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BCHM 307 Week 2 Notes

by: Erin VanHoosier

BCHM 307 Week 2 Notes BCHM 30700 - 001

Erin VanHoosier
GPA 3.76

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Chapter 4, Sections 1-4
Stefan Paula
Class Notes
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This 5 page Class Notes was uploaded by Erin VanHoosier on Sunday September 4, 2016. The Class Notes belongs to BCHM 30700 - 001 at Purdue University taught by Stefan Paula in Fall 2016. Since its upload, it has received 44 views. For similar materials see Biochemistry in Chemistry at Purdue University.


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Date Created: 09/04/16
BCHM 307 Week 2 Notes Erin VanHoosier Ch. 4 Protein Structure 4-1: Proteins are Chains of Amino Acids Protein: biological molecule consisting of one or more polypeptides Polypeptides: chains of polymerized (combined) amino acids Amino Acid (AA) : small molecule containing an amino group, carboxylate group and side chain (R group…can be anything!) The 20 AAs have different chemical properties:  The R GROUPS make the 20 AAs UNIQUE  APPHA CARBONS: are the carbons attached to the amino and carboxylate groups  Chirality: the positioning of the molecule in relation to the alpha carbon o Different positioning makes for DIFFERENT molecules (mirror images) o L amino acids vs D amino acids (mirror images) o Both present in solutions  The Hydrophobic AAs o nonpolar o Alanine, valine, leucine, isoleucine, phenylalanine, methionine, tryptophan, proline o Usually located in the interior of molecule o Hydrophobic chains not involved in chemical reactions  The Polar AAs o Interact with water o Serine, threonine, tyrosine: contain hydroxyl groups o Cysteine: thiol group o Asparagine, glutamine: amide group o Histidine o Glycine: no H+ bonds, but neither hydrophobic nor charged o Some polar side chains can ionize at ideal pH o Disulfide bond: two sulfides bonded by a single bond  The Charged AAs o Aspartate, glutamate: carboxylate groups (- charge) o Lysine, arginine (+ charge) o Location: surface  Benefits: act w/ H2O or other polar/ionic substances Peptide bonds link AAs in proteins Condensation reaction: water is eliminated 1 BCHM 307 Week 2 Notes Erin VanHoosier o Involved the carboxylate group of on AA with the amino group of another AA, which then combines to form a peptide bond o Residues: remaining parts of AA o Hydrolyzation: breaking of peptide bonds via exopeptidases (act from end of chain) /endopeptidases ( act from middle of chain) o N-terminus: residue with bond availability amino group is oriented on the L o C-terminus: residue with bond availability carboxylate group on the R Can calculate net charge of protein at given pH via pK value (tendency to ionize) Microenvironment (immediate surroundings) can alter polarity and change tendency to ionize Most polypeptides contain btwn 100-1000 AA residues!!!!! <40 is called oligopeptides or peptides The AA sequence is the 1st level of protein structure: Primary structure = sequence of AA in chain Secondary structure =folding arrangement of polypeptide backbone Tertiary structure = 3-D shape of entire molecule Quaternary structure = >1 polypeptide chain and its spatial arrangement 4-2: Secondary Structure: The Confirmation of the Peptide Group Backbone= everything except for the R group 4 Levels of Protein Structure 1 Primary: list of AA in order 2 Secondary: only contains backbone a Repeated sections 2 Tertiary: 3-dimensional, contains backbone AND R-groups 3 >1 chain of AAs linked together  Two resonance forms for the AA o Amide group=H+ bond donors o Carbonyl Oxygens= H+ bond acceptors  No rotation around N--Alpha Carbon---C bonds; therefore, AA is considered planar o Rotation can occur at N--Alpha Carbon and Alpha Carbon---C bonds separately, but the rotation is limited so Oxygen atoms don’t get too close  Torsion angles  Structures must minimize steric strain The Alpha Helix exhibits a twisted backbone conformation Via Linus Pauling 2 BCHM 307 Week 2 Notes Erin VanHoosier Polypeptide backbone twists in a right-handed helix o 3.6 residues per turn o Height between turns (pitch): 5.4 Angstroms o Carbonyl oxygens forms H+ bond with NH group that is four residues away o Glycine and Proline are rare in alpha helix structures o Backbone forms van der Waals interactions  Atoms touch; therefore interactions=stable The Beta Sheets contain multiple polypeptide strands o H+ bonding is between adjacent strands o Parallel Beta Sheet: adjacent strands run in same direction  Stretch/elongated arrangement  Allows for lots of H+ bonds, but bonds are angled o Anti-parallel Beta Sheet: adjacent strands run in opposite directions  More stable because H+ bonds are straight  Can contain 2 or >12 strands  Each strand has an average length of 6 residues Regular secondary structures= alpha helices & beta sheets  Regular bc backbone conformations are the same from one residue to the next Proteins also contain irregular secondary structure  Loops: connect either Beta strands or Alpha helices o Contain residues with irregular/unique secondary structures ***KNOW THE DIFFERENCE BETWEEN ALPHA HELICES AND BETA SHEETS AND WHAT EACH STRUCTURE MEANS*** 4-3: Tertiary Structure and Protein Stability  3-D Structure contains: o regular & irregular 2ndary structure o Spatial arrangement of side chains  X-ray crystallography: probes the atomic structure of macromolecules Classes of Protein Structure: CATH System (Class, Architecture, Topology, Homology) 1 Alpha structure 2 Beta structure 3 Alpha and Beta Structure 4 A few secondary elements (Beta) Proteins have hydrophobic cores  Globular proteins usually contain two layers of secondary structure 3 BCHM 307 Week 2 Notes Erin VanHoosier o Surface Regions: hydrophilic o Core regions: hydrophobic  Domain: a polypeptide segment that folded into a single structural unit with the core o Small hydrophobic protein=lots of secondary structure  Alpha helices and beta sheets (H+ bonded) minimizes hydrophilicity of polar backbone groups  Irregular structures (loops) on surface of protein/domain  Can form H+ bond with H20 molecules  The greater the residue's hydrophobic tendency, the more likely it is to be placed in the CORE!  CAN PREDICT LOCATION OF AA RESIDUE BASED ON HYDROPHOBICITY!! o Ion pair: when two residues with opposite charges interact (located near each other) Protein structures are stabilized mainly by the hydrophobic effect  Folded confirmation of protein is only a little more stable than its unfolded form  Hydrophobic effects put nonpolar groups in the interior of the protein, which stabilizes the backbone  Hydrogen bonding helps fine-tune the stability, it doesn’t have a major role in providing stability Cross-links help stabilize proteins  Ion pairs, disulfide bonds, and inorganic ions (Zn)=most common cross-link  Doesn’t affect stability very much o Due to increase in free energy but a loss of entropy (disorder) o Doesn’t take much to unfold the 3-D structure; therefore, proteins aren’t very stable  Disulfide bonds o Rare in intracellular proteins o Seen more in extracellular environment  Prevents protein unfolding in harsh environments  Van der Waals interactions: favor the folded form bc interactions are closer  Zinc fingers o Common in DNA binding proteins o 20-60 residues with 1 or 2 Zn^2+ ions o Stabilizes small proteins Protein folding begins with the formation of secondary structures  Polypeptide chains begin folding once they leave the ribosome due to crowding in the cell interior 4 BCHM 307 Week 2 Notes Erin VanHoosier o May reach tertiary structure before whole chain is synthesized o Secondary structure elements are found in the core  Denature: to chemically unfold a polypeptide chain o Via salts or urea  Renature: to refold a polypeptide chain  Native structure is the protein's tertiary structure o Built in an organized fashion: hydrophobic effect o Folding is determined via the AA sequence  Molecular chaperones: proteins that assist other proteins in the folding process in a cell o Improper folding from genetic mutations can lead to disease  Processing: alters the chain before reaching mature form  Intrinsically unstructured proteins: are very flexible in their structure 4-4: Quaternary Structure  Occurs when protein has more than one polypeptide chain  Spatial arrangement makes up the quaternary structure o Subunits: individual chains o Homodimer, homotetramer, etc. : when subunits within the polypeptide chain are identical  Interface is the area of contact between two subunits o Interface is often hydrophobic o H+ bonds, ion pairs, and disulfide bonds determine shape of subunits connections  Symmetry of 2 or more identical subunits=most common  Symmetry of non-identical subunits is based on the groups of subunits  Some proteins have more than one quaternary structure  Multi-subunit proteins o Can build large proteins via small additions  Small additions help decrease errors in the construction of the protein o Subunits influence other subunits behavior/function 5


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