Can be produced by the body
what groups can essential amino acids be subdivided into
glucogenic
ketogenic
glucogenic and ketogenic
what can non essential amino acids be sub divided into
glucogenic
glucogenic and ketogenic
how is alanine converted to pyruvate
Alanine loses its amino group by transamination to form pyruvate catalysed by alanine aminotransferase
how is asparagine converted to oxaloacetate
Asparagine is hydrolysed by asparaginase, liberating ammonia and aspartate.
Aspartate loses its amino group by transamination via the enzyme aspartate aminotransferase to form oxaloacetate.
how is phenylalanine converted to tyrosine
by phenylalanine hydroxylase
how is tyrosine converted to fumarate
A multi-step reaction:
Transamination:
- Tyrosine –> Hydroxy-phenylpyruvate
- ⍺-ketoglutarate –> Glutamate
Dioxygenation:
- Hydroxy-phenylpyruvate –> Homogentisate
- O2 + Ascorbate–> CO2 + H2O
Dioxygenation:
- Homogentisate –> 4-Maleylacoacetate
Isomerisation:
- 4-Maleylacoacetate–> 4-Furmarlacoacetate
Hydrolysis:
- 4-Furmarlacoacetate—-> Fumarate and Acetoacetate
what do Aminotransferases do
Catalyse the reversible transamination (Swap of the amino group and carbonyl group)
between an amino acid and a keto acid, giving rise to one of three non-essential amino acids
⍺-ketoglutarate –> Glutamate
Pyruvate –>Alanine
Oxaloacetate—> Aspartate
what is Pyridoxal Phosphate (PLP)
Is a Prosthetic group = Compounds bound to enzymes (covalently or not) and their change from one form to another and back takes place in a single catalytic cycle
Fe is probably the most well-known prosthetic group – Haemoglobin
Pyridoxal phosphate is the active form of what
Pyridoxine (Vitamin B6)
PLP enzymes (such as aminotransferases) form what intermediates with the amino acid substrate
form covalent Schiff-base intermediates
what is schiff base
A compound with the general structure of R1R2C=NR3
R1 and R2 can be a H, but R3 cannot
what does PLP become during the metabolism transition
PLP will transiently become PMT (Pyrodoxamine phosphate)
what happens to Pyridoxal Phosphate during metabolism
Enzyme bound to the PLP accepts the amino acid substrate and loses the enzyme
- Internal (enzyme-bound) to external (substrate-bound) aldimine
The external aldimine loses a proton to become a Quinoid intermediate
Quinoid intermediate becomes re-protonated, producing a ketimine
Ketimine is hydrolysed, producing PMP and the relevant ⍺-keto acid
This process happens in reverse to reproduce PLP, using a different ⍺-keto acid
how is PLP reproduced from metabolism
the metabolism process happens in reverse to reproduce PLP using a different alpha-keto acid
Glutamine is converted to glutamate and ammonia by what enzyme
in the conversion of Glutamine —> alpha -Ketoglutarate
enzyme glutaminase
explain the conversion of Glutamine —-> alpha-Ketoglutarate
Glutamine is converted to glutamate and ammonia by the enzyme glutaminase
Glutamate is converted to alpha-ketoglutarate by oxidative deamination by glutamate dehydrogenase
what essential and non essential amino acids can have their amino group converted to ammonium (NH4+)
The essential amino acid threonine and the non-essential amino acid serine can have their amino group directly converted to ammonium (NH4+)
how can The essential amino acid threonine and the non-essential amino acid serine have their amino group directly converted to ammonium (NH4+)
Serine–> Pyruvate + NH4+
by, Serine dehydratase
Threonine—> ⍺-ketoglutarate + NH4+
by, Threonine dehydratase
explain Dehydratase enzymes
H2O is lost in these reactions
Serine, for example: loses an H+ and an –OH group from its ⍺- and β- carbons respectively, forming the unstable intermediate aminocrylate. H2O is then added back,
PLP is the cofactor
name the enzymes in the mitochondria of the urea cycle
① Carbamoyl phosphate synthase I
② Ornithine transcarbamylase
name the enzymes in the cytosol of the urea cycle
③ Arginosuccinate synthase
④ Arginosuccinate lyase
⑤ Arginase
explain the mitochondrial steps 1 and 2 of the urea cycle
CO2 and the first Ammonium ion group lost in the urea cycle react with a phospho- group donated by ATP to produce Carbamoyl phosphate
- Carbamoyl phosphate synthase I
Carbamoyl group is transferred to Ornithine, releasing the organic phosphate and producing Citrulline
- Ornithine transcarbamylase
Aspartate donates the second amino group lost in the urea cycle and undergoes a condensation reaction with Citrulline. This produces Argininosuccinate
- ATP to AMP by hydrolysis, and the water produced is used in the condensation reaction.
explain the mitochondrial steps 3, 4 and 5 of the urea cycle
Aspartate donates the second amino group lost in the urea cycle and undergoes a condensation reaction with Citrulline. This produces Argininosuccinate
- Argininosuccinate synthetase
- ATP to AMP by hydrolysis, and the water produced is used in the condensation reaction.
Argininosuccinate is cleaved into Arginine and Fumarate
- Argininosuccinase
- 2 step reaction:
1. Transfer of the amino group to form arginine
2. Preservation of the Carbon skeleton in the form of fumarate
Arginine is hydrolysed to produced Ornithine and Urea
- Arginase
The Urea Cycle and the Krebs Cycle are interlinked through what
through Argininosuccinate
what in the C3 family is converted to pyruvate
Serine
Alanine
Cysteine
what are the different pathways to generate pyruvate
Cysteine can be oxidised to produce Cysteinesulfinate, which loses an amino group in an amino transferase reaction to produce β-sulfinylpyruvate. Hydrolysis then produces pyruvate
Cysteine can lose an amino group in an amino transferase reaction, producing Mercapto-pyruvate. Mercapto-pyruvate sulfurtransferase produces pyruvate
what do c5 enter the citric acid cycle as
cycle as ⍺-ketoglutarate through Glutamate
what c5 Enter the Citric Acid cycle as ⍺-ketoglutarate through Glutamate
Proline
Histidine
Glutamine
Arginine
how do the non polar amino acids Leucine, Isoleucine, and Valine form succinyl CoA
The first step is a transaminase reaction, producing the appropriate ⍺-keto acid.
Branched-chain ⍺-keto acid dehydrogenase complex
- Homologous to the pyruvate dehydrogenase complex. The E3 component is identical -regenerates oxidised lipoamide
Followed by a series of oxidation/reduction reactions similar to TCA cycle
Isoleucine and Valine:
Propionyl-CoA –> Succinyl-CoA
Leucine:
Acetoacetate and Acetyl-CoA for ketone body production
