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`Protein Structure
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`Each successive level of protein folding ultimately contributes to its shape and
`
`therefore its function.
`
`LEARNING OBJECTIVE [ edit ]
`
`- Summarize the four levels of protein structure
`
`KEY POINTS [edit |
`
`Protein structure depends on its Emino acid sequence and local, low-energy chemical bonds between atoms
`in both the polypeptide backbone and in amino acid side chains.
`
`Protein structure plays a key role in its function; if a protein loses its shape at any structural level, it may
`
`no longer be functional.
`
`Primary structure is the amino acid sequence.
`
`Secondary structure is local interactions between stretches of a polypeptide chain and includes E—heli§ and
`B-pleated sheet structures.
`
`Tertiary structure is the overall the three-dimension folding driven largely by interactions between R
`gI'Ol1pS.
`
`Quarternary structures is the orientation and arrangement of subunits in a multi-subunit protein.
`
`TERMS [ edit |
`
`Mylan v. Genentech
`Mylan v. Genentech
`IPR2016-00710
`Genentech Exhibit 2083
`
`IPR2016-00710
`
`Genentech Exhibit 2083
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`Protein Structure
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`- E-pleated sheet
`
`secondary structure of proteins where N—H groups in the backbone of one fully—extended strand establish
`
`hydrogen bonds with C=O groups in the backbone of an adjacent fully-extended strand
`
`. or-helix
`
`secondary structure of proteins where every backbone N—H creates a hydrogen bond with the C=O group of the
`amino acid four residues earlier in the same helix.
`
`- antiparallel
`
`The nature of the opposite orientations of the two strands of DNA or two beta strands that comprise a protein's
`
`secondary structure
`
`- disulfide bond
`
`A bond, consisting of a covalent bond between two sulfur atoms, formed by the reaction of two thiol groups,
`
`especially between the thiol groups of two proteins
`
`Give us feedback on this content:
`
`FULL TEXT [ edit
`
`The shape of a protein is critical to its function because
`
`it determines whether the protein can interact with eister for FREE to remove ads and unlock more
`features! Learn more
`
`other molecules. Protein structures are very Eomplex,
`
`and researchers have only very recently been able to easily and quickly determine the structure of complete
`
`proteins down to the atomic level. (The techniques used date back to the 1950s, but until recently they were very
`
`slow and laborious to use, so complete protein structures were very slow to be solved.) Early structural
`
`biochemists conceptually divided protein structures into four "levels" to make it easier to get a handle on the
`
`complexity of the overall structures. To determine how the protein gets its final shape or conformation, we need
`
`to understand these four levels of protein structure: primary, secondary, tertiary, and quaternary.
`
`Primary Structure
`
`Aprotein's primary structure is the unique sequence of amino acids in each polypeptide chain that makes up the
`
`protein. Really, this is just a list of which amino acids appear in which order in a polypeptide chain, not really a
`
`structure. But, because the final protein structure ultimately depends on this sequence, this was called the
`
`primary structure of the polypeptide chain. For example, the pancreatic hormone insulin has two polypeptide
`
`chains, A and B.
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`Protein Structure
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`Primary structure
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`TheA chain 0 insulin is 21 amino acids lon and the B chain is 0 amino acids lon
`
`and each se uence is uni ue
`
`to the insulin protein.
`
`The gene, or sequence of DNé, ultimately determines the unique sequence of amino acids in each peptide chain.
`
`A change in Eucleotide sequence of the gene's coding region may lead to a different amino acid being added to
`
`the growing polypeptide chain, causing a change in protein structure and therefore function.
`
`The oxygen-transport protein hemoglobin consists of four polypeptide chains, two identical (1 chains and two
`
`identical [3 chains. In sickle Eell anemia, a single amino substitution in the hemoglobin [3 chain causes a change
`
`the structure of the entire protein. When the amino acid glutamic acid is replaced by Valine in the [3 chain, the
`
`polypeptide folds into an slightly-different shape that creates a dysfunctional hemoglobin protein. So, just one
`
`amino acid substitution can cause dramatic changes. These dysfunctional hemoglobin proteins, under low-
`
`oxygen conditions, start associating with one another, forming long fibers made from millions of aggregated
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`hemoglobins that distort the red blood cells into crescent or "sickle" shapes, which clog . People affected
`
`by the disease often experience breathlessness, dizziness, headaches, and abdominal pain.
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`Protein Structure
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`Sickle cell disease
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`Sickle cells are crescent sha ed while normal cells are disc-sha ed.
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`Secondary Structure
`
`Aprotein's secondary structure is whatever regular structures arise from interactions between neighboring or
`
`near-by amino acids as the polypeptide starts to fold into its functional three-dimensional form. Secondary
`
`structures arise as H bonds form between local groups of amino acids in a region of the polypeptide chain.
`
`Rarely does a single secondary structure extend throughout the polypeptide chain. It is usually just in a section
`
`of the chain. The most common forms of secondary structure are the or-helix and B-pleated sheet structures and
`
`they play an important structural role in most globular and fibrous proteins.
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`Protein Structure
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`Secondary Protein Structure
`
`B-pleated
`sheet
`
`‘3‘HH
`
`R UHH R
`
`DHH
`
`R
`
`DHH
`
`C-N*C*C-N\c;C-N’c*C-N~c;C-N’c*C-N\c;C-N’c‘C-Nxcxt
`I
`I
`II
`I
`II
`I
`II
`I
`H
`D
`II
`
`5* Rh
`"
`I
`I
`c#C~N-c,C,m
`II
`HH,_':',
`
`Secondary structure
`
`The a-helixand - leated sheet orm becauseo h dro en bondin between carbon 1 and amino rou sin the
`e tide backbone. Certain amino acids have a ro ensi
`to orm an a-helix while others have a ro ensi
`to
`
`form a /3-pleated sheet.
`
`In the a-helix chain, the hydrogen bond forms between the oxygen atom in the polypeptide backbone carbonyl
`
`group in one amino acid and the hydrogen atom in the polypeptide backbone amino group of another amino
`
`acid that is four amino acids farther along the chain. This holds the stretch of amino acids in a right-handed coil.
`
`Every helical turn in an alpha helix has 3.6 amino acid residues. The R groups (the side chains) of the
`
`polypeptide protrude out from the a-helix chain and are not involved in the H bonds that maintain the a-helix
`
`structure.
`
`In [3-pleated sheets, stretches of amino acids are held in an almost fully-extended conformation that "pleats" or
`
`zig-zags due to the non-linear nature of single C-C and C-N Evalent bondst B-pleated sheets never occur alone.
`
`They have to held in place by other B-pleated sheets. The stretches of amino acids in B-pleated sheets are held in
`
`their pleated sheet structure because hydrogen bonds form between the oxygen atom in a polypeptide backbone
`
`carbonyl group of one B-pleated sheet and the hydrogen atom in a polypeptide backbone amino group of
`
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`Protein Structure
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`another B-pleated sheet. The [3—pleated sheets which hold each other together align parallel or antiparallel to
`
`each other. The R groups of the amino acids in a B-pleated sheet point out perpendicular to the hydrogen bonds
`
`holding the [3-pleated sheets together, and are not involved in maintaining the [3-pleated sheet structure.
`
`Tertiary Structure
`
`The tertiary structure of a polypeptide chain is its overall three-dimensional shape, once all the secondary
`
`structure elements have folded together among each other. Interactions between polar, nonpolar, Ecidig, and
`
`basic R group within the polypeptide chain create the complex three-dimensional tertiary structure of a protein.
`
`When protein folding takes place in the aqueous environment of the body, the hydrophobig R groups of
`
`nonpolar amino acids mostly lie in the interior of the protein, while the l_iyd1'ophili9R groups lie mostly on the
`
`outside. Cysteine side chains form disulfide linkages in the presence of oxygen, the only covalent bond forming
`
`during protein folding. All of these interactions, weak and strong, determine the final three-dimensional shape
`
`of the protein. When a protein loses its three-dimensional shape, it will no longer be functional.
`
`Polypeptide badrbune
` Ci
`
`Ii
`cm—cm—cm—cm—Nm“h—c—cm
`
`CIIM
`I
`5
`Hrdrouen 'i'
`hand
`-
`
`DH
`
`r: — NH:
`I
`EH2
`
`
`
`-
`Enrssullide
`"“""*
`
`as
`
`.
`
`'
`.1’
`_
`'i,
`
`'._
`
`.1‘
`
`
`
`Ionic hand
`
`
`
`..
`
`*'
`
`CH
`_,
`..__
`$
`xi: 3
`
`5
`
`-1-"
`
`Hydrophobic
`
`1
`
`Tertiary structure
`
`The tertia
`
`structureo
`
`roteins is determinedb h dro hobic interactions ionic bondin
`
`h dro en bondin
`
`and disulfide linkages.
`
`Quaternary Structure
`
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`Protein Structure
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`The quaternary structure of a protein is how its subunits are oriented and arranged with respect to one another.
`
`As a result, quaternary structure only applies to multi—subunit proteins; that is, proteins made from one than
`
`one polypeptide chain. Proteins made from a single polypeptide will not have a quaternary structure.
`
`In proteins with more than one subunit, weak interactions between the subunits help to stabilize the overall
`
`structure. Enfles often play key roles in bonding subunits to form the final, functioning protein.
`
`For example, insulin is a ba1l—shaped, globular protein that contains both hydrogen bonds and disulfide bonds
`
`that hold its two polypeptide chains together. Silk is a fibrous protein that results from hydrogen bonding
`
`between different B—p1eated chains.
`
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`Protein Structure
`
`Amino Ellildfi
`
`Primary Protein structure
`sequence of a chain of
`
`animo acids
`
`\
`
`Pleated sheet é-'
`'
`
`"
`
`Alpha helix —'~
`
`pattern ‘
`‘
`4»
`
`.
`
`Secondary Protein structure
`hydrogen bonding of the peptide
`backbone causes the amino
`
`acids to fold into a repeating
`
`Pleated sheet
`
`'
`
`'
`
`Alpha helix
`
`Tertiary protein structure
`three-dimensional folding
`pattern of a protein due to side
`chain interactions
`
`Quaternary protein structure
`protein consisting of more
`than one amino acid chain
`
`Four levels of protein structure
`
`The four levels of protein structure can be observed in these illustrations.
`
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`Protein Structure
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`Referenced in 4 quiz questions
`
`Which of the following would probably happen if the insulin protein folded in oil
`instead of water?
`
`Which of the following protein structures forms primarily because of hydrogen
`
`DOLJS?
`
`Which of the following would be true if insulin folded in oil (nonpolar) instead of
`
`water (polar)?
`
`Which of the following structures is formed from the interactions of the amino acid R
`
`groups?
`
`KEY TERM REFERENCE
`
`DNA
`
`— Appears in these related concepts: Supercoiling, The Diversity of Life, and The Relationship
`Between Genes and Proteins
`
`R group
`
`—
`
`acidic
`
`— Appears in these related concepts: pH, Buffers, Acids, and Bases, Classification of
`
`Prokaggotes, and Male Reproductive Anatomy
`
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`Protein Structure
`
`amino acid
`
`— Appears in these related concepts: Peptide Bonding between Amino Acids,
`
`Properties of Nitrogen, and The Incorporation of Nonstandard Amino Acids
`
`artery
`
`— Appears in these related concepts: Blood Flow Through the Body, Blood Vessel Function,
`
`and Arteg Function
`
`cell
`
`— Appears in these related concepts: Cells as the Basic Unit of Life, Citric Acid Cycle, and Levels
`
`of Organization
`
`complex
`
`— Appears in these related concepts: Transduction of Sound, Introduction to Complex
`
`Numbers, and Electron Transport Chain
`
`covalent bond
`
`— Appears in these related concepts: Types of Bonds, Introducfion to Lewis
`
`Structures for Covalent Molecules, and Covalent Cgstals
`
`element
`
`— Appears in these related concepts: Development of the Periodic Table, Elements and
`
`Compounds, and The Periodic Table
`
`enzyme
`
`— Appears in these related concepts: Regulatog Mechanisms for Cellular Respiration,
`
`Nuuition and Health, and Carbon Dioxide Transport
`
`gene
`
`— Appears in these related concepts: Genomic DNA and Chromosomes, Genes as the Unit of
`
`Heredig, and The Influence of Behavior on Genes
`
`hemoglobin
`
`— Appears in these related concepts: Physical Characteristics and Volume, RBC
`
`Anatomy, and Components of Blood
`
`hormone
`
`— Appears in these related concepts: Functions of the Nervous System, Biological
`
`Influences on Sexual Motivation, and How Stress Impacts our Health
`
`hydrogen bond
`
`— Appears in these related concepts: Dipole-Dipole Force, Hydrogen Bonding,
`
`and Special Properties of Water
`
`hydrophilic
`Mosaic Model
`
`— Appears in these related concepts: Water’s Polarity, Functional Groups, and Fluid
`
`hydrophobic
`
`— Appears in these related concepts: Hydrophilic and Hydrophobic Colloids,
`
`Signaling Molecules, and Soaps & Detergents
`
`insulin
`
`— Appears in these related concepts: Types of Cells in the Pancreas, Hormonal Regulafion
`
`of Metabolism, and Pancreas
`
`linkage
`
`— Appears in these related concepts: Genetic Linkage and Violafion of the Law of
`
`Independent Assortment, Genetic Linkage and Distances, and History of DNA Research
`
`— Appears in these related concepts: Molecules, Levels of Organization of Living Things,
`molecule
`and Chemical Reacfions and Molecules
`
`nucleotide
`
`— Appears in these related concepts: DNA and RNA, The Structure and Sequence of
`
`DNA, and Transcripfion in Prokagotes
`
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`Protein Structure
`
`polar
`
`— Appears in these related concepts: Polar Coordinates, Area and Arc Length in Polar
`
`Coordinates, and Selective Permeabilig
`
`polypeptide
`
`— Appears in these related concepts: Types and Functions of Proteins, Amino Acids,
`
`and The Endocrine System
`
`protein
`
`— Appears in these related concepts: Purimng Proteins by Affinifl Tag, Centrosome, and
`
`Proteins: Sources, Uses in the Body, and Dietag Requirements
`
`sickle cell anemia
`
`— Appears in this related concept: Transport of Oxygen in the Blood
`
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`"Boundless."
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`"Boundless."
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`httg://www.bound|ess.com//biology/definition/antiparallel
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`Boundless Learning CC BY-SA 3.0.
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`"hydrogen bond."
`
`http://en.wiktionag/.org/wiki/hydrogen bond
`
`Wiktionary CC BY-SA 3.0.
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`''disulfide bond."
`
`http://en.wiktionag.org/wiki/disulfide bond
`
`Wiktionary CC BY-SA 3.0.
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`"OpenStax College, Biology. October 16, 2013."
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`http://cnx.org/content/m44402/latest/?collection=col11448/latest
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`Openstax CNX CC BY 3.0.
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`"OpenStax College, Proteins. October 16, 201 3."
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`httg://cnx.org/content/m44402/latest/Figure 03 04 04.igg
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`"OpenStax College, Proteins. October 16, 2013."
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`"OpenStax College, Proteins. October 16, 2013."
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`http://cnx.org/content/m44402/latest/Figure 03 04 07.iQg
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`"OpenStax College, Proteins. October 16, 2013."
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`http://cnx.org/content/m44402/latest/Figure 03 04 08.iQg
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`"OpenStax College, Proteins. October 16, 2013."
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`Protein Structure
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`Source: Boundless. “Protein Structure.” Boundless Biology Boundless, 08 Aug. 2016. Retrieved 17 Dec. 2016 from
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