Bio 212 Unit 2

Describe dehydration synthesis and hydrolysis. What does each accomplish?

Dehydration synthesis joins amino acids together with the removal of a water molecule. Hydrolysis breaks peptide bonds and requires a molecule of water. Special hydrolytic enzymes called proteases break peptide bonds. (Digestive enzymes)

Elastin

Elastin, as its name implies, enables your skin to stretch and bounce back; it is elastic. It's a protein in connective tissue that is elastic and allows many tissues in the body to resume their shape after stretching or contracting. It helps skin to return to its original position when it is poked or pinched.

Enzymes

Enzymes are biological molecules (proteins) that act as catalysts and help complex reactions occur everywhere in life. It helps break down protein into amino acids. They speed up the rate of a chemical reaction and are responsible for the entire metabolism of a protein

Gene Regulatory Proteins

Gene Regulatory Proteins activate or deactivate specific genes in a cell.

Oxido-reducase

General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced. Enzymes of this type are often called oxidase, reductases, or dehydrogenases

Hydrolase

General term for enzymes that catalyze a hydrolytic cleavage reaction

ATPases

Hydrolyze ATP. Many proteins have an energy-harnessing ATPase activity as part of their functions, including motor proteins such as myosin and membrane transport protein such as the sodium pump

9 classes of biological molecules:

1) Enzymes = catalyze covalent bond breakage or formation 2) Structural Proteins = provide mechanical support to cells and tissues 3) Transport Proteins = carry small molecules or ions 4) Motor Proteins = generate movement in cells and tissues 5) Storage Proteins = store amino acids or ions 6) Signal Proteins = carry extracellular signals from cell to cell 7) Receptor Proteins = detect signals and transmit them to the cell's response machinery 8) Gene Regulatory Proteins = bind to DNA to switch genes on or off 9) Special-Purpose proteins

Describe the general steps in an enzyme catalyzed reaction.

36) E + S (ES) Transition state where chemistry occurs) E + P. The enzyme is then free to catalyze another reaction.

Coiled-coiled motiff

A coiled-coiled motif is the intertwining of two polypeptide chains. Keratin is an example.

Disulfide Bond

A disulfide bridge (bond) is a bond between two cysteines at different locations along a polypeptide chain. These add additional stability to a protein and are often seen in proteins that are exported from a cell.

Peptide Bond

A peptide bond is a covalent bond between the amino group of one amino acid and the carboxyl group of another amino acid. This bond had double bond characteristics, it is strong and inflexible. Proteins are composed of amino acids bound together by peptide bonds.

Prion

A prion is a misfolded protein that will cause other proteins to misfold causing a chain reaction and form protein aggregates that disrupt cell function. Amyloid fibrils found in nerve cells are an example.

Protein Abducts

A protein adduct is another molecule covalently bound to a protein that provides additional function to that protein. Retinal allows the protein rhodopsin to respond to light, Heme allows hemoglobin to bind to oxygen.

Protein Domain

A protein domain is a localized region in a polypeptide chain that has a specific function. It may be a DNA binding domain, or ATP binding domain.

Protein family

A protein family is a group of related proteins with similar amino acid sequences that have a common origin. However these related proteins may have quite different functions.

How do mutations (amino acid substitutions) influence protein folding? Give an example.

A replaced amino acid will often disrupt the proper electrostatic interactions responsible for the proper folding of a protein. This will either cause the protein to fold incorrectly or cause the proteins to aggregate. A single amino acid substitution is responsible for hemoglobin to aggregate in red blood cells, causing the cells for form a sickle shape disrupting blood flow.

Describe 5 ways proteins and enzymes can be regulated.

A) Feedback Inhibition- a downstream product in an enzymatic pathway inhibits an upstream enzyme in the pathway. B) Allosteric Inhibition- a molecule (sometimes a product) will bind to an enzyme and turn off its activity. C) Protein Phosphorylation- Phosphorylation of a protein or enzyme will either activate or deactivate that protein. It requires a kinase that will phosphorylate the protein and a phosphatase that will dephosphorylate the protein. D) G-protein is a critical signaling protein. It is turned on while bound to GTP but after a given amount of time the G-protein will hydrolyze GTP to GDP this will turn off the G-protein. To reactivate the G-protein the GDP will be exchanged with GTP thereby activating it until the GTP is again hydrolyzed to GD

4 classes of amino acids

A) Polar (hydrophilic) amino acids (mix with water) B) Non-Polar (hydrophobic) amino acids (avoid water) C) Basic (positively charged) amino acids D) Acidic (negatively charged) amino

Amino Acids

Amino acids are the monomer units of proteins. They consist of a basic amino group (NH2) an acid carboxyl group (COOH), and an R-group. The R-group defines the amino acid and it is a molecule of a specific structure. These three parts of an amino acid are bound to a central alpha carbon. H2N—C—COOH R The bonds between the amino group and the alpha carbon and the bond between the carboxyl group and alpha carbon can freely rotate.

How do amino acids differ from each other?

Amino acids differ from each other by the R group. The R group defines the amino acid. There are 20 different R groups so there are 20 different amino acids.

Antibody

An antibody is a tetramer consisting of two light chains and two heavy chains. The variable region allows an antibody to specifically bind to an antigen. There can be thousands of different antibodies each with a variable region that binds to a specific antigen.

What is an enzyme pathway and how are pathways regulated?

An enzymatic pathway, is a multi-step, multi enzyme reaction where there is an initial substrate that undergoes multiple chemical changes to produce a final product. E1 E2 E3 Initial Substrate P1 P2 Final Product These pathways are often regulated where the build-up of the final product will inhibit the first or second enzyme in the pathway. (Feedback Inhibition)

What are the four ways to represent the 3 dimensional shape of a protein?

Backbone model, Ribbon model, Wire model, Space -filling model.

Nuclease

Breaks down nucleic acid by hydrolyzing bonds between nucleotides

Protease

Breaks down proteins by hydrolyzing peptide bonds between amino acids

Polymerase

Catalyzes polymerization reaction such as the synthesis of DNA and RNA

Kinase

Catalyzes the addition of phosphate groups of molecules. Protein kinases are an important group of kinases that attach phosphate groups to proteins

Phosphatase

Catalyzes the hydrolytic removal of a phosphate group from a molecule

Isomerase

Catalyzes the rearrangement of of bonds within a single molecule

Ligase

Joins two molecules together. DNA ligase joins two DNA strands end to end

What are only a small fraction of possible amino acid sequences actually seen in cells?

Most amino acid sequence combinations can result in multiple conformations. These are unstable and would not be good for a reliable protein with a specific function. Only a fraction of amino acid sequence combinations results in only one stable conformation. These are selected for.

Motor Proteins

Motor Proteins pull, push, or spin creating mechanical force. Kinesin and Myosin are two examples.

How do proteins bond with other molecules?

Proteins can bind with huge numbers of other molecules through electrostatic interactions and Van der Waals forces. Affinity is the measure of the strength of attraction between molecules.

Quaternary structure

Quaternary Structure is the conformation of a protein comprised of two or more polypeptide chains. The may contribute to large protein complexes. The protein coat of some viruses is an example.

Receptor Proteins

Receptor Proteins bind to specific signal molecules and transmit the information from outside of the cell to inside of the cell.

Signal Proteins

Signal Proteins are proteins when convey information to a cell. These are hormones.

How do proteins fold? What is responsible for the folding and shape of a protein?

Since there is free rotation of the bonds of the alpha carbon and the amino group or carboxyl group, the peptide backbone of a protein is flexible and can bend and turn. Electrostatic interactions between atoms of the protein backbone or R groups are responsible for the protein folding.

What do molecular chaperones accomplish?

Some proteins following translation need assistance adopting their native conformation because they're too complex. Molecular chaperones assist with these foldings by pushing them into their correct shape.

Special Purpose Proteins

Special Purpose Proteins- these are proteins found in different cells or organism that take on unique functions.

How do many proteins composed of many subunits organize themselves?

Spontanously

Storage Proteins

Storage proteins store molecules for future use. Ovalbumin stores amino acids in eggs for the developing organism to build proteins.

Structural Protein

Structural Proteins holds the cell together. They provide mechanical support to cells and tissues. Collagen and elastin are examples.

What is the most important factor that determines a protein's function?

The biological function of a protein is dependent on the molecules it binds with. It's dependent on the shape of the protein. If you change the shape, you change the function.

Primary structure of protein

The primary structure of a protein is the amino acid sequence of a protein. It is represented by the one letter amino acid representation. ASQWTSSCGP as an example. The primary structure determines all other levels of protein structure and is responsible for how a protein folds and the 3 dimensional shape of a protein and also the function of the protein.

Secondary structure of protein

The secondary structure of a protein is the localized folding of the peptide backbone in a polypeptide. It can be an alpha helix, a beta-sheet, or a hairpin turn. Hydrogen bonding is responsible for most secondary structure.

Tertiary structure of protein

The tertiary structure of a protein is the global, 3 dimensional shape of a polypeptide chain. It is comprised of all the secondary structure in that polypeptide chain.

Why are proteins and enzymes regulated?

Their activity is regulated to allow a cell to maintain a state of homeostasis. Saves energy and keeps molecules from building up or over exhausting critical substrates.

Transport Protein

Transport Proteins carry small molecules and ions. They provide channels for hydrophilic molecules to pass across the membrane and to pump molecules across the membrane against their gradient (low to high) using ATP as energy. For example, Serum albumin, found in the bloodstream, carries lipids. Hemoglobin is an example. These proteins move nutrients, gasses, and other molecules in and out of cells and from one specific location to another specific location.