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Peptides and Proteins are covalent, linear chains of amino acids. This defines their primary structure.
Proteins are typically described as N-terminus (free amino terminus) to C-terminal. This is also the direction of synthesis on the ribosome.
**Another aspect of protein structure is whether they are transmembrane. Proteins, with the help of intracellular machinery, can insert hydrophobic regions into the membrane with parts of the protein protruding into the luminal and cytosolic spaces.
Amino acids are conjoined through peptide bonds. Peptide bonds are amide bonds (bonds between a carboxylate group and an amine).Peptide bonds do not rotate along the C-N bond because they have partial double bond characteristics. Therefore, 6 atoms lie within a plane: the carbonyl oxygen, the alpha-carbon (central carbon of the amino acid), the carbonyl carbon)
Secondary, tertiary, and quaternary structure is acquired through non-covalent interactions: – Hydrogen bonding – Hydrophobic interactions – Ionic interactions – Van der waalsinteractions
String, betta pleated sheet, or alpha helix, folding, combine folding
Primary structure define
Sequence of amino acid and any modifications made to them
Secondary structure defined and characteristics
Folding proteins helps acquire a certain structure (alpha helices, beta sheets, turns and bends)
Arises from wanting to satisfy Hydrogens Bonds on the main chain carboxyl groups and amide groups
H bonds + or – 1 kcal/mol per bond to the stability of the secondary structure element. Alpha-helices and beta-sheets are often connected via turns as linkers, and can occur in many patters (eg, helix-turn-helix).
Alpha-helices and beta-sheets, tend to maximize the hydrogen bonding in the core of the protein. The regular repeat structures form hydrogen bonds for all the available backbone amide carbonyl and nitrogen groups
Tertiary structure characteristics 2
Organization of secondary structures into a domain – only a single peptide
Domain structures are held in place through hydrophobic interactions, disulfide bonds, ionic bonds (rare), and sometimes hydrogen
What occurs if the secondary structure cannot form an H bond (no interaction with a main chain carbonyl or amide)?
a cost in stability of ~ +7 kcal/mol, unless it can interact with water instead. So, failing to satisfy H-bonding is destabilizing. So, the protein will optimize (make huge use of) Hbonding in a manner consistent with the secondary structures to the extent possible. The side chains, R-groups, determine what kind of secondary structure is favored. Some proteins have all these secondary structures, while other proteins have predominately one kind of secondary structure.
Quaternary structure define
Several peptides into a functional protein that incorporates second and tert into assembly (ex hemoglobin)
Is a RNA molecule that catalyzes and chemical reaction (ex peptidyl transferase in polypep chain formation)
How the polypeptides grows from the amino to carboxyl terminus
AA in the ribosome are attached to their tRNAs by an ester bond (R’CO - O - R) between the carboxyl terminus and either the 2’ or 3’ OH groups of the ribose sugar of an adenosinethe ester bond in the (P)eptidyl site is cleaved, and peptidyl transferase catalyzes a condensation reaction between its carboxyl terminus and the amino terminus of the amino acid in the (A)mino site
5 structures that the amino acid is composed of
Central alpha carbon atom
R group (side chain)
4 diff groups connected to tetrahedral alpha carbon atom
**mirror images = L isomer and D isomer (only L in proteins)
AA are categorized based on 5 properties
**some AA have specific effects on secondary structure (Pro Gly)
**chemical reactivity associated with diff groups is essential function of enzymes
The proteins that catalyze specific chemical reactions
Small amino acids name & characteristics 2
Form twisted helices with other pro
Very flexible backbone
Smallest AA R group (allows tight packing of strands to form helix
Often found in turns and active sites
Single methyl group
Cyclic amino acid name and characteristics
Breaks or kinks α-helices in secondary structure
Major constituent of collagen
Branched chained AA name and characteristics:
Hydrophobic and found in cores of proteins
How BCAA relates to glycolysis:
When a muscle protein breaks to AA, the amino group of BCAA is sent to pyruvate to make alanine and the carbons are sent to TCA to extra E for the muscles
Hydroxyl AA name and function 4
SER Serine: hydroxyl groups are very reactive and can be phosphorylated or glycosylated easily.
THR Threonine: **same as above** participate in active sites to carry out covalent chemistry or acid/base chemistry
CYS Cysteine: form a “disulfide” bond with another cysteine, oxi rxn, red is reverse. critical in protein tertiary structure formation and sometimes in quaternary structure.
** cys-SH + cys-SH > cys-S-S-cys + 2H (note – the Hydrogens are incorporated into other molecules). • Reducing agents specific for disulfides can reverse this, such as glutathione, which is part of the intracellular redox system.
MET Methionine: methyl is attached to sulfur of methionine to give molecules that need 1 carbon group to grow larger
Aromatics name and function 3
PHE Phenylalanine: can be converted to tyrosine by hrdoxylation rxn
TYR Tyrosine: precursor for other compounds, is phosphorylated during growth factor receptor activation, is a docking site for proteins with SH2 domain
TRP Tryptophan: **can be converted to B vitamin, niacin
Somewhat hydrophobic, large
Stabilize binding of aromatic rings (ex ATP)
Stacking interaction with substrates
Tyrosine phosphorylation (is the addition of a phosphate (PO43−) group to the amino acidtyrosine on a protein)
Acidic residues names and functions 2
On the exterior to impact solubility
In active sites
Acidic residue derivatives name and function 2
ASP Asparagine (or aspartic acid)
GLU Glutamine (or glutamic acid)
Can be reactive
Asparagine is the site of N-linked glycosylation
Basic amino acids name and function 3
LYS Lysine: undergoes modifications
ARG Arginine: part of urea cycle
HIS Histidine: often in active sites, pKis near neutral and can be readily protonated, can bind or release protons (act as buffer(mechanism that keep the pH in the optimal required range all the time)) near physio PH
Charged at neutral PH
Typically found on the exterior to render the protein soluble
Aliphatics names and important functions 5
Valine, Leucine, isoleucine, methionine, alanine
Important in folding
Alcohols names important functions 3
Serine, threonine, tyrosine
Can be phosphorylated – critical in signaling
Can be glycosylated, important for many functionals and structural aspects of proteins
Important in many enzymatic reactions.
Aromatics names and important functions 4
Tyrosine, phenylalanine, tryptophan (histidine also has aromatic ring properties)
Often found in binding sites, stabilize other aromatic ring systems
Carboxylic acids names and important functions:
Glutamate and Aspartate
Bases names and important functions 3
Lysine, Arginine, Histidine
Participate in enzymatic reactions.
Sulfhydryl names and important functions
Can form disulfide bonds – critical for tertiary structure and sometimes quaternary structure.
Similar to serine; also participates in enzymatic chemistry.
The Henderson–Hasselbalch equation defined and what is it used for
describes the relation of pH to the acid and conjugate base forms of a titratable group, in biological systems.
The equation can be used to do the following: Estimate the pH of a buffer solution
Find the equilibrium pH in acid-base reactions Calculate the isoelectric point of proteins pKa is the pH where the acid and conjugate base forms of a compound are equal in concentration. The pKa is the best buffering point of a pH buffer.
The amino and carboxylic acid pKa values of amino acids are only relevant for the two residues at the ends. The rest are in amide bonds and not tritratable. For most proteins, that is a minor contribution to the over-all charge proterties.
pKa of an Amino group is about 9 to 10 for individual amino acids. pKa of the Carboxy group is about 2.0, for individual amino acids
pKa values of the side chain define and important pKa residues name and pKa
determine the overall charge and solubility of a protein.
A: asp 3.9 glu 4.3
B: lys 10.5 arg 12.5 his 6.0
Cysterine: cys 8.3
pKa is the best buffering point of PH buffer
isoelectric point defined
pI, is the pH value where the molecule is net neutral (net charge is zero).
pH that proteins are net neutral at often makes them less soluble, and they may precipitate out of solution.
** Most proteins (but by no means all), are more acidic, meaning that they have a pI of less than 7; typical values are 5-6. However, the pI values can range up**
Net protein charge defined
The overall charge of a polypeptide/protein is the sum total of all the +and charges on the side chains of the amino acids constituting the protein
** N-terminus is always a +1 at pH 7.4 and the C-terminus is always a -1 atpH 7.4, unless they are modified
** One exception is histidine. Side chain pKa is 6, so it should be deprotonated most of the time, often times near the surface of the proteins, the local effect chane the pKa enough that it is charged. Some will count a His as a + 0.5 charge
CA: two angles of rotation associated with each Amino acid: N-Cα (alpha C on N of AA) and Cα-CO (Carbonyl oxy and C, the alpha C). These are restricted by the R groups
NH: amide bond has double-bond character, and does not rotate: This is a key aspect of higher order structure. Is planar, planarity is of 6 atoms (key characteristic of pro structure)
Alpha helices characteristics 4
right-hand helices stabilized by H-bonds running roughly parallel to the helix axis, require H bonding to residues nearby in the sequence (4 AA distant)
Certain amino acids preferentially form α-helices
The R-groups, side chains, all point out from the helix
α-helices satisfy all backbone (main chain) Hydrogen bonds.
is a rod-like structure with the peptide chain tightly coiled and the side chains of amino acid residues extending outward from the axis of the spiral
**hemoglobin (soluble, quaternary structure 2a globin 2b globin, affect one another to cause release or binding of oxygen) and rhodopsin (transmembrane protein) are 2 alpha helical proteins
alpha helices structure characters 3
Each carbonyl group is hydrogen-bonded to the amide-hydrogen of a peptide bond that is four residues away along the same chain
There are 3.6 amino acids per turn
The helix winds as a right-handed screw.
Beta helices characters 3
β-sheets form flat sideby-side planes of amino acids and is extended which implies H bond interactions can occur among residues that are distant in primary sequence
The R-groups point up and down (alternating) from the plane of the sheet
All main chain hydrogen bonds are satisfied, except edges
**porin (transmembrane protein form beta barrels in soluble proteins) & IgI (held together by disulfide bonds into its quaternary structure all structures folded make Y shape)
Beta helices structures 5
It is pleated because the alpha-carbon-carbon bonds are tetrahedral and cannot exist in a planar configuration
This causes the structure to appear “pleated” viewed from the side
If the polypeptide chains runs in the same direction, it forms a parallel β-sheet
If the polypeptide chains runs in opposite direction, they form an antiparallel structure
Parallel and anti-parallel beta-sheets have somewhat different hydrogen bonding patterns.
Tertiary bonds 4 structures
Disulfide bridges (only covalent bond and can be broken by reducing agents)
**denaturing agents can damage all bonds except disulfide
Myoglobin function and characteristic
Molecules that stores oxygen in tissues such as muscle
Smaller, single peptide, and single domain
Binds and releases oxygen in a non-cooperative fashion
Contains secondary and tertiary structures, alpha helices only!
Post-translational modification has cyclic phosphorylation and dephosphorylation, serves as a regulatory role, other modifications can serve other roles
Enzyme characteristics 3
Most rxns are catalyzed by enzymes which are regenerated during the course of the reaction
Speed up reaction rates
How enzymes can diagnose pathology?
Measurement of the serum levels of numerous enzymes is used diagnostically. This is because the presence of these enzymes in the serum indicates that tissue or cellular damage has occurred resulting in the release of intracellular component into the blood.
Superoxide dismutase function and cofactors
catalyzes the dismutationofthe superoxide(O2.-)radicalinto either molecular oxygen, O2 or to hydrogen peroxide,H2O2
Cu and Zn
**has a dimeric structure
Major Structural protein, in 1/3 of body proteins
Unusual Triple Helical structure
Has high 35% Gly and 21% Pro plus (hydroxyproline)
Atypical 2nd and quaternary structure
Other structural proteins also rely on structures atypical for globular proteins
Major component of connective tissue such as cartilage, tendons, the organic matrix of bones, and the cornea of the eye
amino acid sequence in collagen is generally a repeating tripeptide unit, GlyXaa-Pro or Gly-Xaa-Hyp, where Xaa can be any amino acid and adopt a left-handed helical structure with 3 aa per turn
tropocollagen form and function
Three of these helices wrap around one another with a right-handed twist to form
molecules self-assemble into collagen fibrils and are packed together to form collagen fibers
** Scurvy, osteogenesis imperfecta, and Ehlers-Danlos syndrome result defects in collagen synthesis and/or crosslinking*
- ** To mature collage, prolines on collagen are converted to hydroxyproline. This is carried out by the enzyme prolyl hydroxylase. Prolyl hydroxylase requires vitamin C, ascorbate, for it’s activity. If you have a deficiency in vitamin C, you will be unable to resynthesize collagen, and get the disease scurvy.