Peptides and Peptide Bonds

Topic: Peptide Bond

Peptides and Peptide Bonds

A polypeptide is formed by the _____ interaction of two amino acids

covalent

Topic: Peptide Bond

Peptides and Peptide Bonds’

A polypeptide is formed by the covalent interactions of two _____ ______

amino acids

Topic: Peptide Bond

Peptides and Peptide Bonds

• A molecule of _____ is eliminated for each peptide bond formed and the product is called a peptide

water

Topic: Peptide Bond

Peptides and Peptide Bonds

• A molecule of _____ is eliminated for each peptide bond formed and the product is called a peptide

• The remaining portion of the AA in the peptide is called an ____ ___ _____

amino acid residue

Topic: Peptide Bond

Peptides and Peptide Bonds

• A molecule of water is eliminated for each peptide bond formed and the product is called a peptide

• The remaining portion of the AA in the peptide is called an amino acid residue

• The _______ and _____ ends are available for further reaction

N-terminal and C-terminal

Topic: Peptide Bond

Peptides and Peptide Bonds

• The condensation reaction to form peptide bonds is catalyzed by the _________

ribosome

Topic: Peptide Bond

Peptides and Peptide Bonds

• The condensation reaction to form peptide bonds is catalyzed by the _________

• How do amino acids get into the ribosome?

tRNA molecules transport amino acids to the ribosome

Topic: Peptide Bond

Peptides and Peptide Bonds

What is happening in the highlighted orange

The amino group from the amino acid is added to the carboxyl group of the growing peptide aka amino acids are added successfully to the carboxyl terminal end of the growing peptide

Topic: Peptide Bond

Peptides and Peptide Bonds

The _____ _____ _____ is the primary structure of the protein

amino acid sequence

Topic: Peptide Bond

Peptides and Peptide Bonds

The amino acid sequence is the _____ ______ of the protein

primary structure

Topic: Peptide Bond Structure

________ and ________ analyzed the geometry and dimensions of peptide bonds in crystal structures of molecules containing one or a few peptide bonds

Linus Pauling and Robert Corey

Topic: Peptide Bond Structure

_______ bond length is 10% shorter than found in usual amines

C-N

Topic: Peptide Bond Structure

The C-N bond length is _____ shorter than found in usual amines

10%

Topic: Peptide Bond Structure

Planar Structure of Peptide Bonds

• Why is the peptide bond (C-N) shorter than the others

because the C-N bond has some double bond character, resonance with the C=O group

Topic: Peptide Bond Structure

Planar Structure of Peptide Bonds

• The peptide bond is short because the C-N bond has some double-bond character (40%) due to resonance with the C=O group

• All peptide bonds are approximately _______

coplanar

Topic: Peptide Bond Structure

Planar Structure of Peptide Bonds

• The peptide bond is short because the C-N bond has some double-bond character (40%) due to resonance with the C=O group

• All peptide bonds are approximately coplanar

• The ______ of the peptide bond reduces the degrees of freedom durin gfolding

rigidity

Topic: Peptide Bond Structure

Peptide Bond Torsion Angles

• The 3 main torsion angles of a polypeptide backbone are

  • ______, C-N

  • _______, C=O to C (α)

  • ________, peptide bond

• phi ( ϕ)

• psi (Ψ)

• omega (ω)

Topic: Peptide Bond Structure

Peptide Bond Torsion Angles

• The three main torsion angles of a polypeptide backbone are phi ( ϕ), C (α)- N ; psi (Ψ), C=O to C (α), and omega (ω) peptide bond

• The planarity of peptide bonds restrict ω to _____ (trans) in nearly all the main chain peptide bonds

180 degrees

Topic: Peptide Bond Structure

Peptide Bond Torsion Angles

• The three main torsion angles of a polypeptide backbone are phi ( ϕ), C (α)- N ; psi (Ψ), C=O to C (α), and omega (ω) peptide bond

• The planarity of peptide bonds restrict ω to 180 (trans) in nearly all the main chain peptide bonds

• In rare cases, ω=0 degrees for a ___ peptide bond which usually involves proline

cis

Topic: Peptide Bond Structure

Peptide Bond Torsion Angles

• The three main torsion angles of a polypeptide backbone are phi ( ϕ), C (α)- N; psi (Ψ), C=O to C (α), and omega (ω) peptide bond

• The planarity of peptide bonds restricts ω to _180_ (trans) in nearly all the main chain peptide bonds

• In rare cases, ω=0 degrees for a cis peptide bond which usually involves _____

proline

Topic: Peptide Bond Structure

Peptide Bond Torsion Angles

what does the phi ϕ torsion angle connect to in a polypeptide backbone

• C (α)- N

Topic: Peptide Bond Structure

Peptide Bond Torsion Angles

what does the psi Ψ torsion angle connect to in a polypeptide backbone

C=O to C(α)

Topic: Peptide Bond Structure

Peptide Bond Torsion Angles

what does the omega torsion angle connect to in a polypeptide backbone ω

peptide bond (C-N)

Topic: Peptide Bond Structure

Peptide Bonds Cis and Trans Configuration

The two C(α) carbons , C=O and N-H are nearly _______

coplanar

Topic: Peptide Bond Structure

Peptide Bonds Cis and Trans Configuration

The _____ _____ is always nearly in the trans configuration because it is favorable over cis

peptide bond

Topic: Peptide Bond Structure

Peptide Bonds Cis and Trans Configuration

• The peptide bond is nearly always in the ________ configuration because it is favorable over cis

trans

Topic: Peptide Bond Structure

Peptide Bonds Cis and Trans Configuration

• The peptide bond is nearly always in the trans configuration because it is favorable over cis

• C(α) atom sare on the opposite sides of the C-N peptide in the ______ ______ and the same side in the _____ _____

trans isomer; cis isomer

Topic: Peptide Bond Structure

Peptide Bonds Cis and Trans Configuration

• The peptide bond is nearly always in the trans configuration because it is favorable over cis

• C(α) atoms are on the opposite sides of the C-N peptide in the trans isomer and the same side in the cis isomer

• _______ ________ between fucntional groups attached to C(α) atoms are greater in the cis configuration

steric hinderance

Topic: Peptide Bond Structure

Peptide Bonds Involving Proline

The _________ nature of the proline chain allow both the cis and trans configurations to have nearly equivalent energies. Thus, proline is found in the cis configuration

cyclic nature

Topic: Peptide Bond Structure

Peptide Bonds Involving Proline

The cyclic nature of the proline chain allow both the cis and trans configurations to have nearly equivalent energies. Thus, proline is found in the _____ configuration

cis

Topic: Peptide Bond Structure

Formation and Stability of Peptide Bonds

• In aqueous solution, formation of a peptide bond is ___ _______ ___________ (Δ)G = 10kJ/mol at room temperature )

not favored thermodynamically

Topic: Peptide Bond Structure

Formation and Stability of Peptide Bonds

• In aqueous solution, formation of a peptide bond is ___ _______ ___________ (Δ)G = 10kJ/mol at room temperature )

• Instead, the reverse reaction, ________ of a peptide bond is favored

hydrolysis

Topic: Peptide Bond Structure

Formation and Stability of Peptide Bonds

• In aqueous solution, formation of a peptide bond is not thermodynamically (Δ)G = 10kJ/mol at room temperature )

• Instead, the reverse reaction, hydrolysis of a peptide bond, is favored

• The energy _____ is used during translation

ATP

Topic: Peptide Bond Structure

Polypeptide Nomenclature

• The convention is always to represent the ____ terminus on the left and the ___ terminus on the right

N; C

Topic: Peptide Bond Structure

Polypeptide Nomenclature

• The convention is always to represent the ____ terminus on the left and the ___ terminus on the right

• Short peptides of a few residues are called ______ peptides , while longer peptides are called polypeptides, and proteins are very long-chain polypeptides folded into regular structures

oligopeptides

Topic: Peptide Bond Structure

Polypeptide Nomenclature

• The convention is always to represent the N terminus on the left and the C terminus on the right

• Short peptides of a few residues are called oligopeptides, while longer peptides are called ______ , and proteins are very long chain polypeptides folded into regular structures

polypeptides

Topic: Peptide Bond Structure

Polypeptide Nomenclature

• The convention is always to represent the N terminus on the left and the C terminus on the right

• Short peptides of a few residues are called oligopeptides, while longer peptides are called polypeptides , and proteins are very long chain polypeptides folded into regular structures

• The term polypeptide refers simply to a chain of amino acids while the term protein refers to ________ ________ and is ( in some cases ) modified. Proteins may consist of more than one polypeptide chain ( multimer)

the chain of amino acids after it folds properly

TOPIC: Ionization of Peptides and Proteins

Protein Size

• the avergae molecular weight of an amino acid is about 138. When accoutning the abundance of AA’s in known proteins, the molecular weight of an average AA in protein is about ___

128

TOPIC: Ionization of Peptides and Proteins

Protein Size

• The average molecular weight of an amino acid is about 138. When accounting for the abundance of AA’s in known proteins, the molecular weight of an average AA in protein is about 128

• Peptide bond formation removes a water molecule ( molecular weight of 18) so the avergae weight of an amino acid reside in a protein is ___

110

TOPIC: Ionization of Peptides and Proteins

Protein Size

• The average molecular weight of an amino acid is about 138. When accounting for the abundance of AA’s in known proteins, the molecular weight of an average AA in protein is about 128

• Peptide bond formation removes a water molecule ( molecular weight of 18) so the average weight of an amino acid reside in a protein is 110

• Estimate the number of residues in a protein by dividing the molecular weight by 110

  • ex- 619,000/110=

5627

TOPIC: Ionization of Peptides and Proteins

Peptide Sequence

____________________. Simply choosing the most common amino acids as monomers is a polypeptide, the number of sequences possible is given by the following

• Number of sequence = ( number of possible AAd)^( peptide length)

The number of unique sequences possibilities is enormous

TOPIC: Ionization of Peptides and Proteins

Peptide Sequence

• . Simply choosing the most common amino acids as monomers is a polypeptide, the number of sequences possible is given by the following

• Number of sequence = ( number of possible AA)^( peptide length)

• Ex- For any of the 20 common amino acids in a tetrapide ( four amino acid residues ) results inthe following number of possible peptide sequences ______

20^4= 160,000

TOPIC: Ionization of Peptides and Proteins

Peptide Sequence

• The number of unique sequences possibilities is enormous.. Simply choosing the most common amino acids as monomers is a polypeptide, the number of sequences possible is given by the following

• Number of sequence = ( number of possible AA)^( peptide length)

• Ex- For any of the 20 common amino acids in a tetrapide ( four amino acid residues ) results inthe following number of possible peptide sequences 20^4= 160,000

• Organisms typically rely on _____ to ______ sequences, so necessary function will determine which sequences are constructed. As we will see, polypeptides ( proteins) do not contain an equal distribution of amino acids

30,000- 35,000

TOPIC: Ionization of Peptides and Proteins

AA’s sequence in Polypeptide Chain Define Structure

• Each of the amino acids, joined together by peptide bonds, in proteins ( or polypeptides ) have different properties determine dby their __ group side chains:

  • acidic, basic, neutral, hydrophobic

R

TOPIC: Ionization of Peptides and Proteins

AA’s sequence in Polypeptide Chain Define Structure

• Each of the amino acids, joined together by peptide bonds, in proteins ( or polypeptides ) have different properties determined by their _R_ group side chains:

  • acidic, basic, neutral, hydrophobic

• The amino acid side chains direct the folding of the nascent polypeptide into___________ and ________

a functional protein and stabilize its final conformation

TOPIC: Ionization of Peptides and Proteins

Some proteins Contain Chemical Groups Other Than Amino Acids

• Conjugated proteins:___________

  • non amino acid part = prosthetic group

contain permanently associated chemical components

TOPIC: Ionization of Peptides and Proteins

Some proteins Contain Chemical Groups Other Than Amino Acids

• Conjugated proteins: contain permanently associated chemical components

  • non amino acid part = ______

prosthetic group

TOPIC: Ionization of Peptides and Proteins

Some proteins Contain Chemical Groups Other Than Amino Acids

• Conjugated proteins:contain permanently associated chemical components

  • non amino acid part = prosthetic group

• lipoproteins:______

contain lipids

TOPIC: Ionization of Peptides and Proteins

Some proteins Contain Chemical Groups Other Than Amino Acids

• Conjugated proteins:contain permanently associated chemical components

  • non amino acid part = prosthetic group

• Lipoproteins contain lipids

• glycoproteins:_______

contain sugars

TOPIC: Ionization of Peptides and Proteins

Some proteins Contain Chemical Groups Other Than Amino Acids

• Conjugated proteins:contain permanently associated chemical components

  • non amino acid part = prosthetic group

• lipoproteins

• glycoproteins: contain sugars

• metalloproteins: ______

contain specific metals