Cell Bio Chapter 4 Protein Structure and Function

Enzymes

catalyze covalent bond breakage or formation (highly variable)

Structural proteins

provide mechanical support to cells and tissues (ex: collagen, elastin)

Transport proteins

carry small molecules or ions (ex: albumin, hemoglobin)

Storage proteins

store amino acids and ions (ex: ferritin, ovalbumin)

Signal proteins

carry extracellular signals from cell to cell (ex: insulin, growth factors)

Receptor proteins

detect signal (ex: rhodopsin, insulin receptor)

Transcriptional regulators

bind to DNA to switch genes or off (ex: a huge variety of transcription factors and epigenetic regulators)

Special purpose proteins

highly variable (from preventing blood from freezing to glue proteins in marine organisms that attach them firmly to rocks)

Types of noncovalent bonds that help proteins fold

electrostatic attractions, van der Waals attraction, hydrogen bonds, and hydrophobic forces

On the surface

polar amino acid side chains are displayed ____

Buried on the inside

nonpolar amino acid side chains are ____ to form a tightly packed hydrophobic core

Chaperone proteins

special proteins that aid in protein folding in cells by binding to newly synthesized/ partially folded protein chains and help them fold in an energetically favorable way; requires ATP

Chaperonin barrels

provide an enclosed chamber in which a newly synthesized poly peptide chain can fold without the risk of aggregating; requires ATP to associate and disassociate the closing of this chamber

Alpha helix

folding pattern, common in many proteins, in which a single polypeptide chain twists around itself to form a rigid cylinder stabilized by hydrogen bonds between every fourth amino acid

Beta sheet

folding pattern found in many proteins in which neighboring regions of the polypeptide chain associate with each other through hydrogen bonds to give a rigid, flattened structure; can be parallel or antiparallel

How do membrane bound proteins cross the lipid bilayer?

they cross in the shape of an alpha helix with the hydrophobic side chains on the exterior and hydrophilic parts of the polypeptide on the interior

Amyloid structure

structure formed by beta sheets where the beta sheets are stacked together in long rows with their amino acid size chains interdigitated like the teeth of a zipper

Amyloid structure function

structure adopted by hormones to allow for efficient packaging of peptide or protein hormones

Parkinson’s disease

can occur due to insoluble aggregates of alpha synuclein which kills nerve cells in brain regions that regulate movement

Prions

misfolded proteins that are infectious that can cause diseases such as Alzheimer’s, Parkinson’s Huntington's disease, mad cow disease, and creutzfeldt Jakob disease; can spread by eating the infected

Protein domains

segment of a polypeptide chain that can fold into a compact stable structure and that often carries out a specific function

Protein families

a group of polypeptides that share a similar amino acid sequence or three dimensional structure, reflecting a common evolutionary origin; individual members often have related but distinct functions such as kinases that phosphorylate different target proteins ex. Serine proteases

Hemoglobin

example of a protein containing multiple polypeptide chain subunits including 2 alpha globulin and 2 beta globulin subunits that each bind a heme molecule containing oxygen

Identical proteins

form complex structures such as dimers, filaments, sheets, or spheres

Dimer

formed from two identical protein subunits with just one binding site

Filament

formed from identical protein subunits with two different binding sites to form this long helical structure (ex. actin filament)

Closed ring

formed from identical proteins that have binding side positioned appropriately in relation to each other]

Tubulin

protein subunits that form hollow microtubules

Intermediate filament proteins

made from 70 different human genes and consists of keratins, lamins etc.

Capsid

spherical shell that encloses a viral genome made from virus proteins

Collagen

a molecule that is a triple helix formed by three extended protein chains that wrap around one another that is the most abundant fibrous extracellular protein

Elastin

fibrous protein formed from loose and unstructured polypeptide chains that are covalently cross linked into a rubberlike elastic meshwork that enable skin and other tissues to stretch and recoil without tearing

Disulfide bonds

covalent cross link formed between the sulfhydryl groups on two cysteine side chains; often used to reinforce a secreted protein’s structure or to join two different proteins together

Ligand

general term for a small molecule that binds to a specific site on a macromolecule; must fit precisely into a protein’s binding site to form noncovalent interactions with the protein

Binding site

region on the surface of a protein, typically a cavity or groove, that interacts with another molecule (a ligand) through the formation of multiple noncovalent bonds; allows proteins to interact with specific ligands

Antibodies

protein produced by B lymphocytes in response to a foreign molecule or invading organism; binds to the foreign molecule or cell extremely tightly thereby inactivating it or marking it for destruction

Antibody structure

composed of two identical heavy chains and two light chains (the v part of the Y structure); antibodies bind to the light chain’s variable domain

Hydrolase

General term for enzymes that catalyze a hydrolytic cleavage reaction

Nuclease

Breaks down nucleic acids by hydrolyzing bonds between nucleotides

Protease

Breaks down proteins by hydrolyzing peptide bonds between amino acids

Ligase

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

Isomerase

Catalyzes the rearrangement of bonds within a single molecule

Polymerase

Catalyzes polymerization reactions such as the synthesis of DNA and RNA

Kinase

Catalyzes the addition of phosphate groups to 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

Oxidoreductase

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 oxidases, reductases, or dehydrogenases

ATP ase

hydrolyzes ATP. Many proteins have an energy

Michaelis constant, KM

the concentration of substrate at which an enzyme works at half its maximum velocity; serves as a measure of how tightly the substrate is bound

Vmax

the maximum rate of an enzymatic reaction, reached when the active sites of all of the enzyme molecules in a sample are fully occupied by substrate; not changed in presence of competitive inhibitor as y intercept is identical for both curves on a double reciprocal plot

Competitive inhibitor

directly blocks substrate binding to an enzyme; can be overcome by increasing the substrate concentration

Lysozyme

enzyme that severs the polysaccharide chains that form the cell walls of bacteria; found in many secretions including saliva and tears; where it serves as an antibiotic.

Enzymes can encourage a reaction by ____

holding reaction substrates together in a precise alignment, rearranging the distribution of charge in a reaction intermediate, or altering bond angles in the substrate to increase the rate of a particular reaction

Tightly bound small molecules

required by some proteins to function. Some examples are retinal for rhodopsin and heme for hemoglobin

Feedback inhibition

a form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway.

Protein phosphorylation

the covalent addition of a phosphate group to a side chain of a protein, catalyzed by a protein kinase; serves as a form of regulation that usually alters the activity or properties of the target protein

Protein kinase

enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein

Protein phosphatase

enzyme that catalyzes the removal of a phosphate group from a protein, often with high specificity for the phosphorylated site

GTP binding protein

intracellular signaling protein whose activity is determined by its association with either GTP or GDP; includes both trimeric G proteins and monomeric GTPases, such as Ras; function as molecular switches

GTP cycle

GTP binds to GTP binding protein activates, hydrolysis of GTP to GDP + phosphate inactivates, GDP dissociation, repeat

GTP binding

activates GTP molecule

GTP hydrolysis

inactivates GTP molecule by turning GTP into GDP and phosphate

GDP dissociation

the release of GDP from GTP binding molecule required for GTP to bind and reactivate the cycle

Motor proteins

protein such as myosin or kinesin that uses energy derived from the hydrolysis of a tightly bound ATP molecule to propel itself along a protein filament or other polymeric molecule; generate movements in cells and tissues

Three motor protein conformations

ATP binding, ATP hydrolysis, release of ADP and products; irreversible process that causes the protein to move to the right along the filament

Scaffold protein

protein with multiple binding site for other macromolecules, holding them in a way that speeds up their functional interactions

Biomolecular condensate

a large aggregate of phase separated macromolecules that creates a region with a special biochemistry without the use of an encapsulating membrane

Phase separation

interaction created as a result of weak interactions (hydrogen bond, hydrophobic interactions, and electrostatic interactions) that allows molecules to come and go while the condensate remains intact and separated from its surroundings