ch.4- protein structure & function

what are the different things proteins can be?

• enzymes

• structural proteins

• transport proteins

• motor proteins

• storage

• signal

• receptor

• gene regulation

what are examples of structural proteins

• extracellular matrix:

  • collagen

  • elastin

• cytoskeleton

  • tubulin

  • actin

  • keratin

what are examples of transport proteins?

• hemoglobin- carries oxygen

• transferrin- carries iron

what is an example of motor proteins?

• myosin- found in skeletal muscles and helps with movement

• kinesin- interacts with microtubules to move cargo

• dynein- allows cilia and flagella to beat

give examples of storage proteins

• iron binds to ferritin

• casein in mil

• ovalbumin in egg whites

give examples of signal proteins

• insulin- regulates blood sugar

what does a protein need to do in order to carry out its proper function?

maintain its specific shape

what is the shape of a protein initially specified by?

its amino acid sequence

what allows polypeptide chains to fold?

non-covalent bonds

what are some noncovalent bonds that allow polypeptide chains to fold?

• electrostatic attractions (ions)

• hydrogen bonds

• van der waals

• hydrophobic interactions

what happens to all the nonpolar side chains in a polypeptide chain?

they cluster in the middle together away from water

the type of folding that takes place in a polypeptide chain depends on what?

the amount of energy required

what is an example of something that can denature proteins?

urea

what are the 2 types of secondary protein structures?

• alpha helix

• beta pleated sheets

what happens when a protein isnt folded correctly, besides the fact that it wont function properly?

it could cause disease

what is a protein’s typical structure?

globular

what happens if a protein becomes fibrous?

it flattens and lose their ability to carry out their function

what happens if flattened proteins start building up?

an amyloid fibril is formed which can lead to various diseases, including Alzheimer's

what structure do good prions have?

alpha helical

what structure do bad prions have?

beta pleated sheets

what do chaperone proteins do?

help the process of folding by binding the polypeptide chain and molding into shape

what do chamber proteins do?

isolates the protein from the environment and allows it to fold inside

what are the 4 3D protein models?

1. backbone-

2. ribbon- adding secondary structure

3. wire

4. space-filling

what is a backbone model?

a line representation of the main chain of a protein

what is a ribbon model?

arrows are beta pleated sheets and ribbons represent alpha helices in the protein's secondary structures

what is a wire model?

adding the different carbons and side chains

what is a space-filling model?

a complete 3D model of the proteins structure and how it sits in space

what is the most common alpha helix (Right or Left)?

right

every 4 amino acid undergoes what bond with the previous one?

hydrogen bonds

what do alpha helices do with their hydrophobic amino acids on the outsides exposed?

they cluster together through hydrophobic interactions, forming a coiled-coil structure to isolate the hydrophobic amino acids on the backbone

what are some structures that beta pleated sheets undertake?

• zipper

• antiparallel

• parallel

• extended polypeptide backbone

what do serine proteases do?

enzymes that cleave peptide bonds in proteins using a serine residue in their active site

examples of serine proteases

• trypsin

• chymotrypsin

• elastase

how many domains is hemoglobin made out of?

4 different ones

what is an example of a protein that has a long elongated fibrous shape?

collagen and elastin

what are extracellular proteins usually stabilized by?

covalent cross-linkages

what is an example of a cross-linkage that stabilizes extracellular proteins

disulfide bonds

why arent there a lot of proteins with disulfide bonds inside the cytoplasm?

the cytoplasm contains many reducing agents (breaks disulfide bonds and adds H)

how are proteins able to bind to other molecules?

noncovalent interactions

what does hydrolase do?

catalyzes the hydrolysis of chemical bonds, often breaking down complex molecules into simpler ones by adding water

what do nucleases do?

breaks down nucleic acids by hydrolyzing bonds between molecules

what do proteases do?

breaks down proteins by hydrolyzing peptide bonds between amino acids

what do ligases do?

joins two molecules together; DNA ligase joins 2 DNA strands together end-to-end

what do isomerases do?

catalyzes the rearrangement of bonds within a single molecule

what do polymerases do?

catalyzes polymerization reactions such as the synthesis of DNA and RNA

what do kinases do?

add phosphate groups to molecules

what do phosphatases do?

remove phosphate groups from molecules

what does oxido-reductase do?

catalyzes oxidation-reduction reactions, transferring electrons between molecules

what does ATPase do?

hydrolyzes ATP into ADP

what is lysozyme?

enzyme found in secretions that destroys the bacterial cell wall

what do statins do?

they fit in the active site of the enzyme involved in cholesterol synthesis

how do you regulate enzymes?

• regulate gene expression

• regulate protein degredation

• allosteric regulation

what are allosteric proteins

enzymes that have 2 or more binding sites that influence one another

what are regulatory sites?

regions on an enzyme where molecules can bind to regulate activity by changing its shape

what is feedback inihibition?

when the end product of a metabolic pathway inhibits an earlier step, preventing the overproduction of that product

how does the last product in a metabolic pathway act as a feedback inhibitor and function allosterically?

the last product binds to an allosteric/regulatory site on the enzyme, reducing its activity and preventing overproduction of the initial product

how can phosphorylation control protein activity?

by causing a conformational change since phosphate groups carry a -2 charge, affecting the overall charge of the protein and therefore its shape

what type of amino acids do kinases usually phosphorylate?

tyrosine, serine or threonine

what are protein machines?

a collection of protein that come together and fold in specific ways to form a large structure that carries out a sophisticated function