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The hydrolysis of each polypeptide yields a set of amino acids , referred to as the molecules
amino acid composition
The 20 amino acids that are commonly found in naturally occurring polypeptides are referred to as
standard amino acids.
Note that 19 of the standard amino acids have
the same general structure.
The exception, __, differs from the other standard amino acids in that its amino group is secondary, formed by ring closure between the R group and the amino nitrogen.
These amino acids consist of amino acid residues that have been chemically modified after incorporation into a polypeptide or amino acids that occur in living organisms but are not found in proteins
Nonstandard amino acids
Amino acid can behave as either an acid or a base
Molecules that bear both positive and negative charges on different atoms are called
The ___, however, gives each amino acid its unique properties
The R group
The __ determines the final three-dimensional configuration of each protein
sequence of amino acids.
Amino acids are classified according to their capacity to interact with water. 4 classes
The nonpolar amino acids contain mostly
hydrocarbon R grops that do not bear a charge.
These play an important role in maintaining the three dimensional structures of proteins,
They interact poorly with water
Two types of hydrocarbon side chains are found in non polar.
aromatic and aliphatic
These hydrocarbons containing cyclic structures that constitute a class of unsaturated hydrocarbons with unique properties.
This refers to nonarmatic hydrocarbons such as methane and cyclohexane.
Phenylalaine and Tryptophan contain
Glycine, alanine, valine, leucine, isoleucine, proline
A ___ appears in the aliphatic side chains of methionine and cysteine
Have aliphatic R groups.
These amino acids have functional groups capable of hydrogen bonding, they easily interact with water.
Polar amino acids (hydrophilic)
Serine, Threonine, Tyrosine, Asparagine, and Glutamine belong to this category
Serine, threonine, and tyrosine contain a
Polar amino acids.
polar hydroxyl group.
These standard amino acids have side chains with carboxylate groups
Acidic Amino Acids. Negatively charged
These amino acids bear a positive charged at physiological ph. They can therefore form Ionic bonds with acidic amino acids
Basic Amino acids.
Substances released from one nerve cell that influences the function of a second nerve cell or a muscle cell
Chemical signal molecules produced in one cell that regulate the function of other cell
-Amino acids are precursors of a variety of complex nitrogen-containing molecules. Nitrogenous base components of nucleotides and nucleic acids, heme and h chlorophyll.
Because the alpha carbons of 19/20 standard amino acids are attached to for different groups, they are referred to as
Molecules with chiral carbons can exist as ___, molecules that differ only in spatial arrangement of their atoms.
These two isomers are mirror images of each other. Such molecules are called ___, cannot be superimposed on each other
asymmetric, or chiral, carbons
Enantiomers( identical physical properties, except they rotate plane-polarized light in opposite directions. Optical isomers
Most asymmetrical molecules found in living organisms occur in only one
Stereoisomeric form, either D or L. Few exceptions, only L- amino acids are found in proteins.
__ has had a profound effect on the structural and fictional properties of biomeolcules
-Right-handd helices observed in proteins result form the exclusive presence of L- amino acids.
Chiral molecules- most bind substrate molecules in only one enantiomeric form.
Once the carboxyl group has lost its proton, alanine has no net charge and is electrically neutral. THe ph at which this occurs wis called the
When amino acids are incorporated in polypeptides, the alpha amino and alpha carboxyl groups
isoelectric point (pI).
PI= Pk1 + Pk2
Lose their charges( all ionzable groups of proteins are side chain groups of seven amino acids
histidine, lysine, arginine, aspartate, glutamate, cystenine and tyrosine.
-pka values of individual R groups are affected by their positions within protein microenviroments.
These aspects of organic molecules determine which reactions they may undergo
These are linear polymers composed of amino acids linked together by peptide bonds
These are amide linkages formed when the unshared electron pair of the alpha amino nitrogen atom of one amino acid attacks the alpha carboxyl carbon of another in a nucleophilic acyl substituion reaction
The type of reaction for peptide bond formation
Linked amino acids are referred to as
When two amino acids are linked--
dehydration, water molecule is removed.
amino acid residues
Characterized the peptide bond as
rigid and plana( flat). C-N bonds are shorter than normal C-N bonds. Partial double b-bond character. Rigidity of peptide has consequences- bonds in polypeptide backbone cannot rotate freely, limits on number of conformational possibilities.
These can help stabilize many polypeptides and proteins
Molecules such as amino acids that posses primary amine groups can reversibly react with carbonyl groups. The imine products of this reaction are often referred to as
The most important examples of schiff base formation in biochemistry occur in amino acid metabolism. Schiff bases, referred to as ___, formed by reversible reaction of an amino group with an aldehye group, are intermediates in transamination reactions
Examples of structural support in regards to protein
collagen(major components of connective tissue), fibroin (silk protein)
movement - tubulin-actin
These promote the correct refolding of damaged proteins
heat shock proteins (hsps)
Proteins have multiple and often unreleated functions
These are heat shock proteins that protect cells from physiological stress
These are composed of protein molecules that are related by amino acid sequence similarity
Proteins that are more distantly related are classified into
Protein families. Common ancestry.
Because of their diversity, proteins are often classified in two additional ways
shape and composition
Proteins are classified into two major groups based on their shape, Fibrous proteins and Globular Proteins.
These are long, rod-shaped molecules that are insoluble in water and physically tough. Found in skin, hair and nails (keratins). Structural and protective functions
These are compact spherical molecules that are usually water soluble. Typically have dynamic functions
Globular Proteins(hemoglobin and albumin)
On the basis of composition, proteins are classified as either
These proteins contain only amino acids.
These proteins consist of a simple protein combined with a non protein component. The non protein component is called
A protein without its prosthetic group is called an
A protein molecule combined with its prosthetic group is refered to as a
simple and conjugated
Conjugated proteins are classified according to the nature of their
prosthetic groups. Glycoproteins contain carbohydrate component. lipoproteins contain lipid molecules.
The amino acid sequence, is specified by genetic information
As the polypeptide chain folds, it forms certain localized arrangements of adjacent amino acids that constitute the
The overall three-dimensiona shape that a polypeptide assumes is called
Proteins that consists of two or more polypeptide chains are said to have a quaternary structure
Every polypeptide has a
specific amino acid sequence.
The interactions between ___ determine the protein's three dimensional structure and its functional role and relationship to other proteins
amino acid residues
Polypeptides that have similar amino acid sequences and have arisen from same ancestral gene are said to be __
Sequence comparisons among homologous polypeptides have been used to trace the genetic relationship of different species(cytochrome C- mitochondria)
Each type of polypeptide folds into its own unique and functional conformation. Over time, however, as the result of evolutionary processes, the amino acid sequences of polypeptides change owing to the random and spontaneous alterations in DNA sequences called
A significant number of primary sequence changes do not affect a polypeptide's function. Some of these subsitutions are said to be___ because an amino acid with a chemically similar side chain is substituted.
Some sequence positions are significantly less stringent. These residues, referred to as variable, apparently perform nonspecific roles in the polypeptide's function
Substitutions at either sites have been used to _____
Quite often overall 3d structure does not change despite numerous amino acid sequences.
Trace evolutionary relationships)Longer the time since two species diverged, larger number of differences in certain polypeptide's primary structure", supported by cytochrome C primary sequence in chimps/humans
Whales,sheep, differ by 10 residues from the human protein. 50 million years ago
molecule diseases HbA Human adult hemoglobin, composed of two identical alpha chains and 2 identical beta chains.
Sickle-cell results form a single amino acid substitutions in the beta chain of HbA. substitutions of a hydrophobic valine for a negatively charged gluatmic acid. Aggregate to form rigid rodlike structures in oxygen free state, susceptible to hemolysis
The most commonly observed types of secondary structure are the
What influences o/ V/ angles?
alpha-helix and the beta-pleated sheet. Stabilized by localized hydrogen bonding between carbonyl and N-H groups in polypeptide's backbone
peptide bonds are rigid, alpha carbons are swivel points for polypeptide chain.
Several properties of R groups (size/charge) attached to alpha carbon influence the angle. Certain amino acids foster or inhibit specific secondary structures. Most fibrous proteins are composed almost entirely of secondary structural patterns.
The ___ is a rigid, rodlike structure that forms when a polypeptide chain twists into a right-handed helical conformation. Hydrogen bonds form between the N-H group of each amino acid and the carbonyl group of the amino acid four resides away
- Some amino acids do not foster alpha helical formation, why?
-Peptide bonds, allowed limits on the o/ v/ angles.
Amino acid sequences with a large number of charged amino acids and bulky R groups, are incompatible with alpha helix structures. Alpha bonds are crucial in alpha helix structure.
These form when two or more polypetide chain segments line up side by side
B pleated sheets. Each segment is referred to as beta-strand. Each is fully extended not coiled. Stabilized by hydrogen bonds that form between polypeptide backbone n-h and carbonyl groups of adjacent chains.
B-pleated sheets are either
parellel or antiparallel.
In these, B-pleated sheet structures, the hydrogen bonds in polypeptide chains are arranged in the same direction
In these, these bonds are arranged in opposite directions
Many globular proteins contain combinations of alpha helix and beta pleated sheet secondary structures. These patterns are called
Supersecondary structures or motifs.
The structure of BAB unit consists of
The b-turn is common in proteins rich in
two parallel B-pleated sheets are connected by alpha helix segment. Stabilized by hydrophobic interactions between non-polar side chains projecting from interacting surfaces of t each aspect (a/b)
A process in which unorganized (newly synthesized) molecule acquires a highly organized structure, occurs as consequence of interactions between side chains in their primary structure
Globular proteins are compact because of efficient packing as the polypeptide folds. During this process...
most water molecules are excluded from proteins interior, making interactions between polar/nonpolar groups possible
Large globular proteins often contain several compact units called
domains. Typically structurally independent segments that have specific functions (binding an ion small molecule).
The core-three -dimensional structure of a domain is called a
Domains are classified on the basis of their
core motif structure
Alpha domains = alpha helices and
B-domains consists of anti parallel B strands
a/b domains- various combinations of a helix alternating with b strands
A+B domains are primarily B - sheets with one or more outlying alpha helices
Most proteins contain two or more domains
A number of eukaryotic proteins, reffered to as ____, contain numerous duplicate or imperfect copies of one or more domains that are linked in a series
Hydrophobic interactions-electrostatic interactions-hydrogen bonds-covalent bonds
The strongest electrostatic interaction in proteins occur s between
ionic groups of opposite charge.. Salt bridges, nonequivalent bonds are significant only in regions of the protein where water is excluded because of the energy required to remove water molecules from ionic groups near surface.
In proteins that consists of more then one polypeptide chain, each polypeptide is a called a
subunit. Ligand-binding pockets are water-depleted regions of the protein.
Tertiary- presence of water
precludes the formation of hydrogen bonds with other species
The stabilization contributed by small structural water molecules may free polypeptide from some of its internal interactions. The resulting increased flexibility of polypeptide chain is believed to play a critical role in the binding of molecules called
3d- covalent linkages are created by
What are the most prominent covalent bonds in tertiary structure? benefits? What lacks these features
chemical reactions that alter a polypeptide's structure during of after its synthesis.
The most prominent covalent bonds in tertiary structure ate the disulfide bridges found in many extracellular proteins. Protect protein from adverse changes in PH.
Intercellular proteins do not contain disulfide bridges because of high cytoplasmic concentrations of reducing agents.
3d - dynamic hydration shell that forms around a protein, also contributes to the
flexibility required for biological activity
Folding of proteins is
As polypeptide folds, favorable (negative ) H values are the result in part of the sequestration of hydrophobic side chains within the interior of the molecule and the optimization of other non covalent interactions. Opposing these factors is the unfavorable decrease in entropy that occurs as the disorganized polypeptide folds into its highly organized native state. The change in entropy of the water that surrounds the protein is positive because of the decreased organization of the water in going from the unfolded to the folded state of protein.
* the precarious balance between favorable and unfavorable forces allow proteins the flexibility they require for biological function
thermodynamically favorable (-g)
3D- Multisubunit proteins in which come of all subunits are identical are referred to as
oligomers. They are composed of promoters.
*large number of oligomeric proteins contain two or four subunit promoters, referred to as dimers and tetramers, respectively.
3d- Reason for occurrence of multisubunit proteins (3)
Synthesis of separate subunits may be more efficient than increasing length of single polypeptide chain.
-replacement of smaller, worn out components can be managed more effectively(collagen)
-Complex interactions of multiple subunits help regulate a protein's biological function
Polypeptide subunits assemble and are held together by
non-covalent interactions such as the hydrophobic effect, electrostatic interactions and hydrogen bonds.
Ligand-induced conformational changes in such proteins are called.
What triggers them and what are they called
The kind of reaction
allosteric transitions, and the ligands that trigger then are called effectors/modulators.
* Allosteric effects can be +/-, depending on whether effector binding increase or decreases the proteins affinity for other ligands.
IF there is a complete lack of ordered structure, the term
natively unfolded proteins. Most unstructured proteins are eukaryotic. Folding of IUPs into stable 3d, is prevented by biased amino acid sequences that have polar/charged amino acids.
* diversity of functions. Many are involved in regulated of signal transduction, transcription, translation, cell proliferation
Denaturation- strong acids bases
Changes in ph result in pronation of some side chain groups. Alters hydrogen bonding and salt bridges. Reaches isolectric point= may precipitate from solution.
Denauration organic solvents
Water soluble organic solvents (enthanol) interfere with hydrophobic interactions because they interact with non polar R groups, form hydrogen bonds. Non polar solvents also disrupt hydrophobic interactions
Substances that disrupt hydrophobic interactions ,causing proteins to unfold into extended polypeptide chains. These molecules are called amphibpahtic (both ilic)
Denaturtion- reducing agents
Urea, reducing events convert disulfide bridges i to sulfhydrl groups. Disrupts hydrogen bonds and hydrophiv interactions
Denautration- salt concentration
some h2o interact with izoniable grops are attracted rto salt ions. Solvent molecules available to interact decreases, protein-protein interaction sin crease. Solvation spheres surrounding protein io ionized groups are removed. Protein precipitates. Salting out(process) Usually reversible, used in protein purification
mercury, lead, a disrupt salt bridges by forming ionic bonds with negatively charged groups., bond with sulfhydryl groups, result in significant change in structure/function
vibration increases, , interactions are disrupted, protein unfolds. Can use in purification procedures, some more resistant
Forces that drive folding process
bond rotations ,free energy considerations, behavior of amino acids in aqueous environments
Is a recomindant Dna tecniqque i which specific sequence changes can be introduced in to a predetermined position in cloned genes
site-directed mutagensis ( revealed that protein folding is a step wise processes in which secondary structure formations appear to be an importance force infolding) Showed that amino acid subsitutions reveled that changes in surface amino acids rarely affect protein's structure
subsituional of amino acids within hydrophobic core often lead to serious changes
Folding is not a random processed based on primary sequence, also too complex, of protein folding
*numerous routes that polypeptide can take to forld into native state.. Low energy state
Type of spectroscopy in which relationship between molecular motion and structure is probed with eletromagnetic radiation
The folding of larger polypeptides typically involves
the formation of several intermediates.
The term___ refers to a partially organized globular state of a folding polypeptide that resembles the molecules' native state.
Within the interior of a molten globule, tertiary interactions among amino acid side chains are fluctuating; that is, they have not yet stabilized.
It has also become increasingly clear that the folding and targeting of many proteins in living cells are aided by a group of molecules now referred to as
molecular chaperones(found in bacteria to higher animals/plants) mitochondria, chloroplasts, ER
Two major molecular chaperone classes
The ___ are a family of molecular chaperones that bind to and stabilize proteins during the early stages of folding. numerous __monomers bind to short hydrophobic segments in unfolded polypeptides thereby preventing molten globule formation. Each type posses two binding sites, one for an unfolded protein segment and another for ATP. Release of polypeptide from this involves ATP hydrolysis. Mito-ER localized variables required for transmembrane translocation of some polypeptides.
Once an unfolded polypeptide has been released by ___, it is passed on to a member of a family of molecular chaperones referred to as ____, which mediate protein folding. These form a large structure composed of two stacked seven-ssubunit rings. The unfolded protein enters the hydrophobic cavity of the hsp60 complex. When folding is complete, ATP hydrolysis converts the cavity to a hydrophilic surface and the folded protein domain moves out of the cavity. When the cavity is empty, it reverts to the hdroyphbic surface in which form it can accept ATP and an unfolded protein for a repeat of the cycle.
Fibrous proteins typically contain
high proportions of secondary structures, such as alpha helices, or b-pleated sheets. Rod like sheet like shapes. Have structural rather than dynamic roles.
Keratin(bundles of alpha helices) Fibroin antiparallel b-pleated sheets.
Collagen is composed of
three left-handed polypeptide helices that are twisted around each-other to form a right-handed cripple helix.
The assembly of collagen fibers in their extracellular locations, such as tendons and bone
Two aldehydes from an a, b-unsatured aldehyde linkage
The biological functions of ___usually involve precise binding of small ligands, or large macromolecules such as nucleic acids or other proteins.
As the first o2 binds to hemoglobin, the binding of additonal o2 to the same molecule is enchained.
mygobloin gives up oxygen only when
muscle cell's oxygen concentration is very low. Has a greater affinity for o2 than does hemoglobin
dissociation of oxygen from hemoglobin is enchanted if
ph decreases, Bohr effect.
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