- the 3D arrangement of a protein chain over a short stretch of adjacent amino acid residues - includes a-helices and b-sheets

- the 3D structure of a complete protein chain

- rotation angle around the peptide bond

Lecture 5 - Protein Strucute Flashcards by Becky Ross

When amino acids are bonded together in a peptide of protein, they are referred to as…

… amino acid residues

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How are the amino acid residues in a polypeptide chain numbered?

From the amino terminus to the carboxy terminus

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How many chains do proteins have

Anywhere from one to several chains
- proteins with one chain are the most common variety

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Because proteins are mostly globular, the main chain must….

Be able to form a more compact shape and be able to double back

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Globular proteins will be mainly comprised of..

Primarily a-helix, B-helix structure and turns

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How ,any levels of protien structure

4
primary, secondary, tertiary and quanternary

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All proteins have….
Some proteins have…..

All proteins have primary, secondary and tertiary structure
Some proteins have quanternary structure

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Primary structure

The linear sequence of amino acids that make up the polypeptide

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Secondary structure

the 3D arrangement of a protein chain over a short stretch of adjacent amino acid residues
includes a-helices and b-sheets

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Tertiary structure

the 3D structure of a complete protein chain

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Quanternary structure

interchain packing and structure for a protien that contains multiple polypeptide chains (e.g haemoglobin)

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The protein main chain and side chains atoms have bond which can…. And are somewhat….

The protein main chain and side chains atoms have binds which can rotate and are somewhat flexible

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The main chain atoms in a protein are

N
Ca
C’

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Bond angle between N and Ca is called

phi

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Bond angle between Ca and C’ are called

Psi

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Bong angles take on values ranging from

0 to +/- 180*

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The chain angle between ‘ and N is called

w (omega)

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W (omega) bond have the angle..

Very close to either 180 or 0

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Main chain bond angles

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Phi angle

Rotation around the N-Ca bond

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Psi angle

Rotation angle around the Ca-C’

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Omega

rotation angle around the peptide bond

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Main chain angles in the polypeptide shown

180

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Phi-phi restrictions

Phi-Phi angles have restrictions in their values because of steric hinderance

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What collision results form phi rotation

O-O collision

Phi rotation can lead to

O-O collision

Psi rotation can lead to collisions of

NH-NH

Psi rotation can lead to

NH-NH collisions

O-O collisions result from

Phi rotation

NH-NH collisions result from

Psi rotation

Steric hinderance between the hydrogen on the amide nitrogen and the carbonyl oxygen

What is w - omega

- third main chain angle - angle of rotation around the peptide bond

Most peptide bonds are cis/trans

Trans

Angle of omega bond for a trans peptide bond

- w is about 180 - Ca atoms are found on opposite sides of the peptide bond

Steric crowding is increased for cis/trans peptide bonds

Cis

Bond angle of cis peptide omega bond angle

- in a cis peptide bond, the Ca atoms are found on the same side of the peptide bond, w is about 0

Once formed, the peptide bond angle usually does/does not rotate very much

Does not rotate very much

The combination of all the ____ and ____ around all of the ___ in a ___ leads to its overall ____ ____, which in turn, leads to the arrangement of all the side chains in the protien, which in turn leads to its function

The combination of all the rotations and twists around all the bonds in a protien leads to its overall 3D structure, which in turn, leads to the arrangement of all the side chains in the protien, which in turn leads to its function

Two canonical structures that are protien secondary structures

B-strand/B-sheet a-helix

Strucutre of the a-helix

- the main chain spirals around the central axis like a spiral staircase - no covalent interaction (hydrogen bond) between the carbonyl of residue “n” and the N-H of residue “n+4” - hydrogen bonds help stabilise the a-helix structure - slightly positive charge on the hydrogen - slightly negative charge on the oxygen

Key properties of the a-helix

-3.6 residues/turn; 5.5A rise/turn; d=1.5A residue - spiral is right handed - side chains point out from the helix axis; help stabilise the a-helix - stabilising hydrogen bond, 3-7kcal/mol or 12-28kj/mol - some residues are ‘helic breakers’ e.g glycine, proline - helic dipole exists, positive at N-terminus

Which way do the side chains point in an a-helix

Outwards

Energy in a-helix hydrogen bonds

- 3-7 kcal/mol - 12-28 kj/mol

a-helix rotations

Which residues are considered “helix breakers”

- glycine - proline

Do a-helixes have dipoles

Yes Positive at N-terminus

Helix dipole depiction

Helix wheel

-3.6 residues/turn -one full turn is 360* - in an a-helix each amino acid side chain is separated by 100*

B-structure

• Stretches of residues with a more extended structure than the a-helix. • Each section of B structure is called a B-strand • Hydrogen-bonding occurs between adjacent chains (strands) • Adjacent chains can often form a B- sheet, ≥ two B-strands • 2 to 10 strands per sheet • Average strand length contains ~ 6 amino acid residues • Each strand may have up to 15 residues • Two types of hydrogen bonding interaction in a B-sheet:

each seaction of B strucutre os called a

B strand

Hydrogen bonding occurs between

Adjacent chains (strands)

Adjacent chains can often form

B-sheet

How many stands per B-sheet

2-10

How many amino acid residues in the average B-strand

6 amino acid residues

How many residues can a B-stand have

Two types of hydrogen bonding interaction in a B-sheet

Antiparallel: strands run in the opposite direction - hydrogen bonding pattern is optimal (vertical) Parallel: strands run in the same direction - hydrogen bonds are zig zagged

B-pleated sheet

- extended - pleated

B-sheet vs B-strand

- sheets not planar, pleated with R-handed twist

B- strucutre location of side chains

- side chains point above and below the sheet

Any NP-P-NP-P* stretch of residues commonly will form a

B-strand

B-structure in silk

- model sequence is (-Gly-Ser-Gly-Ala-Gly-Ala-) n - all from one sheet is interdigitate with ala from other sheet - silks from different species have different interdigitating groups and have differing physical properties

What is needed to form globular proteins

Turns

Structure of turns

Often short and hair pin like

How many residues are involved in turns

3 or 4

Almost __% of residues are involved in turns

300

High amounts of ____ and ____ in turns

Gly and pro

Turns often have an H-bon across _____

Width

Which types of turns are very common

Type 1 and type 2

How many types of turns are there

Features of glycine good for turns but not helies

- small side chains make glycine very flexible. It has a lot of conformational freedom.

What makes proline good for turns and bad for helicies

- proline is too rigid for helices but has a built-in turn because of the bonding between the R-group and the amino group

Why are protein structures challegenign to display clearly

- there are lots of atoms - detailed internal cavities - complicated shapes - all the elements of protein structure - a-helix, b-stands, turns, loops

Protein display structure

- helices shown as spirals (or cylinders) - strands shown as arrows, pointing form N to C - turns and random coil, shown as loops or rope like stretches

Protien structure shorthand

Protein short hand advantages

- easily visualise the main chain path of protein - identify elements of secondary strucutre - allows an appreciation of proteins as 3D objects - allows comparison to other proteins

Lecture 5 - Protein Strucute Flashcards

(75 cards)