Bio Chem Chapter 4: Protein structures

What determines protein function?

Amino acid sequence

What can many human genetic diseases be traced to?

Defective proteins

What do functionally similar proteins from different species have in common?

similar amino acid sequences

What is a similar protein seen in fruit flies and humans?

Ubiquitin

Is the amino acid sequence absolutely fixed for a particular protein?

Not necessarily. some flexibility is possible without disruption of function.

What are 20-30% of human proteins?

polymorphic: have amino acid sequence variants

What are the crucial regions in most proteins that are essential for their function?

Conserved regions

What is the ultimate goal for protein sequences?

To be able to design a protein sequence that possesses a desired function.

What is the primary structure?

Specified by the order of the amino acid sequence (N to C) linked by covalent bonds.

What does the primary structure give insight into?

Proteins three-dimensional structure and its function

What do some sequence that serve as signals determine?

-Cellular location

-Chemical modifications

-Half-life of a protein

How are proteins grouped into families?

Analysis of function, structure, and sequence

Can the function, structure, and sequence of a protein be recognized by the primary sequence?

Yes, some of the features can be

Consensus sequences

reflects the most common amino acids at each position

What can regions that have good agreement represent?

Evolutionary conserved functional domains

If two organisms are related, what should be similar?

The sequence of their genes and proteins

When the evolutionary distance between the two organism increases, what happens to the sequences?

The sequences increasingly diverge

Residues that are essential for the activity of proteins?

Conserved over time

What happens to residues that are less important to function?

May vary over time

Different proteins can evolve___.

at different rates

Homologous proteins (homologs)

Two proteins in a family with a common ancestor.

Orthologs

Two proteins in a family from different species with a common ancestor

Paralogs

Two proteins in a family that are present in the same species with a common protein ancestor.

How can homologs be identified?

Through the use of increasingly powerful computer programs that directly compare two or more protein sequences.

How does electronic search pricesses work?

-Sliding one sequence past the other unit a section with a good match is found

-Sometimes gaps must be added to the alignment

Penalties in electronic searching

Are added to the score for gaps to prevent too many from being added to force an alignment.

% idenity

Exact residue matches

% similarity

conserved residue functionality

What does the process also consider?

-Also consider the function/chemical properties of substituted amino acids.

-ex: glu is replaced with Asp at a specific residue

What are the length of lines connecting the nodes proportional to?

To the number of amino acids substitutions separating one species from another.

What are molecular evolutionary trees based on?

Based on sequence divergence for members of a single protein family from different species.

How can molecular evolutionary trees be refined?

With additional data on the unique biochemical and physiological properties of the protein(s) from each species.

What is the secondary structure of a protein?

local conformation of the polypeptide backbone stabilized hydrogen binds between the functional groups of peptide bonds.

What determines the type of repeated secondary structure formed?

Amino acid sequence

What chemistry is taking place in the secondary structure?

-Partial double bond character of the peptide bond

-Unshared electron pair on N is delocalized to the carbonyl

-True structure is a resonance hybrid

Is there rotation around the double bond?

No

What is the partial double bind character of the peptide bond?

Planarity of the peptide bond-all six atoms lie in a plane.

With partial double bond character, the peptide bond is _____ reactive?

less, compared to esters.

With partial double bond character, what is the result on the peptide bond?

The bond is “relatively rigid” prohibiting free rotation.

Due to the rigidity of the partial double bond, what are the possible geometric isomers?

Trans: different sides

cis: same side

What is the predominant configuration for proteins?

99.9% of proteins are trans

What is trans more common than cis in proteins?

Steric hinderance when in cis

What is the exception cis vs. trans?

Proline has about 6% cis, both have steric hindrance

What is proline isomerization catalyzed by?

Proline isomerases

Where is the bond rotation in proitiens?

Along the polypeptide backbone

Rotation around bons connected to the alpha carbon are what ______?

Permitted

What is the phi angle?

Angle around the alpha-carbon-amide nitrogen bond

What is the psi angle?

Angle around the alpha carbon-carboxyl carbon bond.

In a fully extended polypeptide, what are the angles for phi and psi?

180

Where are the R-groups in a fully extended polypeptide?

The R-groups alternate above and below the plane.

Why are some phi and psi combinations unfavorable?

Due to steric crowding of backbone atoms or side chains.

Why are some phi and psi combinations favorable?

The chance to form favorable hydrogen bonding interactions along the backbone.

What does a Ramachandran plot show?

-Shows the distribution of phi and psi angles that are found in a protein.

-Black dots = pyruvate kinase

What do Ramachandran plots demonstrate?

-Common secondary structure elements.

-Reveals regions with unusual backbone structure

What are the two regular arrangements of the backbone commonly found?

alpha-helix and beta-sheets

On a Ramachandran plot, where are the beta-sheets?

Around 120-180

On a Ramachandran plot, where are the right-handed alpha-helix?

around -60

What is the structure of an alpha-helix?

Rod-like structure with R groups on the outside, main chain on the inside.

How are alpha-helix stabilized?

Stabilized by hydrogen bonds between the nearby backbone amides.

What direction are the hydrogen bonds in regard to the axis of the helix?

parallel

What direction are the side chains in regard to the axis of the helix?

perpendicular

What are the inner characteristics of an alpha-helix?

-The inner diameter of the helix (no sidechains) is about 4-5

-Filled to van der Waal’s radii-too small for anything to fit “inside”

What are the outer characteristics of an alpha-helix?

-The outer diameter of the helix (with side chains) is 10-12

-Happens to fit well into the major groove of dsDNA

What direction of alpha-helix are predominantly formed in proteins?

Right handed

What are amphipathic helices?

-One side is facing the outside (hydrophilic) and one side is facing the inside (hydrophilic)

Can all polypeptide sequences adopt an alpha-helical structure?

No

What are the stabilizing factors of alpha helix?

-Favorable interactions between side chains 3-4 residues apart of opposite charge or capable of H-bonding

-Size and shape- smaller hydrophobic R-groups

What some of the destabilizing factors in an alpha helix?

-Electrostatic repulsion between like charges at pH 7 (Glu)

-Bulk and shape (Asn, Ile, Thr)

Why can glycine be a destabilizing factor?

Because the small R-group readily supports other conformations.

Why is proline a destabilizing factor?

-Because the required rotation around the N-C alpha bond is impossible and the amide nitrogen lacks an N-H for hydrogen bonding

What would happen if proline was introduced in the middle of an alpha-helix?

-Introduce a kink in the alpha-helix

Where are prolines usually found in alpha-helix?

the end

What is the typical length of an alpha-helix?

4-40 residues

Beta-sheets

Backbone is in a more extended conformation with multiple sections aligned side-by-side

What causes the pleated sheet-like structure?

Planarity of the peptide bond and tetrahedral geometry of the alpha carbon.

How are beta-sheets stabilized?

By H-bonds between peptide bonds that are “in the plane” of the sheet.

How many sections are usually in a sheet?

Sheets are commonly made up of 4-7 backbone sections.

What direction do the side chains protrude from the sheet?

The side chains protrude from the sheet alternating in an up and down direction.

What are two orientations that a beta-sheet can be in?

Parallel or antiparallel

What is a parallel beta sheet?

Strands run in the same direction

What is a anti-parallel beta sheet?

Strands run in opposite directions

Can beta-sheets be both parallel and anti-parallel in the same sheet?

yes

What kind shape do sheets often adopt?

Twisted

When do beta-turns occur?

Occur frequently whenever strands in beta-sheets change the direction

What do beta-turns allow for?

Reverse of the direction (common for antiparallel)

How many amino acids does it take to turn 180?

4 amino acids

How are beta-turns stabilized?

H-bonds from a carbonyl oxygen to amide protein three residues down the sequence.

What amino acids are common in beta-turns?

Proline and glycine

What is Circular Dichroism (CD) analysis?

-Common secondary structure can be assessed by CD

-CD measures the molar absorption difference

What do CD signals from peptide bonds depend on?

Chain conformation

Chromophores

The chiral environment produces characteristics signals

How are amino acids grouped?

Based on their preference for forming alpha-helices, beta-sheets, and turns

Which amino acid shows no significant preference for any of the structures?

Arginine

Can sequence adopt other conformations?

Yes, some sequences can adopt alternative conformations in different proteins.

What is the tertiary structure of a protein?

Long-range conformation of the polypeptide backbone.

often brings together groups that are far apart in the primary structure.

What is the biologically active structure?

Stabilized by multiple weak interactions.

What bond do tertiary structures have?

disulfide bonds (covalent)

Where are the disulfide bonds perdominatly?

-Intracellular proteins generally do not have disulfides

-Extracellular proteins can have several

What are the two major classes of tertiary structure?

Fibrous and globular proteins

Fibrous proteins

Typically insoluble, made from a single secondary structure