Peptide Bonds Chapter 4 - Part 1

Polar Amino Acids are

Polar amino acids are Hydrophilic. like water

Prions (PrP) is hard to stop because

PrP is hard to stop because once it is misfolded, it will infect other healthy PrP proteins, rapidly.

When it is turned upside Alpha Helix has same or different handedness?

Same handedness. only changes when reflected in a mirror

Covalent Bonds

Share electrons

Prion protein - PrP

Found by Dr Stanley Prusiner. incorrectly folded protein PrP when eaten cause neurodegenerative disorders such as Alzheimers.

Who proposed structures of helix and sheet first?

Pauling and Corey 1954

Binding site

A cavity in a protein where specific ligand can attach like a key into a modern car.

Single Protein subunits can form 3 shapes

A filament, tube, or sphere

Many large structures such as viruses and ribosomes are built with

A mixture of different proteins plus DNA or RNA molecules

Polypeptide Chain

A protein is made of amino acids linked together into a polypeptide chain.

Antibodies are in the shape of the letter

An antibody is Y shaped and has two identical binding sites for antigens on arms. There are two identical heavy chains and two identical light chains held together by disulfide bonds. mutates when needed.

Denatured protein

An unfolded protein. Can usually recover it's shape, (unlike proteins in cooked eggs). renaturation works best for small proteins

Beta Structures come in two varieties

Anti-Parallel and Parallel

Ligand

Any substance that is bound by a protein, due to the formation the three set of weak non-covalent bonds.

anitfreeze proteins formed of

Beta sheets

Carboxyl group

C-terminal, negatively charged Carbon side of amino acid

How Proteins Work

Each proteins conformation endows it with unique function based on chemical properties. Activity of proteins depends on ability to bind specifically to other molecules, allowing them to act as catalysts, structural supports, signal receptors, and tiny motors.

Beta sheets are formed by H-bonds between:

H-bonds between peptide bonds of different strands, and side chains project alternately above and below the plan of the strand

Some Proteins are often formed as a symmetrical assembly of different sub units.

Hemoglobin contains two copies of alpha-globin and two copies of beta-globin. abundant in red blood cells. Each subunit contains a heme molecule for O2 binding.

Homodimers and Heterodimers in Prion Diseases

Homo = same. Hetero = Different. Dimer =A structure composed of two halves A normal PrP with a bad PrP causes a Heterodimer, which creates a Homodimer. Converting more PrP to misfolded form creates aggregate.

Segment of a Alpha helix can cross Lipid Bilayer in Cell. how many amino acids can span membrane this way

Hydrophobic non-polar side chains on helix help it attract to hydrocarbon tail of phospho-lipid of membrane. About 20 amino acids required to span membrane this way.

why is tip of Y antibody so versatile?

It is because there is a light chain and heavy chain variable domain there.

Protein Families

Like Serine proteases. each family member has similar amino acid sequence, and 3-d structure

COVALENT Disulfide bonds help stabilize a favored protein conformation.

Like a Staple. Can either join parts of same chain or two different chains. Because the energy to break one covalent bond is higher than many non-covalent bonds. Like in Endo Reticulum. Also in Lysozyme which protects tears from bacteria.

Collagen is a triple helix formed by three protein chains that wrap around one another

May rod-like collagen molecules are cross-linked together in extracellular space to form collagen fibrils that have the tensile strength of steel.

Alpha Helices are formed by hydrogen bonds between:

N-terminal of one amino acid H-BONDS to the C-terminal FOUR amino acids away in same chain. side chains not involved.

Amino Group

N-terminal, positively charged Nitrogen side of amino acid

Non-polar Amino Acids are

Non-polar amino acids are Hydrophobic. do not like water

Proteins in a Molecular cell is helped by Molecular Chaperones

Vital in crowded conditions of cytoplasm, make proteins avoid wrong partners.

Hydrogen Bonds

When a hydrogen atom is "sandwiched" between electron-attracting atoms (like oxygen or nitrogen want hydrogen's electron, compete for it)

Prion diseases include

When they eat same or simillar species. Sheep - scrapie. Cows- bovine spongeform encephalopathy or madcow. Humans - Creutzfeldt Jacob disease CDJ (forms in places like africa after eating monkeys).

Serine proteases comprise:

a family of proteolytic enzymes that has the same looking structure, and has an active site both for serine. Cuts peptide bonds with hydrolysis.

What gives each amino acid its unique property

amino acid side chain gives unique properties such as hydrophobia for non-polar

Protein Domain

any segment of a polypeptide chain that can fold independently into a compact, stable structure, like the SH2 domain

Protein Domain

any segment of polypeptide chain that can fold independently into a compact stable structure.

van der Waals attractions

attractions between two atoms at very short distances. This most likely should happen between non-polar side-chain facing inside of the molecule.

Alpha Helices usually formed from a structural bond called

backbone to backbone

Electrostatic Bonds

between charged groups. like when a positive and negative charge get close together, they attract.

Hydrogen Bonds within a protein molecule help stabilize it's shape. can bond 3 ways.

can bond three ways backbone to backbone backbone to side chain side chain to side chain

Peptide Bonds

covalent bond between amino acids. the Carboxyl group of one amino acids shares electrons with amino group of another amino acid.

Structure and Shapes of proteins determine -

determines their function

Polypeptide Backbone

each polypeptide chain consists of a backbone that supports both amino acids held together by peptide bonds. excludes side chains

Conformation

final folded structure of protein

Hydrophobic interaction in water

hydro-philic polar side chains face water and hydrogen bonds can be formed. hydrophobic non-polar side chains stay inside of protein both usually cluster into groups of polar or non-polar

When proteins fold incorrectly

incorrectly folded proteins can form aggregates that damage cells and even whole tissues

many proteins often contain multiple copies of

multiple copies of a single polypeptide chain or subunit. my even have one identical, or two non-identical sites on each monomer to create dimers or tertramers, etc.

four types of weak bonds (three are non-covalent bonds) help proteins fold

non-covalent bonds include hydrogen bonds, electrostatic attractions, and van der Waals attractions. The fourth is Hydrophobic Interaction

Side Chains

parts of amino acids that do not form the peptide bond. give amino acids their unique proteins

The four structures are primary, secondary, tertiary and quaternary

primary = amino acid sequence secondary = helices and sheets tertiary = whole 3-d polypeptide quaternary = more than one polypeptide

secondary structure of a protein is

secondary structures are alpha helices and beta sheets

Many Proteins are composed of separate functional__

separate functional domains. each domain has different functions like organs

Lysozyme enzyme works by

severs polysaccaride chain that form cell walls of bacteria. it binds to sugar with Enzyme Substrate complex ES. Bends critical bonds causing reactions between added Aspartic acid and c1 carbon on distorted sugar. Asp links to site of clevage. It adds glutamic acid and water molecule between two sugar groups. a hydrolysis reaction occurs and the bond breaks off both Asp to original state, Gul, and sugars. This forms enzyme product EP when released

Intertwined alpha helix form coiled coils by

the alpha helices touch along a similar non-polar line, wrap around each-other, and leave polar side exposed. Most stable structure in water

Common enzymes names are

the name of an enzyme usually indicates the substrate and the nature of the reaction catalyzed. For example citrate synthase catalyzes the synthesis of citrate by a reaction between acetyl CoA and oxaloacetate.

Protein with just one binding site can form a dimer with another identical protein. However identical proteins with two different binding site form

they form a long helical filament, like Actin of the cytoskeleton. With two properly based binding sites they will form a ring instead.

The proteins re-nature in water, and stabilize for what purpose

they stabilize in a shape that is the lowest energy cost. It also determines function.

Dimer

two halves, or two proteins.

Purified protein exposed to high concentrations of urea results in

urea results in denaturation. Urea has a hydrogen bond donor (-NH2) and a hydrogen bond acceptor (-C=O) disrupts hydro bonds inside protein. no more hydrophobic core. removing urea results in original shape in water.

Do all proteins bind to other molecules?

yes they do. it determines how it works