CH 3: C. Peptide Bonds, D. Structure, Folding

Peptide bonds

a type of bond that connects amino acids

so that’s why its polymer is called polypeptide (since its multiple aminoacids peptide bonded)

When does amino acids ionize

when amino acid is put in water it becomes ionsized in order to dissolve

the ionzing makes the amino acids more reactive

What is the ionized form of amino acid?

when water molecule interacts with Amino acid…

Amino group gets 1 extra H (becomes NH3+ a

Carboxyl group looses H becoming COO-

why do Peptide bonds form

when Carboxyl and amino groups become ionized they become attracted to each other.

causing an ionized amino acids’s carboxyl group to bond to another amino acids amino group.

this creates water which is relased and after the C of the carboxyl group and and N of the amino group form a bond which acts like a double bond

what is the structure of a Polypeptide chain

Starts with amino group: N terminus

ends with a carboxyl group: C terminus

can have variation of 8 residues in between

Polypeptide Residue numbering system (8)

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1. Gly

2. Pro

3. Ser

4. Asp

5. Phe

6. Val

7. Tyr

8. Cys

Oligopeptide

polymer made of less than 50 amino acids

Polypeptide

polymer made of more than 50 amino acids

Protein

a functional molecule that cam be used to refer to any amino acid chain

each proteins sequence of amino acids is unique

What are the 5 elements found in a protein?

C, H, N, O, S

What determines a protein’s 3d structure

a proteins sequence of amino acids determines its 3d structure

proteins needs a 3d shape to be functional, there is lots of diversity in shape,

in size, and properties

What determines a protein’s function

a protein’s structure determines the function of a protein

What is the Primary Structure of Protein

the unique sequence of amino acids that will form a polypeptide chain (protein)

the sequence determines the structure and structure determines function, so a single amino acid change can completely change the protein’s function

how does a protein get a Secondary structure?

when the polypeptide chain’s backbone (held by Hydrogen bonds) folds or coils

this structure can only occur when polypeptide bends, as C=O and N-H groups are then close enough to hydrogen bond

when this happens they warp and fold into each other creating either 2d or 3d shapes

ex. beta and alpha

2 types of secondary structures (Protein)

alpha-helix

Beta-pleated sheets

traits of the alpha-helix

• coiled in a single chain

• Hydrogen bonds within the polypeptide chain

• the hydrogen bonds are between N-H and a C=O

• R groups are oriented outside the helix

traits of the Beta-pleated sheets

• has flat/sheet structure. needs 2 strands to not bend

• formed when two or more beta strands Hydrogen bond

• H bond formed between N-H and C=O

R groups are oriented inside and outside the sheets

Tertiary structure (Protein)

this structure happens when the r group interacts with each other and the peptide backbone

this results in the bending and folding of alpha helixes and beta sheets making more unique 3d shapes

5 R group interactions in the (Tertriary structure)

• Hydrogen Bonds:

  • Description: Hydrogen bonds can form between two polar side chains or between a side chain and the carboxyl group on the backbone.

  • Example: Hydrogen bonding between the side chain of serine and the backbone carbonyl group.

• Hydrophobic Interactions:

  • Description: Hydrophobic interactions occur when non-polar amino acid side chains cluster together to avoid contact with water.

  • Example: Interaction between the side chains of valine and leucine.

• Van der Waals Interactions:

  • Description: These are weak attractions between non-polar amino acid side chains due to temporary dipoles created by the movement of electrons

  • Example: Interaction between the side chains of alanine and isoleucine.

• Covalent Disulfide Bonds:

  • Description: Disulfide bonds are strong covalent bonds that form between the sulfur atoms of two cysteine residues.

  • Example: Disulfide bond between two cysteine side chains, stabilizing the protein structure.

• Ionic Bonds:

  • Description: Ionic bonds, also known as salt bridges, form between the positively charged side chains of basic amino acids and the negatively charged side chains of acidic amino acids.

  • Example: Ionic bond between the side chain of lysine (basic) and the side chain of aspartic acid (acidic).

Quaternary structure (Protein)

happens when two or more polypeptide chains make one macromolecule (full function protein)

Dimer

two polypeptide chains interacting to form a protein

teramer

the protein has 4 polypeptide chains

What if the protein has 1 polypeptide chain

with one chain it has a tertiary structure not quaternary

Protein folding

when proteins fold due to hydrogen bonds and van der waals interactions.

are more energentically stable than unfolded

Molecular chaperones

specialized proteins which help fold other proteins

shaped like a hollow cylinder with a cap

poly peptide goes it, the protein folds it, and it comes out folded

What happens when proteins have a disordered shape?

the proteins become inactive. as it needs to folded correctly to be active

Regulation of protein shape

the cell can control the shape of the protein and thus its function by activating and deactivating it

Protein denaturation

happens when a protein uncoils/unravels

the intermolecular bond formed in the secondary, tertiary, and quaternary structures are broken

losing its function, may be reversible

their peptide bonds are still together so they are biologically inactive