Exam 1 based off lecture and reading

A Brief History of Studies on Plasma Membrane Structure Cell physiologists determined that there must be more to the structure of membranes than simply a lipid bilayer. Surface tensions of membranes were calculated to be much lower than those of pure lipid structures; explained by the presence of protein in the membrane.

Cell physiology there is something more than lipid because people found from function. because of that they found protein because of surface tension and everything does not add up. presence of a protein lowers the surface tension

sickle cell anemia

Changes Glutamic Acid to Valine within the hemoglobin, resulting in some red blood cells assuming an abnormal sickle shape

PrPc vs PrPsc

-PrPc, normal cellular isoform of prion protein has exactly same AA sequence as scrapie isoform PrPSc, but with different conformation -PrPC is monomeric protein soluble in some detergents and cleaved by proteases -PrPSc insoluble, and N-terminus (AA 90-231) highly resistant to protease digestion. Presence linked to initiation of disease

Protein structures

1. Primary 2. Secondary 3. Tertiary 4. Quaternary

Structures of proteins primary, secondary, tertiary, and quaternary.

1: sequence of protein 2: Partial 3: One chain 4: More than one polypeptide chain

The properties of the side chains The backbone of the polypeptide is composed of that part of each amino acid that is common to all of them. The side chain or r group, bonded to the α‐carbon, is highly variable among the 20 building blocks, which gives proteins their diverse structures and activities. The side chains are important in both intramolecular interactions, which determine the structure and activity of the molecule, and intermolecular interactions, which determine the relationship of a polypeptide with other molecules, including other polypeptides.

20 different amino acids They can go randomly 20 different building blocks that they have some distinctive properties.

heterodimer vs. homodimer

A protein homodimer is formed by two identical proteins. A protein heterodimer is formed by two different proteins.

chaperonin

A protein molecule that assists in the proper folding of other proteins.

x-ray crystallography vs NMR spectroscopy

Both used to determine tertiary structure. X-ray crystallography uses a crystal and mathematics to create an image NMR spectroscopy uses radioactive isotopes to create an image

Aβ42 protein

Causes alzheimers from Ab40,

How the peptide bond is formed?

from linking the carboxyl group of one amino acid to the amino group of its neighbor, with the elimination of water.

Chemical bonds stabilize tertiary structure of the protein.

noncovalent

Chemical bonds stabilize quaternary structure of the protein.

noncovalent bond

Amyloid

protein that is produced in abnormally high levels in Alzheimer's patients

Globular proteins are likely found in?

proteins within the cell

Structure is the function

the (tertiary) structure determines the function of the protein.

Plasma membranes of eukaryotic cells: carbohydrate is 2-10% by weight, with 90% glycoproteins and 10% glycolipids. Carbohydrates face outward into the extracellular space, and internal cellular membranes faces away from the cytosol.Glycoproteins have short, branched hydrophilic oligosaccharides (<15 sugars per chain) with extensive variability in composition and structure.

Glycolipid: If you look at it carefully they are in the plasma membrane of eukaryotic cells. Usually carbohydrate is facing outward in the extracellular space.

Protein Folding The unfolding of a protein is termed denaturation, and it can be brought about by detergents, organic solvents, radiation, heat, and compounds such as urea.Ribonuclease molecules that had re‐formed from the unfolded protein were indistinguishable both structurally and functionally from the correctly folded molecules present at the beginning of the experiment. The linear sequence of amino acids contained all of the information required for the formation of the polypeptide's 3D conformation.

Is protein has to be folded. structure is the function in protein How they form this structure. Linear polypeptide-> fold to form 3D structure like origami. Need to fold it to form a shape. Ribonuclease: has simple structure, has some sort of disulfide bond. if unfolded and denatured and then slowly renature it then can sometimes go back to original confirmation.

The other three amino acids or side chains with unique properties Glycine: small R group that makes backbone flexible so it is useful in protein hinges, and size allows 2 protein backbones to closely approach each otherProline: R group forms ring with amino group (imino acid), and is bulky so doesn't fit into orderly secondary structureCysteine: R group has reactive -SH which forms disulfide (-S-S-) bridge with other cysteines often at some distance away in polypeptide backbone

Glycine is symmetric so L form or D form doesn't matter for them Cysteine: They have Sulfhydryl form a another cystine SH that forms a disulfide bridge. which stabilizes the structure: kind of a covalent bond but not really Proline: not very reactive as a ring so its cylclic. Doesnt really fit so it creates a zig-zag. it is linked to create a loop like structure creating a gap, space.

Plasma membrane: The outer boundary of the cell that separates it from the world is a thin, fragile structure about 5 - 10 nm thick.Need an electron microscope to observe.The 2 dark-staining layers in the electron micrographs correspond primarily to the inner & outer polar surfaces of the bilayer.

So electron microscope has this thickness and you can see it. You can see certain structures generated on the monitor.

The concept that proteins penetrate through membranes was derived primarily from the results of freeze‐fracture replication. Tissue is frozen solid and then struck with a knife blade, which often causes a fracture plane between the two leaflets of the lipid bilayer.

So how do we study and look at the integral membrane protein. Usually you do a freeze fracture replication. Freeze to get very cold and then use a razor to cut and crack open to see what is sticking out. You can find which lipid belongs to and can visualize those proteins.

Integral membrane proteins function as receptors that bind ligands, channels or transporters to move ions/solutes across the membrane, or agents that transfer electrons during photosynthesis and respiration. They are amphipathic, having both hydrophilic and hydrophobic portions; the hydrophobic transmembrane domains form van der Waals interactions with the fatty acyl chains of the bilayer. This (hydrophobic domain of integral protein) preserves the permeability barrier of the membrane, since the protein is anchored within the bilayer and has direct contact with surrounding lipid molecules.

So in here for the integral transporters inside they have a hydrophobic transmembrane domain. and they are forming a very strong interaction with a neighboring lipid thats how they form a very tight structure, so they have no problem with the blocking the work as a barrier. because of the protein. it will not lose its original function of the cell membrane.

Carbohydrate projections play an important role in mediating the interactions of a cell with its environment and sorting of proteins to different cellular compartments. Glycolipid carbohydrates of the red blood cell plasma membrane determine whether a person's blood type (A, B, AB, or O). A: Enzyme adds N-acetylgalactosamine to the end of the chain. B: Enzyme adds galactose to the chain terminus. AB: Both enzymes present. O: Lack enzymes capable of attaching either terminal sugar.

So those membrane carbohydrates. this is an example of the glycolipid. Usually they are added to the spingled end. The hydrophilic side has this sugar in here they are very regular structure. the only difference is the one sugar sticking out.

Additional secondary structures include hinges, turns, loops, or finger‐like extensions.Often, these are the most flexible portions of a polypeptide chain and the sites of greatest biological activity. In a ribbon model showing secondary structure, α helices are represented by helical ribbons, β strands as flattened arrows, and connecting segments as thinner strands.

There are other secondary structures: Hinges, loops turns, and finger like structures (hair pin)

The Asymmetry of the Membrane Lipids Compared to the inner leaflet, the outer leaflet has a relatively high concentration of PC (and sphingomyelin) and a low concentration of PE and PS (graph on the right. "The lipid bilayer is composed of two semi-stable, independent monolayers having different physical and chemical properties."

The Asymmetry: of lipid bylayer: inner leaflet and outer leaflet independent layer that can diffuse and move around independently their composition can be different

What is N-terminal and what is C-terminal of the protein?

The N terminus is the amine NH3 group on the end of the alpha carbon The C terminus is the carboxylic acid group on the alpha carbon

nonpolar amino acids Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, ProlineSide chains are hydrophobic and unable to form electrostatic bonds or interact with water. Side chains of this group generally lack oxygen and nitrogen.Vary in size and shape, which allows tight packing into protein core, associating by van der Waals forces and hydrophobic interactions.

They do not have many features in charge, so usually they are water hating (hydrophobic) Cell is acrocentric water loving property Have a tendency to go inside of the structure and then aggregate. Passing through membrane

Myoglobin: The First Globular Protein Whose Tertiary Structure Was Determined Myoglobin contains no disulfide bonds; the tertiary structure is held together by noncovalent interactions. All of the noncovalent bonds thought to occur between side chains within proteins—hydrogen bonds, ionic bonds, and van der Waals forces—have been found. Unlike myoglobin, most globular proteins contain both α helices and β sheets.

They found that something that stabilizes this bond residue on top of hydrogen bond: Ionic bond, Van der waals bond and some hydrophobic interactions is important in forming this structure here

Protein Misfolding Can Have Deadly Consequences Creutzfeld‐Jakob disease (CJD), is a rare, fatal disorder that can be inherited or acquired that attacks the brain, causing a loss of motor coordination and dementia.Eating contaminated beef from cows suffering from "mad cow disease" caused people to acquire CJD.Islanders of Papua, New Guinea contract "kuru," a spongiform encephalopathy, from eating brain tissue of a recently deceased relative.The infectious agent responsible for CJD lacked nucleic acid and instead was composed solely of protein, called a prion.

This type of protein folding can be very important. Renatures: and folds more/overfold/misfold Wires: the large cords get tangled and cant get undone. If not properly folded and goes into bad formation then no solution to make it properly folded and will acculate and will aggrate and the body cell doesnt know how to destroy it. Carleton Gajdusek: genis jonhopkins medical dr and he studies Kuru and found it was coming from protein "prion". from eating the brain of a dead person. in new guinea. Who ate the muscles were fine but those who ate the organs got kuru. Got nobel prize for this. When very misfolded the cell doesnt know how to deal with it.

Transporting solutes:Membrane proteins facilitate the movement of substances between compartments.Responding to external signals: Membrane receptors transduce signals from outside the cell in response to specific ligands.Intracellular interaction: Membranes mediate recognition and interaction between adjacent cells.Energy transduction: Membranes transduce photosynthetic energy, convert chemical energy to ATP, and store energy.

Transporting solutes respond to external signal because they hold receptors intracellular interaction: within in the cell and between the cell. trafficking the materials Energy Transduction: Mitochondrial membrane that causes the production of energy.

The Nature and Importance of the Lipid Bilayer

all the lipids he talked about and looking at them in different cells their composition is different. This is important in determining the biological function of a certain cell or a membrane of a certain cell. that why they all have a different composition of the membrane lipid

Fibrous proteins are likely found in?

collagen and elastin of connective tissues, and keratin of hair and skin, and silk

pyruvate dehydrogenase

converts pyruvate to acetyl-CoA

domain

domains are often identified with a specific function, and the functions of a newly identified protein can usually be predicted by its domains

Lipid-Anchored Membrane Proteins Numerous peripheral membrane proteins have a glycosyl-phosphatidylinositol linkage that embeds them in the outer leaflet of the lipid bilayer, so are called GPI‐anchored proteins. Examples include the normal cellular scrapie protein PrPC, as well as various receptors, enzymes, and cell-adhesion proteins. Another group of proteins is anchored on the cytoplasmic side of the plasma membrane within the inner leaflet of the lipid bilayer by one or more long hydrocarbon chains. Two proteins associated with the plasma membrane in this way (Src and Ras) are implicated in the transformation of a normal cell to a malignant state.

example: Outer leaflet, GPI anchored proteins Examples include: Normal PrPc, receptors, enzyme, cell adhesion molecules. on the cytoplasmic side they can bind to N- termal or C- bind to fatty acid. Src and Ras are the ancagens anchored to the lipid on the cytosine

Primary Structure The intimate relationship between form and function is best illustrated than with proteins. Protein structure can be described at several levels of organization, each emphasizing a different aspect and each dependent on different types of interactions.Four levels are described: primary, secondary, tertiary, and quaternary. Primary structure, concerns the amino acid sequence of a protein, whereas the latter three levels concern the organization of the molecule in space.

AMino acid sequence Based on mRNA sequence which is from DNA AUG...TAG Determines sequence

Dynamic Changes Within Proteins Proteins are not static and inflexible, but capable of internal movements. The X‐ray crystallographic structure of a protein can be considered an average structure, or "ground state." NMR can monitor shifts in hydrogen bonds, waving movements of external side chains, and the full rotation of the aromatic rings of tyrosine and phenylalanine residues. Non-random movements within a protein triggered by binding of a specific molecule are called conformational changes.

Also via dynamic changes within the protein The reason we are making the X-ray crystal is very rigid ground state picture. Something that your eyes on like a portrait on a drivers license. is a representation of shape but doesn't show you every picture you can have. For example you can have many different faces. there is limitations of the Xray with is overcome by the NRM technique From that you can design many different structures. Conformational changesL non random movement within a protein triggered by the binding of a specific molecule. Taking pictures from so many different angels and supper impose it to see which one is in common. The common movements is probably meaningful not only knowing portrait (ground state) if you know the structure of other shape it can be useful to study structure

polar uncharged amino acids serine, threonine, cysteine, asparagine, glutamineIonization reactions of glutamic acid and lysine at physiologic pH show that their side chains are almost always present in the fully charged state. Consequently, they are able to form ionic bonds with other charged species in the cell.Side chains have a partial negative or positive charge and thus can form hydrogen bonds with other molecules including water. These amino acids are often quite reactive. Asparagine and glutamine are amides of aspartic and glutamic acid.

Amide or hydroxyl group. Depending on the condition it could be charged OH neg and NH2 pos not charged all the time but can be reactive amine and can be modified by other enzymes or activity that provides modification or activation.

Protein-Protein Interactions Different proteins can become physically associated to form a much larger multiprotein complex. Once two molecules come into close contact, their interaction is stabilized by noncovalent bonds.The pyruvate dehydrogenase complex consists of 60 polypeptide chains constituting three different enzymes. The product of one enzyme can be channeled directly to the next enzyme in the sequence without becoming diluted in the cell.

An example of the above is the pyruvate dehydrogenase Makes pyruvate into Acetyl-coA 60 polypeptide complex, a, Beta , gama. they coordinate the reaction.

polar charged amino acids aspartic acid, glutamic acid, lysine, arginine, histidineR groups usually fully charged (lysine, arginine, aspartic acid, glutamic acid) at pH 7; side chains are relatively strong organic acids & bases.Can form ionic bonds due to charges; histones with arginine bind to the negatively charged phosphate DNA backbone.Histidine is usually only partially charged at pH 7; often important in enzyme active sites due to its ability gain or lose a proton in physiologic pH ranges

Aspartic Acid and Glutamate have negatively charged Oxygen: Lysine, Arginine, and Histidine all have plus charge amino group so they can have interactions.

Secondary structure Secondary structure describes the conformation of portions of the polypeptide chain. Depending on the amino acid sequence. the backbone of the polypeptide can assume the form of a cylindrical, twisting spiral called the alpha (a) helix. The backbone lies on the inside of the helix and side chains project outward. The helical structure is stabilized by hydrogen bonds between the atoms of one peptide bond and those situated above and below it along the spiral.

Automatically alpha (a) helix & Beta Sheet Secondary is the confirmation of protein of the polypeptide chain: mostly dealing with a portion of the protein. The portion of the protein automatically forms. Mostly dealing with hydrogen bond only. The hydrogen bond is formed in a cylindrical spiral twisting in the back bone of the polypeptide AKA a helix that is right handed The backbone lies on the inside of the helix and side chains that projects outward. Back bone inside and side chain outside. Hydrogen bonds between atoms situated above and below in the spiral Then it looks like it is coming from the backbone in side chain interaction

The Structure of Amino Acids Proteins are unique polymers made of amino acid monomers. Twenty different amino acids, with different chemical properties, are commonly used in the construction of proteins. All amino acids have a carboxyl and an amino group, separated by a single carbon atom, the α‐carbon. In a neutral solution, the α‐carboxyl group loses its proton and is negatively charged, and the α‐amino group accepts a proton and is positively charged.

Basic structure: Want to memorize the basic structure: amino group NH3, Alpha carbon and Carboxyl group. The side chain makes the amino acid different NCC Protien is polymer of amino acid NCC+NCC Has OH bond in middle. This forms a water and creates a covalent bond or peptide bond.

The beta (b) sheet has several segments of a polypeptide lying side by side that form a folded or pleated conformation. Hydrogen bonds are perpendicular to the long axis and project across from one part of the chain to another. Sheets can be arranged either parallel or antiparallel to each other. β strands are extended and resist tensile forces. Silk has an extensive amount of β sheet, and is five times stronger than steel of comparable weight.

Beta sheet also important structure Hydrogen bonds form in perpendicular to the long axis.

Membrane Lipids: Cholesterol Cholesterol is a smaller and less amphipathic lipid that is only found in animals.A sterol that makes up to 50% of animal membrane lipids.The -OH group is oriented toward membrane surface.Carbon rings are flat and rigid; interfere with movement of phospholipid fatty acid tails

Cholesterol is small. OH group is oriented to the membrane surface. give a little bit of the amphipathic. OH group at end is oriented toward the membrane surface. They are short and dont have much flexibility. so the structure is rigid and decreases fluidity which.

Overview of membrane functions: Compartmentalization:Membranes form continuous sheets that enclose intracellular compartments. Scaffold for biochemical activities: Membranes provide a framework that organizes enzymes for effective interaction.Selectively permeable barrier: Membranes allow regulated exchange of substances between compartments.

Compartmentalize: break into chambers Scafold holding the biochemical reaction/ activites Selective barrier

Membrane Lipids: Phosphoglycerides Lipids with a phosphate group are phospholipids. phosphoglycerides. diglycerides; two hydroxyl groups of glycerol are esterified to fatty acids; the third is esterified to a hydrophilic phosphate group." a small hydrophilic group linked to phosphate: choline, ethanolamine, serine or inositol (head).

Consist of Fatty acid, Glycerol, Phosphate, and a polar all organic compound that gives the charges,

Membranes are lipid-protein assemblies held together by noncovalent bonds. The lipid bilayer is a structural backbone and barrier to prevent random movements of materials into and out of the cell. A unique complement of membrane proteins that contributes to the specialized activities of the cell type.Inner MT membrane: high protein contents - ETC.Myelin sheath cells - high lipid contents and thick - high electrical resistance; insulations..

Contents: composition or ratio. They are important because they specialize the activities of the cell type The inner mitochondrial membrane: high proteins contents because of the electron transport chain. The Myelin Sheath cell- high lipid contents very thick. Provides high electrical resistance or insulation.

CJD

Creutzfeldt-Jakob disease (Mad Cow disease)

The structure of Amino acids Amino acids have asymmetric carbon atoms. With the exception of glycine, the α‐carbon of amino acids bonds to four different groups so that each amino acid can exist in either a D or an L form. Amino acids used in the synthesis of a protein on a ribosome are always L‐amino acids.

Each AMino Acid is the Building BLock of protein They have the asymeitry or sort of chiarity ALL AMINO ACIDS IN THE CELL ARE THE L FORM

All amino acids we have in our cell are D forms (True / False).

False they are L Amino acids used in the synthesis of a protein on a ribosome are always L‐amino acids.

β-sheet

Folding pattern found in many proteins in which neighboring regions of the polypeptide chain associate side by side with each other through hydrogen bonds to give a rigid, flattened structure. Hydrogen bonds form in perpendicular to the long axis.

The Asymmetry of the Membrane Lipids Glycolipids : outer leaflet where they act as receptors for ligands. PE (inner) promotes membrane curvaturefor membrane budding and fusion (shorter fatty acid chain). PS (inner) has a negative charge to bind positively charged lysine and arginine residues on adjacent proteins. PS (outer) on aging lymphocytes marks the cells for destruction by macrophages (please eat me!). PI (inner) can be phosphorylated, which converts the lipid into a phosphoinositide for signal transduction pathways.

Glycolipids: always have to be outer leaflet PE: usually in inside and important in curvature of membrane. they have a shorter fatty acid chain. inside is a little bit more curved because inside is shorter. Needed for shapes. PS: (inner) has a negative charge in inner leaflet PS: sometimes outside too. gives the cell ability to ask for help killing it

Problems arise when membrane proteins (1) are present at low numbers per cell, (2) are unstable in the detergent-containing solutions required for their extraction, (3) are prone to aggregation, (4) are heavily glycosylated and cannot be expressed as recombinant proteins in other types of cells.

Hard to study and isolate the protein. Because of their hydrophobic domain they aggregate. Once they do that they become like rock are heavily glycolated and membrane proteins are not very much present in the membrane. So there is some type of limitation that you cannot test in a test tube

Membrane Lipids: Phosphoglycerides Fatty acyl chains are hydrophobic, unbranched hydrocarbons approximately 16 to 22 carbons in length. A fatty acid may be fully saturated, monounsaturated, or polyunsaturated; one unsaturated and one saturated fatty acyl chain. With fatty acid chains at one end; a polar head group at the other end, all of the phosphoglycerides exhibit a distinct amphipathic character.

Has one fatty acid saturated, and the other one is either monounsaturated or polyunsaturated That is all contributing to this nature. The hydrocarbon the # of fatty acid is 16-22 carbons in length. always a even number.

The Structure of Hemoglobin HemoglobinThe best‐studied multisubunit protein is hemoglobin, the O2‐carrying protein of red blood cells. Hemoglobin consists of two α‐globin and two β‐globin polypeptides, each of which binds a single molecule of oxygen. Binding of oxygen causes a bound iron atom to move closer to a heme group, which leads to increasingly larger movements within and between subunits. This revealed that the complex functions of proteins may be carried out by means of small changes in their conformation.

Hemoglobin is composed of 2 alpha and 2 beta chain Each chain has the ability to bind to oxygen. How they can saturate the binding site in the heme and how it works is one oxygen binds and causes conformational changes and then it allows for more. cooperation: one binds, next molecule easier, and easier on next. This cooperation is controlled by quanterary action polypeptide chain

Studying the Structure and Properties of Integral Membrane Proteins Hydrophobic transmembrane domains make integral membrane proteins difficult to isolate in a soluble form. Their isolation from membranes requires detergents like ionic SDS, which denatures proteins, or nonionic Triton X-100, doesn't alter a protein's tertiary structure.Detergents are amphipathic and can substitute for phospholipids in stabilizing and solubilizing integral proteins. After purification, the protein's amino acid composition, molecular mass, and amino acid sequence can be determined.

How do we study the membrane protein? Usually detergents. Can isolate the membranes. SDS or tritor X 100 and can soap out the lipid from there and isolate the proteins

The Nature and Importance of the Lipid Bilayer The entire lipid bilayer is only about 60 Å (6 nm) thick. membranes are always continuous, unbroken structures. Membranes inter-connect networks within the cell. However, lipid bilayers are flexible, so membranes are deformable and their shape can change, as occurs during locomotion or cell division.

How the lipid composition of the membrane effects the property of the lipid bylayer. it is 6nm thick. and alway continuous and unbroken structures this membrane connects the network in the cell has to be flexible and deformable to change shapes during locomotion of the cell.

The properties of side chains The ionic, polar, or nonpolar character of side chains is very important in protein structure and function. Soluble proteins generally have polar residues at their surface to interact with water. Non-polar residues are found in the core tightly packed together, where water is excluded. Hydrophobic interactions are a driving force during protein folding and contribute substantially to the overall stability of the protein

Hydrophobic and hydrophilic side change Polar charged and polar uncharged are hydrophilic Nonpolar Hydrophobic Inside nonpolar and outside polar which gives stability.

Protein does its job Proteins are macromolecules that carry out a cell's activities. Enzymes accelerate reactions; structural proteins provide mechanical support; hormones have a regulatory functions; receptors determine what a cell reacts to; contractile filaments and molecular motors provide biological movements. Proteins have shapes and surfaces that allow them to interact selectively with other molecules, so they exhibit a high degree of specificity.

If we know the central dogma: Is DNA To RNA To Protein Protein is the one that really does the job Cellular function comes from protein How the protein does in the cell is the major copy of the class Also: Breifly summarize: Protein is where the structure and function comes from forming many shapes having regulatory functions Can be receptor and generates movements in muscles This function is coming from a selective interaction: specificity Protein to protein interaction. Not just any protein is binding to any protein. Has special pairs.

Dynamics of Protein Folding A transient structure during folding resembles the native protein but lacks many of the specific interactions between amino acid side chains.If a protein is closely related at the primary sequence level with another protein whose tertiary structure is known, then one can predict the tertiary structure of the unknown protein.Aligning the amino acids of the unknown protein onto the corresponding amino acids in the protein whose structure is known is called threading.

In principle the primary structure has the 3D folding information. with only that information it is hard to make because it has to be in optimal conditions. pH, temperature, determines and effects so many different possibilities.

Disulfide bridges A strong covalent bond formed when the sulfur of one cysteine monomer bonds to the sulfur of another cysteine monomer.often form between two cysteines that are distant from one another in the polypeptide backbone or even in two separate polypeptides.Disulfide bridges help stabilize the shapes of proteins. When someone gets a "perm" to make their hair curlier, a reducing agent breaks the disulfide bridges, letting the keratin filaments slide past each other. When the reducing agent is washed out, disulfide bridges re‐form, locking the keratin in the new positions.

In the case of a cysteine: forms the S-S You can change the structure by cutting the bridge and renature the protein If denatured the bridge you can move it to for another bridge on the structure. just like a perm. Reshaping the hair. The chemical they use for this purpose is called "cystine"

Tertiary Structure of proteins Describes the conformation of the entire polypeptide. Secondary structure is stabilized by hydrogen bonds, while tertiary structure is stabilized by noncovalent bonds between the side chains of the protein. Secondary structure is limited to a small number of conformations, but tertiary structure is virtually unlimited.The detailed tertiary structure of a protein is usually determined using the technique of X‐ray crystallography.

Is the noncovalent bond is stabilizing this structure Wether the structure is linear or globular So it will have primary or secondary on top of that what other structure is needed to stabilize entire polypeptide chain So, X-Ray Crystallography used to determine what type of tertiary structure proteins have. The diffraction pattern shown allows to see structure.

Lipid-anchored membrane proteins are distinguished both by the types of lipid anchor and their orientation.Glycophosphatidylinositol (GPI)-linked proteins found on the outer leaflet can be released by inositol-specific phospholipases.Some inner-leaflet proteins are anchored to membrane lipids by long hydrocarbon chains.

Lipid-anchored membrane proteins: that is somehow tethered to membrane head. (GPI)-linked: Mostly on the outside/ outer leaflet, on inner leaflet: you can have similar tethering. but not the GPI. Usually covanlent link or something like that is binding to this long hydrocarbon chain. Those integral membranes and why they are important is that those hydrophilic and hydrophobic trans helix domain is forming a very tight interaction. with the lipid. which is van der waal force and also the hydrophobic interaction. The lipid and the protein has a interaction which forms the permeability barriers.

Membrane lipids are amphipathic with three main types: Phosphoglycerides are diacylglycerides with small functional head groups linked to the glycerol backbone by phosphate ester bonds.Sphingolipids are ceramides formed by the attachment of sphingosine to fatty acids.Cholesterol is a smaller and less amphipathic lipid that is only found in animals.

Membranes are AMPHIPATHIC: both hydrophilic and hydrophobic parts 1. Phosphoglycerides: diacylglycerides , small functional head groups , phosphate ester bonds 2. Sphingolipids: Ceramides. They do have phosphate on hydrophyllic side. 3. Cholesterol: small not as amphipathic but is a major component.

Quaternary Structure of Proteins Most proteins have more than one chain, or subunit, linked by covalent disulfide bondsor held together by noncovalent bonds.Proteins composed of subunits are said to have quaternary structure. A protein composed of two identical subunits is described as a homodimer, whereas a protein composed of two nonidentical subunits is a heterodimer.

More than one chain noncovalent bond Covalent disulfide bond (cystine) Homodimer: two identical subunits Heterodimer: Two nonidentical subunits Dimer: structure

Chemical bond stabilizes secondary structure of the protein.

Mostly dealing with hydrogen bond only

Primary Structure The primary structure of a polypeptide is the linear sequence of amino acids that constitute the chain. PEPTIDE BOND stabilizes The degree to which changes in the primary sequence are tolerated depends on the degree to which the shape of the protein or the critical functional residues are disturbed.Sickle cell anemia results solely from a single change (glutamic acid to valine) in amino acid sequence within the hemoglobin molecule.

Mostly the important chemical bonds: peptide bond. If changes in the primary sequence/structure. Protein deletion or replacement Depends on if it can tolerated. Depends of where it happends Not every kind of proteins can tolerate it. One change can sometimes not be bad, but sometimes one change can be drastic Can kill entire animal or function example is sickle cell anemia: Changes Glutamic Acid to Valine within the hemoglobin Glutamic acid is polar charged and Valine is nonpolar. Due to the polarity the red blood cell changes the structure,

Dynamics of Protein Folding Protein folding could arise by secondary structure formation followed by subsequent folding driven by hydrophobic interactions. Alternatively, initial hydrophobic collapse to form a compact structure in which the backbone adopts a native‐like shape, could be followed by secondary structure development. Most proteins probably fold by a middle‐of‐the‐road scheme in which secondary structure formation and compaction occur simultaneously.

Not simple process. Has to be folded very complex. Folding is driven by hydrophobic interactions. aggregate going inside the structure then came from other structures. All the modeling is very descriptive and saying in a very complex way. Not a one time event. just like origami: some instruction follow through and mess up and unfold and retry. and fold and try again.

Membrane proteins attach to the bilayer asymmetrically, giving the membrane a distinct "sidedness"Three classes:Integral proteins:Penetrate and pass through lipid bilayer; make up 25 -30% of all encoded proteins and 60% of current drug targets.Amphipathic-hydrophobic domains anchorthem in the bilayer and hydrophilic regions form functional domains outside of the bilayer.Channel proteins have hydrophilic cores that form aqueous channels in the membrane-spanning region.

Okay so membrane the protein is very important part of the equation. It is important for this Asymmetry or the distinct "sidedness" So there are 3 classes Integral proteins: They are penetrating. through the membrane they look like spirals. They have a hydrophilic residue in the middle and then they are anchored to the bilayer And the hydrophilic side is sticking out Usually they are the receptor like this or they are a channel. Then they are alpha helix like this and the penetrating hydrophobic side can be a beta sheet.

residue (amino acid)

Once incorporated into a polypeptide chain, amino acids the amino acids are residues

Protein Misfolding Can Have Deadly Consequences The prion protein is encoded by a gene within the cell's own chromosomes. In normal brain tissue PrpC (prion protein cellular) is made, while in CJD patients PrpSc (prion protein scrapie) is present.PrpC is soluble and is destroyed by protein‐digesting enzymes, while PrpSc forms insoluble fibrils and is resistant to digestion. Structures are different: PrpC is mainly α‐helical and PrpSc is largely β sheet.PrpSc can bind to PrpC) and cause it to fold into the abnormal form.

PRPC in normal While in CJD patients it becomes PrpSc and cannot form anything. and start to destroy other proteins. Forms insoluble fibers that then destroy other tissues So in this case, they are misfolded. because of that the cell does not know how to destroy it. it is accumulated and brain destroys the tissue.

Peripheral proteins: Attached to the membrane by weak bonds and are easily solubilized.Located entirely outside of bilayer on either the extracellular or cytoplasmic side; associated with membrane surface by non-covalent bonds.

Peripheral proteins: Not really attached to the membrane strongly Usually non-covalent bond. Enzyme or something essential for membrane functions

Properties of Side Chains Ionization reactions of glutamic acid and lysine AT A PHYSIOLOGIC PH show that their side chains are almost always present in the fully charged state "Consequently, (+ to -) side chains are able to form ionic bonds with other charged species in the cell"

Physiologic pH: 7.0 -7.2-4 the + and - side chains interact and maintain charges.

List polar charged amino acids.

Polar Charged Aspartic Acid: D Glutamic Acid: E Lysine: K Arginine: R Histidine: H

I want you to memorize one letter code for amino acids.

Polar Charged Aspartic Acid: D Glutamic Acid: E Lysine: K Arginine: R Histidine: H Polar Uncharged Serine: S Threonine: T Glutamine: Q Asparagine:N Tyrosine:Y Nonpolar: Alanine: A Valine: V Leucine: L Isoleucine: I Methionine: M Phenylalanine: F Tryptophan: W Unique featured Glycine: G Cysteine: C Proline: P

Know One letter Codes

Polar Charged Aspartic Acid: D Glutamic Acid: E Lysine: K Arginine: R Histidine: H Polar Uncharged Serine: S Threonine: T Glutamine: Q Asparagine:N Tyrosine:Y Nonpolar: Alanine: A Valine: V Leucine: L Isoleucine: I Methionine: M Phenylalanine: F Tryptophan: W Unique featured Glycine: G Cysteine: C Proline: P

List polar non-charged amino acids.

Polar Uncharged Serine: S Threonine: T Glutamine: Q Asparagine:N Tyrosine:Y

During protein synthesis, an amino acid is joined to two other amino acids, forming a long polymer called a polypeptide chain. Amino acids are joined by peptide bonds from linking the carboxyl group of one amino acid to the amino group of its neighbor, with the elimination of water. Once incorporated into a polypeptide chain, amino acids are termed residues. The N‐terminus contains an amino acid with a free α‐amino group, ad the residue at the opposite end, the C‐terminus, has a free α‐carboxyl group.

Protein is a poly peptide so it can go on and on Protein can go from 10-20 or to 10000 NCCNCCNCCNCCNCC | R1 Once incorporated into a polypeptide chain, amino acids the amino acids are residues.

chaperones

Proteins that assist in protein folding during posttranslational processing

The Role of Molecular Chaperones Not all proteins can assume their final tertiary structure by self‐assembly. Proteins undergoing folding have to be prevented from interacting non-selectively with other molecules in the crowded compartments of the cell. "Helper proteins", or molecular chaperones, bind to short stretches of hydrophobic amino acids to help unfolded proteins achieve their proper 3D conformation.

SO, usually what they do they use a other protein. Cofactors chaperone proteins. HSP70 is a chaperone protein and then because the heat will mess up folding. that protein comes in and hold structures to preventing then making a random fold. or sometimes it will go through some of the chaperone structure and help fold it.

Tertiary Structure May Reveal Unexpected Similarities in Proteins Similarity in primary sequence is often used to decide whether two proteins may have similar structure and function. Sometimes proteins unrelated at the primary sequence level have similar tertiary structures. Interactions and enzymatic activity of a protein are deduced from the tertiary structure. Actin (eukaryotic) and MreB (prokaryotic) show no similarity at the primary level but do at the tertiary level

So why this structure matters?> The 3D is the final conclusion about the protein research. you crystalize and get structure and see detail of all the corners and edges and getting fine picture of the protein and what it looks like. need to see shape. The structure is strongly related to the function Bacterial protein MreB is isolated and crystalized it looked like actin. The primary structure is not really identical. But once they took the image they look the same and therefore their function is similar. Analogy used many times: 3d printer, you can design a handgun. you load the gun and pull trigger and works. Gun does have to be made of metal can be made of different materials. If it works, it works no matter what material it is made out of.

For many years it was presumed that all proteins had a fixed 3D structure, which gave each protein its unique properties and specific functions; however many proteins have regions that lack a defined shape like the PrP protein. Disordered segments are enriched in charged/polar residues and deficient in hydrophobic residues, and can undergo a physical transformation after binding to an appropriate partner and assume a defined, folded structure.Most proteins are categorized by shape as either fibrous proteins, which are elongated, or globular proteins, which are compact. Extracellular materials are fibrous proteins, like collagen and elastin of connective tissues, and keratin of hair and skin, and silk. In contrast, most proteins within the cell are globular proteins.

Some of the structures are very hard to find. Doesn't make crystals or lacks hydrophobic structure. So basically categorize into two proteins Fibrous proteins: elongated Globular proteins: Which are compact See globular very well and fibrous are not favored

Protein Domains Most eukaryotic proteins have two or more spatially distinct modules, or domains, that fold independently. The different domains often represent parts that function semi‐independently. Protein domains are often identified with a specific function, and the functions of a newly identified protein can usually be predicted by its domains.Shuffling of domains during evolution creates proteins with unique combinations of activities.

Sometimes the functions: where it is coming from there is a unit there or protein domain can be independently crystalized can assign protein domain with specific function. So the function of a newly identified protein can be predicted by its domain. If you know the function of each domain and then you will know the protein function.

Membrane Lipids: Sphingolipids (I will leave this to students) Sphingolipids are derivatives of sphingosine, an amino alcoholthat contains a long hydrocarbon chain. Sphingolipids consist of sphingosine linked to a fatty acid by its amino group, called a ceramide. If the substitution is phosphorylcholine, the molecule is sphingomyelin. If the substitution is a carbohydrate, the molecule is a glycolipid. 'If the carbohydrate is a simple sugar, the glycolipid is a cerebroside; if it is a small cluster of sugars that includes sialic acid, the glycolipid is a ganglioside.'

Sphingolipids structure wise: unique. They do not have glyceral backbone here but have spingosine backbone it is an amino alcohol NH3 OH can add one more branch of amino acids aka cerimide, Ceremide sometimes add myelin Also glycolypid adding a sugar in this case there is N-phosphorous. it is a cerebroside.

Tertiary Structure of proteins Tertiary structure can also be determined by nuclear magnetic resonance (NMR) spectroscopy, which uses a magnetic field to probe proteins with radio waves to determine distances between atoms. X‐ray crystallography provides higher resolution structures for larger proteins but is limited by the ability to get any given protein to form pure crystals. NMR does not require crystallization, provides information about dynamic changes in structure, and can rapidly reveal drug binding sites, but is difficult to use on larger proteins

Tertiary Structure is not only X-ray Cryptography, one of the draw back of the X-Ray cryptography is that is is really hard to get a crystal So sometimes people spend a long time to make the crystal You can use NMR to see it. You need to lable all the backbone atoms with different radio active isotope to run NMR Not only determine the structure but also see the dynamics

Myoglobin: The First Globular Protein Whose Tertiary Structure Was Determined The first glimpse at the tertiary structure of a globular protein was myoglobin.Myoglobin functions in muscle tissue as a storage site for oxygen, bound to an iron atom in the center of a heme group. Approximately 75 percent of the 153 amino acids in the polypeptide chain are in the α‐helical conformation, and no β sheet was found.

The first globular protein that the tertiary structure was determined was myoglobin Small enough and has simple structure. Mostly a helix and no Beta sheet and some of the loops. Has the inorganic compound inserted in there. a hydrogen bond and peptide bond is really important for its primary and secondary structure. No disulfide bridge

Peripheral Membrane Proteins Peripheral proteins associate with the membrane by weak electrostatic bonds,and can usually be solubilized by extraction with high-concentration salt solutions. The best studied are located on the cytosolic surface of the plasma membrane,where they form a fibrillar network that acts as a membrane "skeleton" to provide mechanical support to the membrane and to function as an anchor for integral membrane proteins. Other cytosolic peripheral proteins act as enzymes, specialized coats, or factors that transmit transmembrane signals.

The function of the Peripheral Membrane. the Peripheral Membrane proteins have a very weak electrostatic bond. they bind to a cytosolic surface of a plasma membrane and then they become a skeleton. forming a fiber network and then hold very tightly bound to the membrane surface. important in the formation of certain structures. some times cell membrane itself has to form rigid structure and they have to have this kind of peripheral membrane Those peripheral membrane proteins can be an enzyme, a specialized coat, or factors that transmit transmembrane signals

The Role of Molecular Chaperones Chaperones of the Hsp70 family bind to polypeptides as they emerge from the ribosome and prevent them from binding to other proteins in the cytosol. Proteins can be released by the chaperones to spontaneously fold into their native state, or repeatedly bound and released until they are fully folded. Larger polypeptides are transferred to a different type of chaperone called a chaperonin, acylindrical protein complex that provides a folding environment.TRiC is a chaperonin thought to assist in the folding of up to 15 percent of the polypeptides synthesized in mammalian cells.

The large polypeptides sometimes transfers to a chaperonin: cylinder cone protein complex that provides a proper folding environment and then ejects it.

Protein Misfolding Can Have Deadly Consequences Alzheimer's disease (AD) is a common disorder that strikes as many as 10 percent of individuals who are at least 65 years old. AD patients exhibit memory loss, confusion, and loss of reasoning ability. The brain of a person with AD contains fibrillar deposits of an insoluble material referred to as amyloid.The fibrillar deposits result from the self‐association of a polypeptide composed predominantly of β sheet.

The misfolded protein causes more misfolded proteins and causes this disease. It is 10% had it in over 65. the insoluble material is caused amyloid. is is folded out in the beta sheet and it is

posttranslational modifications (PTMs) Amino acids found in proteins can be altered after their incorporation into a polypeptide chainThe most widespread and important PTM is the reversible addition of a phosphate group to a serine, threonine, or tyrosine residue. Lysine acetylation is another important PTM affecting thousands of proteins in a mammalian cell. PTMs can modify a protein's 3D structure, level of activity, localization within the cell, life span, and/or its interactions with other molecules.

With this type of amino acid and not only adding on sequence based on the instruction from RNA or something But they also modify groups adding modifications to the side chains So Serine, Threonine, or Tyrosine: adding a phosphate group (phosphorylation) Activation to the cell Lysine Acetylation: Histones. adding to lysine NH3 Keytone added and can switch to acekyle group so they can change structures: Activation Really modifies the 3D structure and because of that makes activity stronger, weaker, or move cells. All sorts of things possible by PTM

α-helix,

a delicate coil held together by hydrogen bonding between every fourth amino acid

γ-secretase

causes AB42 overproduction from a mutation in a gene encoding for this

Chemical bond stabilizes primary structure of the protein.

chemical bonds: peptide bond.

Protein Misfolding Can Have Deadly Consequences The amyloid hypothesis contends that the disease is caused by the production of the amyloid /b-peptide (A/b), part of the amyloid precursor protein (APP). Aβ is released after cleavage by β‐secretase and γ‐secretase into a predominant (Aβ40) or minor (Aβ40) species. Aβ42 tends to refold into a conformation that contains considerable β sheet, and can self‐associate to form small complexes.

the precoursor protein is cut off by the exzyme it produces a segment: Ab40 species and the 42 is the problem aggrating and destroys the tissue area.

A Brief History of Studies on Plasma Membrane Structure Protein is present in the form of individual protein molecules and protein complexes that penetrate a fluid lipid bilayer and extend out into the surrounding aqueous environment. Due to lipid bilayer fluidity, membranes are dynamic structures in which the components are mobile and capable of coming together for transient interactions.

this is about the more focused on membrane proteins. How it is involved in the membrane: it is penetrating the lipid bylayer and sometimes sticks out. they can be embedded or attached or pentrating. So if they are not inside of the structure they they are fluidic and can move around so they contribute to fluidity and reduce it. but the membrane lipid is mostly fluidic.

Protein Misfolding Can Have Deadly Consequences Aβ42 overproduction can be caused by duplication of the APP gene, mutations in the APP gene, or mutations in genes (PSEN1/PSEN2) encoding for γ‐secretase. Strategies of new drugs for the prevention and/or reversal of mental decline:(1)Prevent the initial formation of the Aβ42 peptide; (2)Remove the Aβ42 peptide (or amyloid deposits) once it has been formed;(3)Prevent interaction between Aβ molecules to eliminate formation of both oligomers and fibrillar aggregates.

try to prevent this 42 or remove the peptide or preventing it from aggregate. Vaccines to take care of this. hard to make drugs against it. it delays the onset of the alzheimers. only 6 months. if someone takes this then it can only expand about 6 months.