PROTEIN STRUCTURE & FUNCTION (Lec 7) (Set 1)

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Questions and Answers

Which of the following is the correct single letter code translation for the amino acid sequence 'Met-Ala-Ala-Glu-Cys-His-Gly'?

MAECG

MAAECHG

MAAEGCH

MAAECG (correct)

What is the main driving force in protein folding?

To hide hydrophobic side chains from water molecules

To form a hydrophobic core

To neutralize polar C=O and N-H groups

To attain an energetically stable structure (correct)

Which of the following is NOT an important type of secondary structure in proteins?

Alpha helix

Beta sheet

Gamma helix (correct)

Random coil

How many amino acids are usually present in an alpha helix?

5-40 Signup and view all the answers

What is the pitch (turn length) of an alpha helix?

0.15nm Signup and view all the answers

What are the main chain groups in an alpha helix that are hydrogen bonded to one another?

C=O and N-H Signup and view all the answers

What is the vertical distance between two amino acids in an alpha helix?

0.15nm Signup and view all the answers

Which of the following is true about the alpha helix?

All of the above Signup and view all the answers

Which of the following describes the beta sheet?

All of the above Signup and view all the answers

What is the term for the regions that connect anti-parallel beta strands?

Hairpin loops Signup and view all the answers

Which amino acid is often found in loop regions because its locked ring structure introduces a 'kink' into the polypeptide chain?

Proline Signup and view all the answers

What is the term for the final three-dimensional structure of a protein?

Tertiary structure Signup and view all the answers

What are proteins always synthesized using?

20 amino acids Signup and view all the answers

What are the modifications to proteins after synthesis called?

Post-translational modifications Signup and view all the answers

How do parallel beta strands connect?

By alpha helices Signup and view all the answers

The C=O group of amino acid n is hydrogen bonded to the N-H group of amino acid n+4.

True Signup and view all the answers

The α helix is formed from continuous regions of the polypeptide chain.

False Signup and view all the answers

The β sheet is formed from non-continuous regions of the polypeptide chain.

True Signup and view all the answers

Loop regions in proteins are always highly flexible.

False Signup and view all the answers

Proteins can be modified after synthesis in various ways, including the addition of sugars and lipids.

True Signup and view all the answers

Study Notes

Primary Structure

The primary structure of a protein is the sequence of amino acids from N-terminal to C-terminal.
This sequence can be written out using standard abbreviations for amino acids or a single letter code.
Example: Ile-Ala-Met-Ala-Pro-Glu-Pro-Thr-Ile-Asp-Glu can be translated into single letter code.

Secondary Structure

The secondary structure of a protein is the folding of parts of the primary sequence into specific structures.
Two important types of secondary structure are the alpha (α) helix and the beta (β) sheet.

Alpha Helix

The α helix is usually formed from stretches of 5-40 amino acids.
The main chain N-H and C=O groups are hydrogen bonded to one another along the axis of the helix.
The α helix is very stable.
There are 3.6 amino acids per turn.
Each amino acid turns the helix through 100°.
The vertical distance from one amino acid to the next is 0.15nm, so the pitch of the helix (turn length) is 0.54nm.
The C=O group of amino acid n is hydrogen bonded to the N-H group of amino acid n+4.
The amino acid side chains project out from the edge of the helix.
The sequence of amino acids in an α helix can be plotted on a helical wheel diagram.

Beta Sheet

The β sheet is formed from non-continuous regions of the polypeptide chain, called β strands.
The β strands line up and form hydrogen bonds between the C=O groups of one strand and the N-H groups of another.
If the strands all run in the same direction (N → C), the β sheet is described as PARALLEL.
If the strands run in opposite directions, the β sheet is described as ANTI-PARALLEL.
β sheets, including parallel and anti-parallel, are often called β-pleated sheets.

Loop Regions

Loop regions link secondary structures (α helices, β sheets) together.
Loops vary in length, with long loops called random coils and being highly flexible parts of proteins.
Short loop regions that connect anti-parallel β strands are called hairpin loops or β turns.
PROLINE is often found in loop regions because its locked ring structure introduces a ‘kink’ into the polypeptide chain.
GLYCINE is also often found in loops because its small side chain enables it to form turns when other amino acids could not.

Post-translational Modifications

Proteins are synthesised using the same set of 20 amino acids.
However, they can be modified after synthesis in various ways.
Alterations to some produce the “rare” amino acids – hydroxyproline, hydroxylysine.
Sugars/carbohydrates/glycans can be added to some amino acids (asparagine, threonine, serine) – this is called glycosylation – glycoproteins (N-linked, O-linked).
Lipids can also be added – lipoproteins.
These post-translational modifications can contribute to secondary structure.

Tertiary Structure

The final three-dimensional structure of a protein is produced by the association of secondary structures into compact domains.
This is called TERTIARY STRUCTURE.

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Description

Test your knowledge of protein primary structure with this quiz! Translate a sequence of amino acids from standard abbreviations into single letter code. Challenge yourself and improve your understanding of protein structures.