Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry - Foundation Module > Biomolecules - Proteins > Flashcards

Biomolecules - Proteins Flashcards

1
Q

What are “Essential Amino acids”?

A

A.A that must be obtained from the diet. They are amino acids that our body cannot synthesize at the “required amount”.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are “Nonessential Amino Acids”?

A

A.A that the body can synthesize from other sources.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the Amino acid that is specifically essential only for children?

A

Arginine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are “Conditionally Essential Amino acids”?

A

They are amino acids that the body cannot synthesize some a.a in sufficient quantities during certain stages/conditions.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Examples of when an amino acid might become “conditionally essential”.

A

e.g pregnancy, adolescent growth, or recovery from trauma

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Main three component of the structure of Amino Acids.

A

Each a.a has:

  • a carboxyl group
  • a primary amino group (proline 2ry )
  • a distinctive side chain “R group”
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Describe the state of Amino acids during physiological pH conditions.

A

At physiological pH, the carboxyl group is negatively charged (COO-) & the amino group (NH3+) is protonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are the properties of Amino Acids?

A
  1. The α-carbon of a.a is a chiral carbon
  2. Optically active carbon atom except for Glycine.
  3. They have the mirror image form: D & L isomerism Known as enantiomers
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what is a D isomer of an Amino acid?
Where do we typically find this configuration?

A

If the amino group is present on the right side of the asymmetric (α-carbon ) is known as D isomer

In some antibiotics/ bacterial cell walls.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the amino acid configuration in humans?

A

The L configuration

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Amino acids can be configured in 7 ways. what are they?

A
  1. Aliphatic Side chains
  2. Hydroxyl-containing side chains
  3. Side chains containing basic groups
  4. Aromatic side chains
  5. Sufluric side chains
  6. side chains with acidic groups
  7. Imino acids
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

how can the R groups of amino acids be classified?

A
  1. Non-polar R groups
  2. Polar R groups
  3. Negatively charged R groups
  4. Positively charged R groups.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What happens to amino acids with hydroxyl side chains during post-translational modifications?

A

They could be phosphorylated by enzymes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Explain how proline is a unique amino acid in terms of its role in protein biosynthesis.

A

Proline’s imino group allows it to form a cyclic structure with the amino acid backbone, creating a rigid kink in the protein chain that is important for stabilizing protein structures and enabling protein-protein interactions.

can affect; stability; structure and cell signalling activities.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the “Isoelectric point (pI)”?

A

the pH at which a particular molecule or surface carries no net electrical charge.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the applications of isoelectric point?

A
  1. Separation of protein
  2. Solubilizing protein
  3. Isoelectric focusing
  4. Predict R group
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What happens to a molecule’s solubility during the isoelectric point?

A

At the pI, the molecule has minimum solubility.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Describe isoelectric focusing.

A
  • Isoelectric focusing separates proteins based on their pI.
  • The technique uses a gel with a pH gradient, from acidic at one end to basic at the other.
  • An electric field is applied, causing proteins to migrate to the region of the gel that matches their pI. Once they reach their isoelectric point, they become immobilized and can be easily separated from other proteins in the mixture.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

How can isoelectric focusing be applied to amino acids?

A

To predict their behaviour at different pH levels

examining the pKa values of the various R-groups in an amino acid sequence, one can predict the overall charge of the protein at different pH values.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are the features of a peptide bond?

A
  1. Partial double bond structure
  2. Rigid
  3. Exists in trans configuration
  4. Uncharged but polar
  5. Unavailable for chemical reaction except hydrogen bonds
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What are the features of a peptide bond?

A
  1. Partial double bond structure
  2. Rigid
  3. Exists in trans configuration
  4. Uncharged but polar
  5. Unavailable for chemical reaction except for hydrogen bonds
22
Q

Steps for the determination of the amino acid composition of a polypeptide.

A
  1. Cleavage of peptide bonds
  2. Separation of amino acids
  3. Identification of amino acids
23
Q

Explain how cation-exchange chromatography is conducted to separate amino acids after cleavage from a polypeptide.

A

a mixture of amino acids is passed through a column containing a resin that carries a positive charge. The positively charged amino acids bind to the resin and can be separated based on their properties, such as size and charge.

24
Q

What is the chemical process used to determine the sequence of amino acids?

A

Edman Degradation

25
Q

How can DNA sequencing help determine protein’s primary structure?

A
  • The DNA sequence that encodes the protein of interest is determined through DNA sequencing.
  • The genetic code is used to translate the DNA sequence into the corresponding sequence of amino acids.
  • The resulting amino acid sequence represents the primary structure of the protein.
26
Q

Four organizational levels of proteins.

A

Primary, Secondary, Tertiary, and Quaternary.

27
Q

What is the Primary structure of a protein?

A

The sequence of Amino acids in a protein.

28
Q

The basis for the formation of the secondary structure?

A

arrangements are due to the partial double bond character of the peptide bond

29
Q

Examples of secondary structures?

A

α-helix, β-sheet and β-bend

30
Q

What is the secondary structure stabilised by?

A

Hydrogen bonds and Vander Waals force

31
Q

Describe the structure of an Alpha helix (α-helix).

A

Resembles a spring, in which every backbone N-H group donates an H bond to the backbone C=O group.

Has a side chain that extends out

Stabilised by the H bonding between the carbonyl oxygen and amide hydrogen.

32
Q

How can the alpha helix be disturbed?

A
  • proline may insert a kink,
  • charged a.a form ionic bond and disturb the arrangement
  • bulk side chain a.a may also interfere
33
Q

Difference between the alpha helix and the beta sheet?

A

Unlike the alpha helix β-chain are composed of two or more peptide chains (strands) or segments of peptide chain

34
Q

structure of the beta sheet?

A

β-chain are composed of two or more peptide chains (strands) or segments of peptide chain

Hydrogen bonds may be inter or intra chain bonds

They may be parallel (C–terminals on the same side or antiparallel (C-terminals on the opposite side)

35
Q

Explain the difference between parallel and antiparallel beta sheets.

A

Parallel beta sheets:

  • Adjacent strands run in the same direction
  • Hydrogen bonds are at an angle to the strands
  • Less stable than antiparallel sheets due to weaker hydrogen bonds
  • Common in globular proteins

Antiparallel beta sheets:

  • Adjacent strands run in opposite directions
  • Hydrogen bonds are perpendicular to the strands
  • More stable than parallel sheets due to stronger hydrogen bonds
  • Common in fibrous proteins, such as silk and collagen
36
Q

What are β - bends/Reverse turns?

A

β-bends are protein motifs where the polypeptide chain changes direction by approximately 180 degrees in a short segment of 3-5 amino acids.

37
Q

Importance of β - bends/Reverse turns.

A

important for their structural stability and functional properties

37
Q

the common amino acid inβ - bends/Reverse turns?

A

proline (kink), glycine (smallest a.a)

38
Q

where can we find β - bends/Reverse turns?

A

Predominant protein type in globular proteins

Predominantly found in cytosol & surface of the protein molecule

39
Q

where do we see non-repetitive secondary structures?

A

when certain polypeptides have a loop or coil and exhibit less regular structure compared to α-helices or β-sheets. These regions are sometimes referred to as “random coils”.

40
Q

What is a “super secondary structure”?

A

a super secondary structure is a specific arrangement of secondary structures that occur in many different proteins.

41
Q

Explain how the tertiary structure of the protein is stabilised.

A

sequestration of hydrophobic a.a residues in the protein core, from which water is excluded, & by the consequent enrichment of charged or hydrophilic residues on the protein’s water-exposed surface.

42
Q

What is the most common stabilising factor in the tertiary structure for secretory proteins.

A

disulfide bonds; By§ forming disulfide bonds, the protein can maintain its shape and stability, which is important for its function outside the cell.

43
Q

Why are disulfide bonds used to maintain the protein structure of secretory proteins?

A

Because the extracellular environment is often more oxidizing than the cytoplasm, and the disulfide bonds are more stable under oxidizing conditions.

44
Q

What are the four types of bonding interactions between side chains in the tertiary structure?

A
  1. Hydrogen Bonding
  2. Salt Bridges
  3. Disulfide bonds
  4. Non-polar hydrophobic interactions
45
Q

What are Disulphide bonds?

A

Disulfide bonds are covalent bonds that form between two cysteine amino acids in a protein. Cysteine contains a sulfhydryl (-SH) group on its side chain, and when two cysteines come close together, these sulfhydryl groups can undergo oxidation to form a disulfide bond (-S-S-).

46
Q

Examples of protein structures that are held together by disulfide bonds.

A
  1. Insulin: two polypeptide chains that are linked by two disulfide bonds.
  2. Immunoglobulins (antibodies): four polypeptide chains (two heavy chains and two light chains) that are held together by disulfide bonds.
  3. Collagen: to stabilise strcuture
  4. Albumin: to stabilise structure.
47
Q

What are Salt bridges?

A

Salt bridges are a type of electrostatic interaction that can occur between amino acid side chains in proteins. They result from the neutralization of an acid and an amine on adjacent side chains, leading to the formation of a salt bridge.

48
Q

What are Non-polar Hydrophobic interactions?

A

Non-polar groups mutually repel water & other polar groups & results in a net attraction of the non-polar groups for each other.

49
Q

Examples of Non-Polar Hydrophobic interactions?

A

Ala, Val, Leu, and Ile interact in this way.

Biochemistry - Foundation Module (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions