Bio 160 Chapter 3.1 - 3.4

condensation reaction

(aka dehydration) A chemical reaction in which two molecules are joined covalently with the removal of an -OH from one and an -H from another to form water. In biology, most condensation reactions involve the joining of monomers into polymers. Compare with hydrolysis.

What 3 questions do you ask in order to determine what type of R-group an amino acid has?

1. Does the R-group have a negative charge? If so, it is acidic and will lose a proton, like aspartate. 2.Does the R-group have a positive charge? If so, it is basic and will pick up a proton, like lysine. 3. If the R-group is uncharged, does it have an oxygen atom? If so, then the highly electronegative oxygen will form a polar covalent bond in the R-group, thus making it uncharged polar like serine If the R-group in your amino acid does not have a negative charge, a positive charge, or an oxygen atom, then you are looking at a nonpolar amino acid, such as methionine.

why are enzymes good catalysts

1. Enzymes bring substrates together in a precise orientation that makes a reaction more likely to occur (lock-and-key) 2. Enzymes are specific for one reaction

There are three key points to note about the peptide-bonded backbone:

1. R-group orientation: The side chains of each residue extend out from the backbone, making it possible for them to interact with each other and with water. 2. Directionality: There is an amino group (-NH3+) on one end of the backbone and a carboxyl group (-COO-) on the other. The end of the residue sequence that has the free amino group is called the N-terminus, or amino-terminus, and the end with the free carboxyl group is called the C-terminus, or carboxy-terminus. By convention, biologists always write amino acid residue sequences from the N-terminus to the C-terminus, because the N-terminus is the start of the chain when proteins are synthesized in cells. 3. Flexibility: Although the peptide bond itself cannot rotate because of its double-bond nature, the single bonds on either side of the peptide bond can rotate. As a result, the structure as a whole is flexible

What are the proposed ways in which amino acids could have polymerized in the chemical evolution?

1. Researchers have been able to synthesize stable polymers by mixing free amino acids with sources of chemical energy and tiny minerals (which prevent hydrolysis) 2. Amino acids polymerize in the hot, metal-rich environment of undersea volcanoes 3. Amino acids polymerize in cool water with energy rich carbon and sulfur containing gas, similar to that emitted by undersea volcanoes

Amino acid R-groups can be grouped into three general types:

1. charged, including acidic and basic 2. uncharged polar 3. nonpolar

5 types of interactions involving R-groups that help create tertiary structure

1. hydrogen bonding 2. hydrophobic interactions 3. van der Waals interactions 4. Covalent bonding 5. ionic bonding

oligopeptide

A chain composed of fewer than 50 amino acid residues linked together by peptide bonds. Often referred to simply as peptide.

hydrolysis reaction

A chemical reaction in which a molecule is split into smaller molecules by reacting with water. In biology, most hydrolysis reactions involve the splitting of polymers into monomers. It breaks polymers apart by adding a water molecule. The water molecule reacts with the bond linking the monomers, separating one monomer from the polymer chain.

disulfide bonds

A covalent bond between two sulfur atoms, typically in the side chains of certain amino acids (e.g., cysteine). Often contributes to tertiary and quaternary levels of protein structure. frequently referred to as bridges, because they create strong links between distinct regions of the same polypeptide or two separate polypeptides.

protein

A macromolecule consisting of one or more polypeptide chains composed of 50 or more amino acids linked together. Each protein has a unique sequence of amino acids and generally possesses a characteristic three-dimensional shape. Any chain of amino acid residues Complete, often functional form of the molecule

molecular chaperones

A protein that facilitates the folding or refolding of a protein into its correct three-dimensional shape *a heat-shock protein *produced in large quantities after cells experience denaturing effects due to high temperature *recognize unfolded proteins by binding to hydrophobic patches that are not normally exposed when the proteins are folded properly. This interaction prevents the unfolded proteins from clumping together, allowing them to fold into the shape specified by their primary sequence. In this way, chaperones help fold new proteins, and in some cases denatured proteins, before these unfolded aggregates can form.

substrates

A reactant that interacts with a catalyst, such as an enzyme or ribozyme, in a chemical reaction

alpha-helix

A secondary structure in proteins formed when the polypeptide backbone coils into a spiral shape stabilized by hydrogen bonding. H-bonds form between residues that are just four linear positions apart

beta-pleated sheet

A secondary structure in proteins formed when the polypeptide backbone folds into a sheetlike shape stabilized by hydrogen bonding. ( segments of a peptide chain bend 180° and then fold in the same plane ) he distance between residues that form a β-pleated sheet may be larger because folds in the chain can bring them close enough to bond in three-dimensional space

amino acids

A small organic molecule with a central carbon atom bonded to an amino group (-NH3), a carboxyl group (-COOH), a hydrogen atom, and a side chain. When amino acids are linked together to form proteins, they are referred to as residues.

van der Waals interactions

A weak electrical attraction between two nonpolar molecules that have been brought together through hydrophobic interactions. Often contributes to tertiary and quaternary structures in proteins

catalysis

Acceleration of the rate of a chemical reaction due to a decrease in the free energy of the transition state, called the activation energy.

What is the "normal shape" of a protein? Is only one shape possible for each protein, or could there be several different folded shapes?

Although each protein has a characteristic folded shape that is necessary for its function, most proteins maintain a flexible and dynamic shape when they are not actively performing that function. Exist in an assortment of shapes until they are prompted to adopt a single folded and functional form, when they interact with particular ions/molecules, or are chemically modified.

prions

An infectious particle that consists entirely of protein. Prion proteins adopt two differently folded shapes: a normally folded shape and an infectious, often disease-causing shape. The infectious version can bind normally folded prion proteins and cause them to adopt the infectious shape. Also called proteinaceous infectious particles Infectious prions are alternately folded forms of normal proteins that are present in healthy individuals. These infectious and normal proteins do not differ in their primary structure, but their shapes are radically different. e.g. normal and infectious forms of the prion protein (PrP) responsible for "mad cow disease" in cattle, spongiform encephalopathies

hemoglobin

An iron-containing protein in red blood cells that reversibly binds oxygen. This is an example of how the order and types of residues in a polypeptide chain is SO important to function, because if valine is in the 6th position instead of glutamate, then the hemoglobin cells will have a sickle shape, build up in capillaries, and deprive body of oxygen downstream

polarity and charge of R group affects solubility

Both polar and electrically charged R-groups interact readily with water and are hydrophilic. Hydrophilic R-groups dissolve easily in water. Nonpolar R-groups lack charged or highly electronegative atoms capable of forming hydrogen bonds with water. These R-groups are hydrophobic, meaning that they do not interact with water. Instead of dissolving, hydrophobic R-groups tend to coalesce in aqueous solution.

covalent bonding in tertiary structure

Covalent bonds can form between the side chains of two cysteines through a reaction between the sulfhydryl groups. These disulfide ("two-sulfur") bonds are frequently referred to as bridges, because they create strong links between distinct regions of the same polypeptide or two separate polypeptides.

enzyme specificity

Enzyme specificity is the concept that each enzyme catalyzes only one kind of reaction. a product of the geometry and types of functional groups in the sites where substrates bind

hydrogen bonding in tertiary structure

Hydrogen bonds form between polar side chains and opposite partial charges either in the peptide backbone or other R-groups.

hydrophobic interactions in tertiary structure

In an aqueous solution, water molecules interact with the hydrophilic polar side chains of a polypeptide, forcing the hydrophobic nonpolar side chains to coalesce into globular masses. When these nonpolar R-groups come together, the surrounding water molecules form more hydrogen bonds with each other and the polar residues on the surface of the protein, increasing the stability of their own interactions and the disorder of the aqueous solution.

quaternary structure of proteins

In proteins, the overall three-dimensional shape formed from the combination of two or more polypeptide chains (subunits); determined by the number, relative positions, and interactions of the subunits. The individual polypeptides are held together by the same types of bonds and interactions found in the tertiary level of structure.

ionic bonding in tertiary structure

Ionic bonds may form between groups that have full and opposing charges, such as the ionized acidic and basic side chains

van der Waals interactions in tertiary structure

Once hydrophobic side chains are close to one another, their association is further stabilized by electrical attractions known as van der Waals interactions. These weak attractions occur because the constant motion of electrons gives molecules a tiny asymmetry in charge that changes with time. If nonpolar molecules get extremely close to each other, the minute partial charge on one molecule induces an opposite partial charge in the nearby molecule and causes an attraction. Although the interaction is very weak relative to covalent bonds or even hydrogen bonds, a large number of van der Waals interactions can significantly increase the stability of the structure.

proteins involved in transport

Proteins allow particular molecules to enter and exit cells or carry them throughout the body. Hemoglobin is a particularly well-studied transport protein, but virtually every cell is studded with membrane proteins that control the passage of specific molecules and ions

dimer

Proteins with two polypeptide subunits a protein with quaternary structure can consist of just two subunits that are identical. e.g. Cro protein

functional groups affect reactivity

Several of the side chains found in amino acids contain carboxyl, sulfhydryl, hydroxyl, or amino functional groups. Under the right conditions, these functional groups can participate in chemical reactions. In contrast, some amino acids contain side chains that are devoid of functional groups—consisting solely of carbon and hydrogen atoms. These R-groups rarely participate in chemical reactions. As a result, the influence of these amino acids on protein function depends primarily on their size and shape rather than reactivity.

ribosome is an example of how....

Some proteins are found in complexes that include other types of macromolecules. it consists of several nucleic acid molecules and over 50 different proteins.

the purpose of functional groups for amino acid function

The combination of amino and carboxyl functional groups is key to how these molecules behave. In water, amino acids ionize. The concentration of protons at this pH causes the amino group to act as a base, and it attracts a proton to form NH3+. The carboxyl group, in contrast, acts as an acid. The two highly electronegative oxygen atoms in this group pull the electron away from its hydrogen atom, which means that it is relatively easy for this group to lose a proton to form COO− . The charges on these functional groups are important for two reasons: (1) They help amino acids stay in solution, where they can interact with one another and with other solutes, and (2) they affect the amino acid's chemical reactivity.

peptide bonds

The covalent bond formed by a condensation reaction between two amino acids. A covalent bond forms between the carboxyl group of one amino acid and the amino group of another. When a water molecule is removed in the condensation reaction, the carboxyl group is converted to a carbonyl functional group (C=O) and the amino group becomes simply N-H in the resulting polymer.

what is denaturation and how was it discovered?

The loss of a protein's three-dimensional structure due to breakage of chemical bonds and interactions, usually caused by exposure to heat, certain chemicals, or extreme pH conditions. Discovered by Anfinsen when he worked with ribonuclease (which cleaves RNA); when treated w substances that broke hydrogen and disulfide bonds, saw that the protein unfolded, and was rendered unable to perform function, but when denaturing agents were removed, protein refolded & functioned normally showed us that primary structure contains all the info needed for folding

how is protein structure hierarchical?

The order and type of amino acids in the primary structure is responsible for the secondary structures, which then fold up to form tertiary structure. Quaternary structure (if present) is based on interactions between the tertiary structures of the polypeptide subunits.

Tertiary structure of proteins

The overall three-dimensional shape of a single polypeptide chain, resulting from multiple interactions among the amino acid side chains and the peptide backbone results from interactions between residues that are brought together as the chain bends and folds in space The residues that interact with one another are often far apart in the linear sequence form using a variety of bonds and interactions between R-groups or between R-groups and the backbone.

what gives proteins their diversity in function?

The variability in protein size and shape, as well as in the chemical properties of their amino acid residues

why are proteins not the first molecules on earth

To achieve the attributes of life, proteins would need to possess information, replicate, and evolve The information carried in proteins is necessary for their function, but it cannot be used as a template or mold for their own replication. If they cannot replicate, then they cannot evolve on their own

How is it determined which secondary structures will form?

Which secondary structures form, if either, depend on the molecule's primary structure—specifically, the geometry and properties of the amino acids in the sequence. Certain amino acids are more likely to be involved in α-helices than in β-pleated sheets, and vice versa, due to the specific geometry of their side chains

Is protein folding spontaneous?

Yes! In terms of entropy, this result may seem to be in conflict with the second law of thermodynamics. Because an unfolded protein has many more ways to move about, it has much higher entropy than the folded version. Unlike polymerization, however, folding does tend to be spontaneous because the chemical bonds and interactions that occur release enough energy to overcome this decrease in entropy and will also increase entropy in the surrounding environment. As a result, the folded molecule has less potential energy and is thus more stable than the unfolded molecule.

secondary structure of proteins

[interactions between functional groups] localized folding of a polypeptide chain into regular structures (i.e., alpha-helix and beta-pleated sheet) stabilized by hydrogen bonding between atoms of the peptide backbone. Distinctively shaped sections that are stabilized largely by hydrogen bonding that occurs between the oxygen on the C=O group of one amino acid residue and the hydrogen on the N-H groups of another Hydrogen bonding between sections of the same backbone is possible only when a polypeptide bends in a way that puts C=O and N-H groups close together. (Mostly a-helix and b-pleated sheets) The residues that hydrogen-bond to one another are often close together in the linear sequence of a polypeptide's primary structure

why does polymerization of amino acids require energy?

according to the second law of thermodynamics, a pool of free monomers would not be expected to spontaneously synthesize into a polymer, as that would create more order and reduce entropy thus, there needs to be an input of energy into the system in order to make polymerzation spontaneous

R group

also known as a side chain Part of an amino acid's core structure that varies from a single hydrogen atom to large structures containing carbon rings. R-group variability is responsible for the variability in amino acid structure and function. Makes each of the 20 amino acids unique

the monomers of proteins are

amino acids

proteins involved in defense

antibodies - Specialized proteins that aid in destroying infectious agents like bacteria and viruses

Functions of proteins include

catalysis defense movement signalling structure transport

the structure of amino acids

central carbon (a-carbon) forms four covalent bonds with: 1. H - a hydrogen atom 2. NH2 - an amino functional group 3. COOH - carboxyl functional group 4. a distinctive R group, often referred to as a side chain

tetramer

consists of four polypeptides

subunits

each polypeptide in a combo of polypeptides

macromolecular machines

groups of multiple proteins that assemble to carry out a particular function

condensation or hydrolysis: which one dominates and why?

hydrolysis because it increases entropy and is energetically favorable

macromolecule

large molecules made up of smaller molecular subunits (monomers) joined together

monomer

molecular subunit used to build a monomer

proteins involved in movement

motor proteins and contractile proteins move the cell itself (e.g. actin and myosin)

polypeptide

polymers that contain 50 or more amino acid residues linked together by peptide bonds

enzyme

protein that acts as a catalyst, used by living organisms to increase the rate of biological reactions e.g. carbonic anhydrase, salivary amylase

proteins involved in signalling

proteins involved in carrying and receiving signals from cell to cell many reside in cell membrane e.g. small peptide glucagon binds to receptor protein on liver cells, triggering enzymes to release sugar into blood

proteins involved in structure

proteins make up body components such as fingernails and hair, and form the internal "skeleton" of individual cells. Structural proteins keep red blood cells flexible and in their normal disc-like shape

protein folding is often...

regulated Proteins involved in cell signaling, for example, are often regulated in this way. Many of these proteins are disordered and do not complete their folding until after binding to ions or other molecules that are present only during a signaling event.

When amino acids are linked by peptide bonds into a chain, they are referred to as

residues

polymer

structure resulting from the linking together of several monomers in a process called polymerization

Importance of secondary structures

the large number of hydrogen bonds in these secondary structures makes them highly stable. As a result, they increase the stability of the molecule as a whole and help define its shape

active site

the location in an enzyme molecule where substrates (reactant molecules) bind and react where catalysis actually occurs clefts or cavities within the overall shape of the protein

polymerization

the process of linking monomers together

Primary structure of proteins

the unique sequence of amino acids, 20 different types 20^n combo's for a peptide that is n residues long order and type of residues are important because each R-group affects chemical reactivity and solubility, so a change in a single residue could change the overall function of the protein (e.g. sickle-cell anemia)

How do monomers polymerize?

through condensation/dehydration reactions *newly formed bond results in the loss of a water molecule *opposite is hydrolysis