Protein and amino acid metabolism Flashcards by Liviana Pezzaioli

Q

Amino Acid to Polypeptide to Protein: The peptide bond

What is the main enzymatic function of the ribosome and how is it described?

A

Peptidyl transferase

60S (large) subunit of the eukaryotic ribosome

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Q

Amino Acid to Polypeptide to Protein: The peptide bond

Amino acids are joined together during what process?

A

Translation

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Q

Amino Acid to Polypeptide to Protein: The peptide bond

tRNAs bring amino acids, What does this react with?

A

Reacts with the other tRNA held within the ribosome

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Q

Amino Acid to Polypeptide to Protein: The peptide bond

What does the carboxyl group react with?

A

The amino group on the new amino acid

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Q

Amino Acid to Polypeptide to Protein: The peptide bond

What 2 things are lost from where in the condensation reaction that occurs?

A

OH- lost from Carboxyl
H+ lost from the Amino

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Q

Amino Acid to Polypeptide to Protein: The peptide bond

What is the largest and the smallest type of protein? And what size are they both?

A

Largest protein: Titin in humans (34,350 aa)

Smallest protein: TAL in Fruit Flies (11aa)

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Q

Amino Acid to Polypeptide to Protein: Secondary and Tertiary Structure

What types of bonds are formed in the secondary structure?

A

Hydrogen bonds between the N-H
Hydrogen bonds between the C=O

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Q

Amino Acid to Polypeptide to Protein: Secondary and Tertiary Structure

What 2 things is the secondary structure formed of?

A

α-helix
β-sheet

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Q

Amino Acid to Polypeptide to Protein: Secondary and Tertiary Structure

Describe the key features of 1. α-helix and 2. β-sheet within the secondary structure

A

α-helix:
- Right-handed coiled strand
- Hydrogen bonds form intra-strand
- This bonds 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

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Q

Amino Acid to Polypeptide to Protein: Secondary and Tertiary Structure

What are the main key features of the Tertiary Structure?

A

The most stable, lowest energy conformation

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Q

Amino Acid to Polypeptide to Protein: Secondary and Tertiary Structure

What is the tertiary structure held in place by? And provide what all 4 are.

A

Held in place by interactions between the R-groups:

Disulphide bridges
Ionic bonds
Hydrogen bonds
Van der Waals interactions

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Q

Amino Acid to Polypeptide to Protein: Levinthal’s Paradox

Explain what Levinthal’s Paradox is

A

How does the polypeptide find the most energetically favourable conformation for its tertiary structure?

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Q

Amino Acid to Polypeptide to Protein: Levinthal’s Paradox

How many possible folding positions does each amino acid have?

A

3 Possible folding positions

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Q

Amino Acid to Polypeptide to Protein: Levinthal’s Paradox

You cannot measure protein folding on what basis?

A

You cannot measure protein folding by an amino acid to amino acid basis.

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Q

Amino Acid to Polypeptide to Protein: Levinthal’s Paradox

Partially correct intermediates are retained: each correct conformation of an amino acid is maintained, reduces what?

A

Reduces the number of possible positions over time

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Q

Amino Acid to Polypeptide to Protein: Levinthal’s Paradox

Protein intermediates are described as what?

A

Short lived

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Q

Amino Acid to Polypeptide to Protein: Levinthal’s Paradox

What 2 things make protein folding more complex than it may seem?

A

Protein intermediates are short lived
Energy

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Q

Amino Acid to Polypeptide to Protein: Levinthal’s Paradox

Energy:
Intermediated can only be scored by what?

A

The amount of free energy they have, and connect be observed on a residue-by-residue basis

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Q

Amino Acid to Polypeptide to Protein: Levinthal’s Paradox

Energy:
What conformation is used to describe intermediates having a favourable energy but is not on the path to final protein confirmation?

A

Kinetic traps

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Q

Amino Acid to Polypeptide to Protein: The Molten Globule

Why is knowing the biochemistry behind protein folding important? (Give 3 points)

A

KNOWLEDGE:
The knowledge of how the linear sequence of amino acids is translated into spatial information is the “missing link”
INDUSTRIAL/RESEARCH:
There is a tremendous interest in the over-expression of recombinant proteins for industrial, biotechnological, and research applications
DISEASES:
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

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Q

Amino Acid to Polypeptide to Protein: The Molten Globule

How do you figure out how proteins fold?

A

You figure out how they denature, this is the unfolding process.

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Q

Amino Acid to Polypeptide to Protein: The Molten Globule

What does the Levinthal Paradox disprove?

A

The Levinthal Paradox disproves that U ↔ N

U= Unfolded state
N= Native State

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Q

Amino Acid to Polypeptide to Protein: The Molten Globule

α-lactalbumin is what type of protein?

A

α-lactalbumin = Milk protein

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Q

Amino Acid to Polypeptide to Protein: The Molten Globule

To produce the unfolded state of α-lactalbumin, What is it denatured with?

A

6M Guanidine Hydrochloride

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Amino Acid to Polypeptide to Protein: The Molten Globule At pH 4 the protein is still denatured, but has a similar structure to that of the native protein. This suggests an intermediate state, What is this state?

U ↔ M ↔ N Molten Globule

Amino Acid to Polypeptide to Protein: The Molten Globule Many amino acids have what type of groups?

Hydrophobic groups

Amino Acid to Polypeptide to Protein: The Molten Globule Many amino acids have hydrophobic groups, What does this mean for unfolded proteins in water?

- In water the unfolded protein is very unstable

Amino Acid to Polypeptide to Protein: The Molten Globule To avoid water, the hydrophobic groups come together. What is the term for this?

Hydrophobic collapse

Amino Acid to Polypeptide to Protein: The Quaternary Structure Not all proteins have what type of structure?

Quaternary structure

Amino Acid to Polypeptide to Protein: The Quaternary Structure What are oligomeric proteins made up of?

Made up of multiple proteins held together by non-covalent interactions

Amino Acid to Polypeptide to Protein: The Quaternary Structure What are 2 types of oligomeric proteins and how are each of them formed of?

1. Homo-oligomers: formed of identical subunits 2. Hetero-oligomers: formed of non-identical subunits

Amino Acid to Polypeptide to Protein: The Quaternary Structure What is an advantage of oligomeric proteins?

Easier to repair

Alanine ----> Pyruvate How does alanine lose its amino group? And what does this form? The formation of this is catalysed by what enzyme?

By transamination To form pyruvate catalysed by alanine aminotransferase

Asparagine--->Oxaloacetate What is asparagine hydrolysed by? And what does this liberate?

- Asparaginase - liberates ammonia and aspartate

Asparagine--->Oxaloacetate How does aspartate lose its amino group? And this is via what enzyme which then forms?

- By transamination - Via the enzyme aspartate aminotransferase - To form oxaloacetate

Aminotransferases: What do these catalyse? And what does this give rise to?

- Catalyse the reversible transamination between an amino acid and a keto acid - Giving rise to one of three non-essential amino acids

Aminotransferases: What are the 3 non essential amino acids that may give rise during this process?

1. ⍺-ketoglutarate --> Glutamate 2. Pyruvate --> Alanine 3. Oxaloacetate --> Aspartate

Pyridoxal Phosphate (PLP) Describe what a prosthetic group is

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

Pyridoxal Phosphate (PLP) What is the most well known prosthetic group?

Fe=Haemoglobin

Pyridoxal Phosphate (PLP): Pyridoxal phosphate is the active form of what?

Pyridoxine (Vitamin B6)

Pyridoxal Phosphate (PLP): What do PLP enzymes form with the amino acid substrate?

Covalent Schiff-bases

Pyridoxal Phosphate (PLP): What is a schiff base?

A compound with the general structure of R1 R2 C=NR3 R1 and R2 can be a H R3 cannot

Pyridoxal Phosphate metabolism: What will PLP transiently become during transamination?

Pyrodoxamine phosphate (PMT)

Pyridoxal Phosphate metabolism: Enzyme PLP accepts what and loses what in this process?

Enzyme-PLP: - Accepts the amino acid substrate - Loses the enzyme

Pyridoxal Phosphate metabolism: The external aldimine loses a proton to become what?

A Quinoid intermediate

Pyridoxal Phosphate metabolism: Quinoid intermediate becomes re-protonated. What does this produce?

Producing a ketimine

Pyridoxal Phosphate metabolism: Ketimine is then hydrolysed, what does this produce?

Produces PMP and the relevant ⍺-keto acid

Pyridoxal Phosphate metabolism: This process also happens in reverse, why is this?

To reproduce PLP, using a different ⍺-keto acid

Glutamine ----> alpha-Ketoglutarate What is glutamine converted to? and what enzyme is used for this to happen?

- Glutamine is converted to glutamate and ammonia - By the enzyme glutaminase

Glutamine ----> alpha-Ketoglutarate What is glutamate converted to? and what is done to allow for this conversion?

- Glutamate is converted to alpha-ketoglutarate - By oxidative deamination by glutamate dehydrogenase

Serine and Threonine: Are these amino acids essential or non essential?

Threonine= essential Serine= Non essential

Serine and Threonine: What can happen to both of the amino groups of these amino acids?

Can have their amino group directly converted to ammonium (NH4+)

Serine and Threonine: What is the reaction for serine dehydratase?

Serine ---> Pyruvate + NH4+

Serine and Threonine: What is the reaction for threonine dehydratase?

Threonine ---> alpha-ketoglutarate + NH4+

Serine and Threonine: Dehydratase enzymes: What is lost in these reactions?

H2O is lost in these reactions

Serine and Threonine: Serine, for example, loses an H+ and an –OH group from its ⍺- and β- carbons respectively. What does this form? H20 is then added back, what does this produce? What is the cofactor of this reaction?

- Forming the unstable intermediate aminocrylate. - H2O is then added back, producing the products - PLP is the cofactor

The Urea Cycle: What are the mitochondrial steps of the Urea cycle?

1. Carbamoyl phosphate synthase I 2. Ornithine transcarbamylase

The Urea Cycle: What are the cytosolic steps of the Urea cycle?

3. Arginosuccinate synthase 4. Arginosuccinate lyase 5. Arginase

The Urea Cycle: The Mitochondrial Steps What happens in step 1 of the urea cycle? 1. Carbamoyl phosphate synthase I

- CO2 and the first Ammonium ion group lost in the urea cycle react with a phospho- group donated by ATP to produce Carbamoyl phosphate

The Urea Cycle: The Mitochondrial Steps What happens in step 2 of the urea cycle? 2. Ornithine transcarbamylase

- Carbamoyl group is transferred to Ornithine - Releasing the organic phosphate - Producing Citrulline

The Urea Cycle: The Mitochondrial Steps In the mitochondrial steps of the urea cycle, Aspartate goes through a condensation reaction with what? How does this occur and what does it produce?

- Aspartate goes through a condensation reaction with citrulline -Condensation reaction occurs as aspartate donates the second amino group lost in the urea cycle - This produces Argininosuccinate

The Urea Cycle: The Cytosolic Steps What occurs in step 3 of the urea cycle? 3. Arginosuccinate synthase 4. Arginosuccinate lyase 5. Arginase

- Aspartate donates the second amino group lost in the urea cycle - Then undergoes a condensation reaction with Citrulline. - This produces Argininosuccinate .

The Urea Cycle: The Cytosolic Steps 4. Arginosuccinate lyase: What happens in step 4 of the urea cycle? Argininosuccinase is a 2 step reaction, What are these steps?

- Argininosuccinate is cleaved into Arginine and Fumarate 1. Transfer of the amino group to form arginine 2. Preservation of the Carbon skeleton in the form of fumarate

The Urea Cycle: The Cytosolic Steps 5. Arginase: What happens in step 5 of the urea cycle?

- Arginine is hydrolysed to produce Ornithine and Urea Arginase

The Urea Cycle is interlinked with what other cycle through what?

- The Urea Cycle and the Krebs Cycle are interlinked - Through Argininosuccinate

The C3 family: What 3 things are converted to pyruvate?

1. Serine 2. Alanine 3. Cysteine

The C3 family: What are 2 different pathways to generate Pyruvate?

ONE: - Cysteine can be oxidised to produce Cysteinesulfinate - Which loses an amino group in an amino transferase reaction - This produces β-sulfinylpyruvate. - Hydrolysis then produces pyruvate TWO: - Cysteine can lose an amino group in an amino transferase reaction - Producing Mercapto-pyruvate. - Mercapto-pyruvate sulfurtransferase produces pyruvate

The C5 family: What 4 things enter the Citric Acid cycle as ⍺-ketoglutarate through Glutamate?

1. Proline 2. Histidine 3. Glutamine 4. Arginine

Leucine, Isoleucine, and Valine: The first step is a transaminase reaction. What does this produce?

The appropriate ⍺-keto acid

Leucine, Isoleucine, and Valine: Branched-chain ⍺-keto acid dehydrogenase complex is homologous to what?

- Homologous to the pyruvate dehydrogenase complex