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YEAR 2 HUMAN BIOCHEMISTRY > Protein and amino acid metabolism > Flashcards

Protein and amino acid metabolism Flashcards

1
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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2
Q

Amino Acid to Polypeptide to Protein: The peptide bond

Amino acids are joined together during what process?

A

Translation

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3
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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4
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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5
Q

Amino Acid to Polypeptide to Protein: The peptide bond

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

A
  1. OH- lost from Carboxyl
  2. H+ lost from the Amino
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6
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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7
Q

Amino Acid to Polypeptide to Protein: Secondary and Tertiary Structure

What types of bonds are formed in the secondary structure?

A
  1. Hydrogen bonds between the N-H
  2. Hydrogen bonds between the C=O
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8
Q

Amino Acid to Polypeptide to Protein: Secondary and Tertiary Structure

What 2 things is the secondary structure formed of?

A
  1. α-helix
  2. β-sheet
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9
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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10
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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11
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:

  1. Disulphide bridges
  2. Ionic bonds
  3. Hydrogen bonds
  4. Van der Waals interactions
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12
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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13
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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14
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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15
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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16
Q

Amino Acid to Polypeptide to Protein: Levinthal’s Paradox

Protein intermediates are described as what?

A

Short lived

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17
Q

Amino Acid to Polypeptide to Protein: Levinthal’s Paradox

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

A
  1. Protein intermediates are short lived
  2. Energy
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18
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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19
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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20
Q

Amino Acid to Polypeptide to Protein: The Molten Globule

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

A
  1. KNOWLEDGE:
    The knowledge of how the linear sequence of amino acids is translated into spatial information is the “missing link”
  2. INDUSTRIAL/RESEARCH:
    There is a tremendous interest in the over-expression of recombinant proteins for industrial, biotechnological, and research applications
  3. 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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21
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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22
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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23
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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24
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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25
Q

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?

A

U ↔ M ↔ N

Molten Globule

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26
Q

Amino Acid to Polypeptide to Protein: The Molten Globule

Many amino acids have what type of groups?

A

Hydrophobic groups

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27
Q

Amino Acid to Polypeptide to Protein: The Molten Globule

Many amino acids have hydrophobic groups, What does this mean for unfolded proteins in water?

A
  • In water the unfolded protein is very unstable
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28
Q

Amino Acid to Polypeptide to Protein: The Molten Globule

To avoid water, the hydrophobic groups come together. What is the term for this?

A

Hydrophobic collapse

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29
Q

Amino Acid to Polypeptide to Protein: The Quaternary Structure

Not all proteins have what type of structure?

A

Quaternary structure

30
Q

Amino Acid to Polypeptide to Protein: The Quaternary Structure

What are oligomeric proteins made up of?

A

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

31
Q

Amino Acid to Polypeptide to Protein: The Quaternary Structure

What are 2 types of oligomeric proteins and how are each of them formed of?

A
  1. Homo-oligomers: formed of identical subunits
  2. Hetero-oligomers: formed of non-identical subunits
32
Q

Amino Acid to Polypeptide to Protein: The Quaternary Structure

What is an advantage of oligomeric proteins?

A

Easier to repair

33
Q

Alanine —-> Pyruvate

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

A

By transamination

To form pyruvate catalysed by alanine aminotransferase

34
Q

Asparagine—>Oxaloacetate

What is asparagine hydrolysed by? And what does this liberate?

A
  • Asparaginase
  • liberates ammonia and aspartate
35
Q

Asparagine—>Oxaloacetate

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

A
  • By transamination
  • Via the enzyme aspartate aminotransferase
  • To form oxaloacetate
36
Q

Aminotransferases:

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

A
  • Catalyse the reversible transamination between an amino acid and a keto acid
  • Giving rise to one of three non-essential amino acids
37
Q

Aminotransferases:

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

A
  1. ⍺-ketoglutarate –> Glutamate
  2. Pyruvate –> Alanine
  3. Oxaloacetate –> Aspartate
38
Q

Pyridoxal Phosphate (PLP)

Describe what a prosthetic group 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

39
Q

Pyridoxal Phosphate (PLP)

What is the most well known prosthetic group?

A

Fe=Haemoglobin

40
Q

Pyridoxal Phosphate (PLP):

Pyridoxal phosphate is the active form of what?

A

Pyridoxine (Vitamin B6)

41
Q

Pyridoxal Phosphate (PLP):

What do PLP enzymes form with the amino acid substrate?

A

Covalent Schiff-bases

42
Q

Pyridoxal Phosphate (PLP):

What is a schiff base?

A

A compound with the general structure of R1 R2 C=NR3

R1 and R2 can be a H

R3 cannot

43
Q

Pyridoxal Phosphate metabolism:

What will PLP transiently become during transamination?

A

Pyrodoxamine phosphate (PMT)

44
Q

Pyridoxal Phosphate metabolism:

Enzyme PLP accepts what and loses what in this process?

A

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

45
Q

Pyridoxal Phosphate metabolism:

The external aldimine loses a proton to become what?

A

A Quinoid intermediate

46
Q

Pyridoxal Phosphate metabolism:

Quinoid intermediate becomes re-protonated. What does this produce?

A

Producing a ketimine

46
Q

Pyridoxal Phosphate metabolism:

Ketimine is then hydrolysed, what does this produce?

A

Produces PMP and the relevant ⍺-keto acid

47
Q

Pyridoxal Phosphate metabolism:

This process also happens in reverse, why is this?

A

To reproduce PLP, using a different ⍺-keto acid

48
Q

Glutamine —-> alpha-Ketoglutarate

What is glutamine converted to? and what enzyme is used for this to happen?

A
  • Glutamine is converted to glutamate and ammonia
  • By the enzyme glutaminase
49
Q

Glutamine —-> alpha-Ketoglutarate

What is glutamate converted to? and what is done to allow for this conversion?

A
  • Glutamate is converted to alpha-ketoglutarate
  • By oxidative deamination by glutamate dehydrogenase
50
Q

Serine and Threonine:

Are these amino acids essential or non essential?

A

Threonine= essential
Serine= Non essential

51
Q

Serine and Threonine:

What can happen to both of the amino groups of these amino acids?

A

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

52
Q

Serine and Threonine:

What is the reaction for serine dehydratase?

A

Serine —> Pyruvate + NH4+

53
Q

Serine and Threonine:

What is the reaction for threonine dehydratase?

A

Threonine —> alpha-ketoglutarate + NH4+

54
Q

Serine and Threonine:

Dehydratase enzymes: What is lost in these reactions?

A

H2O is lost in these reactions

55
Q

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?

A
  • Forming the unstable intermediate aminocrylate.
  • H2O is then added back, producing the products
  • PLP is the cofactor
56
Q

The Urea Cycle:

What are the mitochondrial steps of the Urea cycle?

A
  1. Carbamoyl phosphate synthase I
  2. Ornithine transcarbamylase
57
Q

The Urea Cycle:

What are the cytosolic steps of the Urea cycle?

A
  1. Arginosuccinate synthase
  2. Arginosuccinate lyase
  3. Arginase
58
Q

The Urea Cycle: The Mitochondrial Steps

What happens in step 1 of the urea cycle?

  1. Carbamoyl phosphate synthase I
A
  • CO2 and the first Ammonium ion group lost in the urea cycle react with a phospho- group donated by ATP to produce Carbamoyl phosphate
59
Q

The Urea Cycle: The Mitochondrial Steps

What happens in step 2 of the urea cycle?

  1. Ornithine transcarbamylase
A
  • Carbamoyl group is transferred to Ornithine
  • Releasing the organic phosphate
  • Producing Citrulline
60
Q

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?

A
  • 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
61
Q

The Urea Cycle: The Cytosolic Steps

What occurs in step 3 of the urea cycle?

  1. Arginosuccinate synthase
  2. Arginosuccinate lyase
  3. Arginase
A
  • Aspartate donates the second amino group lost in the urea cycle
  • Then undergoes a condensation reaction with Citrulline.
  • This produces Argininosuccinate
    .
62
Q

The Urea Cycle: The Cytosolic Steps

  1. Arginosuccinate lyase:
    What happens in step 4 of the urea cycle?

Argininosuccinase is a 2 step reaction, What are these steps?

A
  • 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
63
Q

The Urea Cycle: The Cytosolic Steps

  1. Arginase: What happens in step 5 of the urea cycle?
A
  • Arginine is hydrolysed to produce Ornithine and Urea
    Arginase
64
Q

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

A
  • The Urea Cycle and the Krebs Cycle are interlinked
  • Through Argininosuccinate
65
Q

The C3 family:

What 3 things are converted to pyruvate?

A
  1. Serine
  2. Alanine
  3. Cysteine
66
Q

The C3 family:

What are 2 different pathways to generate Pyruvate?

A

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

67
Q

The C5 family:

What 4 things enter the Citric Acid cycle as ⍺-ketoglutarate through Glutamate?

A
  1. Proline
  2. Histidine
  3. Glutamine
  4. Arginine
68
Q

Leucine, Isoleucine, and Valine:

The first step is a transaminase reaction. What does this produce?

A

The appropriate ⍺-keto acid

69
Q

Leucine, Isoleucine, and Valine:

Branched-chain ⍺-keto acid dehydrogenase complex is homologous to what?

A
  • Homologous to the pyruvate dehydrogenase complex
70
Q
A

YEAR 2 HUMAN BIOCHEMISTRY (12 decks)

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