BIOCHEM: CH 2
Terms in this set (126)
The word protein is derived from the Greek
word proteios meaning ...?
"in the lead" or
"standing in front."
The unfolded state is a population of _____ whereas the folded state is always only ____. Thus, for protein function to occur, it is critical that the folded state be ______. One major question we need to address then, is how is this achieved? (slide 5)
many distinct conformations; one conformation; more stable than the unfolded one.
some functions of proteins
catalysts, transport and store other molecules such as oxygen, provide mechanical support and immune protection, generate movement, transmit nerve impulses and control growth and differentiation (27)
proteins are ___ polymers built of amino acids
-- sequence is called ___ structure
-- 3D structure formed by ____ btw ____ near one another is called _____ structure
-- tertiary structure is formed by...?
-- quaternary structure?
-- H bonds, amino acids, secondary
-- long-range interactions btw AAs
-- composed of several distinct PP chains
Proteins contain a wide range of functional groups
-- most of these groups are chemically stable/reactive?
-- what accounts for broad spectrum of protein function?
-- when groups are combined in various sequences
some proteins are quite rigid whereas others display considerable flexibility
: rigid units can function as ...?
: flexible units can function as..?
: conformational changes within proteins enable the regulated ___ of larger protein complexes as well as the _______ within and and between cells
: structural elements in the cytoskeleton or in connective tissue
: hinges, springs, or levers
: assembly, transmission of information
an α-amino acid consists of a central ___ atom called the _____ linked to an ___ group, a _____ group, a ____ atom and a distinctive ___ group making it a ____ compound
: may exist as __ or ___ isomers
carbon, α carbon, amino, carboxylic acid, hydrogen, R, chiral
: L, D
Proteins are linear polymers of amino acids.
: All naturally occurring proteins on Earth are constructed with __ isomers.
what is the basis for the preference of L amino acids?
it is possible that the preference for L over D was a consequence of chance selection. There is evidence that L AAs are slighly more soluble than a racemic mixture of D and L which tend to form crystals
what are zwitterions?
when amino acids in solution at neutral (physiological) pH exist predominantly as dipolar ions
in dipolar form (as zwitterion), the _____ is protonated and the ____ is deprotonated
amino -NH3+, carboxyl group -COO-
the ionization state of an amino acid varies with pH
: in acid solution (pH=1), amino group is protonated/deprotonated and the carboxyl group is not _____ (_________)
: as the pH is raised, the _____ is the first group to give up a proton
: dipolar form persists until the pH approaches 9, when the protonated amino group gains/loses a proton
: protonated, dissociated (-COOH)
: carboxylic acid
: loses a proton
Learning Check: pH v. pKa
: What is the pH of a glutamic acid solution if the a-carboxyl group is ¼ dissociated?
: What is the pH of a lysine solution if the side chain amino group is 3/4 dissociated?
20 side chains vary in
: ____ character
: _____ capacity
: _____ reactivity
: hydrogen bonding
20 amino acids are commonly found in the proteins of living organisms
: Distinguished by their ____
Linear arrays of amino acids can make a huge number of molecules
: Consider a peptide with two amino acids
- AA1 - AA2 can create ___ different molecules
- AA1 - AA2 - AA3 can create __ different molecules
The 20 standard amino acids are divided into categories based on the properties of their side chains (PPT)
1. _____ side chains
2. ___, _____ side chains
3. ____ side chains
4. ____ side chains
2. polar, uncharged
3. positively charged
4. negatively charged
The 20 standard amino acids are divided into categories based on the properties of their side chains (30)
1. _____ amino acids with ____ R groups
2. ____ amino acids with ___ R groups but the charge is not _____
3. _____ charged amino acids with R groups that have a _____ charge at physiological pH
4. ____ charged amino acids with R group that have a ____ charge at physiological pH
1. hydrophobic, nonpolar
2. polar, neutral, evenly distributed
3. positively, positive
4. negatively, negative
hydrophobic amino acids part 1
hydrophobic amino acids part 2
the larger aliphatic side chains are especially ____ and tend to cluster ____ rather than contact _____
hydrophobic, together, water
simplest amino acid is ____
: unique in that it is ____
glycine (Gly, G)
next simplest amino acid is ___
Alanine (Ala, A)
methionine contains a largely ___ side chain that includes a ___ group
(Met, M) aliphatic, thioether -S-
the side chain of isoleucine includes an additional ___ center
(Ile, I) chiral
Proline also has an aliphatic side chain but differs from other members in that its side chain is bonded to both N and the α-carbon atoms yielding a ____ ring
(Pro, P) pyrrolidine
Tryptophan has an ___ group joined to a methylene. Less hydrophobic than pheylalanine because of its ___ group
(Trp, W), indole- 2 fused rings containing an NH group; NH
Polar but Uncharged Amino Acids
slide 16 diagram
purpose of hydroxyl group on polar but uncharged amino acids
makes these amino acids much more hydrophilic and reactive than hydrophobic amino acids
Positively charged amino acids.
: Have positively charged side chains because _____ in their side chains
- highly ____
- Have the potential for _____ interactions
- Tend to be found on the ____ of proteins (or ____ in the interior)
- Have potential for _____ formation
- which amino acids are they?
: biological pH is less than the pKa of the amino groups
- surface, paired
- Lysine, Arginine and Histidine
Histidine contains an ___ group, an aromatic ring that can also be ____ charged
: often found in ____ sites of enzymes where the ____ can bind and release protons in enzymatic reactions
(His, H) imidazole, positively
: active, imidazole ring
The negatively charged amino acids.
: Have negatively charged side chains because ____ in their side chains
- Have the potential for _____ interactions
- Tend to be found on the _____ of proteins (or ____ in the interior)
- Have potential for _____ formation
: biological pH is greater than the pKa of the carboxyl groups
- surface, paired
Asparagine or Aspartic Acid
(Asx, B) slide 21
Glutamine or Glutamic Acid
(Glx, Z) slide 21
These "residues" are commonly found in the active sites of enzymes.
: Table 2.1 Typical Pka values of ionizable groups in proteins
the formation of a peptide/amide bond is followed by..?
a loss of a water molecule (slide 22)
despite requiring an input of free energy, why are peptide bonds very stable?
they are kinetically stable because the rate of hydrolysis is extremely slow (backward reaction is extremely slow) (35) (slide 22)
a series of amino acids joined by a peptide bond form a _____ and each amino acid unit in a polypeptide is called a ____
polypeptide chain, residue (35)
Polypeptide chains are further subdivided into the main-chain and side-chain
: α-amino, α-carbon, and α-carboxyl groups are linked to form the protein "______"
: Side chains ("______") are connected to the backbone
: Notice all of those _______. This has BIG-TIME consequences.
: hydrogen-bond donors and acceptors
A polypeptide chain has directionality because ...?
its ends are different: an α-amino group is present at one end and an α-carboxyl group at the other (slide 24)
Peptides and proteins have an N-terminus and a C-terminus.
: By convention, peptides and proteins are named, drawn, and discussed from ___-terminus to ___-terminus (___ --> ____)
: N, C (L-->R) (slide 24)
largest single PP known is the muscle protein ___
polypeptide chains made of small numbers of amino acids are called ____ or simply _____
Di-sulfide bonds sometimes form between ____ residues in _____ environments
cysteine, oxidizing (slide 25)
intracellular/extracellular often have several disulfide bonds whereas intracellular/extracellular proteins usually lack them
why was Frederick Sanger's work in sequencing insulin a landmark in biochemistry?
it showed for the first time that a protein has a precisely defined amino acid sequence consisting of only L amino acids linked by peptide bonds (37)
4 reasons why amino acid sequence is important
1. essential to elucidate its function
2. determines the 3D structures of proteins
3. alterations can lead to diseases
4. reveals much of its evolutionary history
Polypeptide chains are ____ yet ____ _____
flexible, conformationally restricted
Polypeptide chains are flexible yet conformationally restricted
: peptide bond is essentially ____
: the bond resonates btw a ___ bond and a ___ bond
: because of this ____ double bond character, ____ about this bond is prevented and thus the conformation of the peptide backbone is ____
: single, double
: partial, rotation, constrained
typical bond lengths within a peptide unit
the peptide bond is uncharged allowing ____ of amino acids linked by peptide bonds to form tightly packed ___ ____
polymers, globular structures
Almost all peptide bonds in proteins are cis/trans? this is due to..?
trans; steric clashes (slide 29)
The peptide bond can in principle adopt the cis or trans conformation, however the trans form is strongly favored due to steric clashes.
: _____ residues are lone exceptions
proline (slide 30)
ond rotation is possible for the two single-bonds in the main-chain: these are called ____ angles.
torsion (slide 31)
A measure of the rotation about a bond is between -180 and +180 degrees.
: angle of rotation bout the bond btw the nitrogen and α-carbon atoms is called ____
: angle of rotation about the bond btw the α-carbon and the carbonyl carbon atoms is called ____
: a clockwise rotation about either bond as viewed from the N atom toward the α-carbon atom or from the α-carbon atom toward the carbonyl group corresponds to a positive/negative value?
: phi (φ)
: psi (ψ)
The consequence of resonance: residue backbone atoms are _____ which restricts the conformational _____ of the polypeptide chain.
coplanar, flexibility (slide 33)
The Ramachandran plot shows us that many torsion angle combos are forbidden because they result in _____ of atoms.
steric collisions (slide 34)
o the take-home message is that polypeptide chains are flexible yet conformationally restricted. What is the consequence?
"The rigidity of the peptide unit and the restricted set of allowed phi and psi angles limits the number of structures accessible to the unfolded form sufficiently to allow protein folding to take place." (pg 40) slide 35
Levels of Protein Structure: The Basics
: Protein structure is complicated, so we discuss four different levels of structure
- Primary structure: ______ of amino acids linked by ____
- Secondary structure: ______ conformations/structures of the peptide ______
- Tertiary structure: ____ conformation/shape of the _____ peptide or protein.
- Quaternary structure: 3-D relationships between _____ polypeptide chains (subunits).
- sequence/order, peptide bonds
- local, regular, repeating, backbone
- 3D, overall, folded
: _____ segments of a polypeptide chain with repeating, characteristic ___, ___ backbone _____ angles, that are stabilized by a regular pattern of ____ _____ between the peptide _____ and _____ groups that are near each other in the ______ sequence
folded, Ψ,Φ, torsion, hydrogen bonds, -N-H, C=O, primary (slide 37)
Regular, repeating structures formed by the protein backbone as a result of hydrogen bonding.
3 main types:
- β-pleated sheets
- Turns and Loops
look at notes revisions!
The α-helix was predicted by ____ in 1948...on a piece of paper!
Linus Pauling (slide 39)
Ways of visualizing the α-helix: ribbon, ball-and-stick, and space-filling.
name the models (slide 40)
Hydrogen bonding in an α-helix involves the CO group in residue ___ and the NH group in residue _____.
i, i+4 (slide 44)
except for amino acids near _____, all the main-chain CO and NH groups are H bonded
the ends of an α-helix
each residue is related to the next by by a ___ , also called ____
The periodicity of the α-helix has important consequences
: ~ _____ residues per turn of the helix
: the pitch is the length of _____ turn along the helix axis and is equal to the product of the ____ and the number of ___ per turn
: ___ Å rise per residue yields a pitch of ____ Å.
: one complete, rise, residues
:5.4 (slide 45)
The Rakmachandran plot reveals that both the right-handed and left-handed helices are among allowed conformations. However, right-handed helices are energetically more favorable. Why?
because there is less steric clash between the side chains of the backbone. (slide 46)
Ribbon and cylindrical depictions of α-helices
diagram of ferritin
If the peptide +NH3-ASGHYTRLW-COO- forms an α-helix, then
A) The NH group of Ser makes a H-bond with the CO group of The
B) The CO group of Tyr makes a H-bond with the NH group of Arg
C) The NH group of Tyr makes a H-bond with the NH group of Arg
D) The CO group of Ser makes a H-bond with the NH group of The
E) A and C
D (slide 48)
Ramachandran plot for β strands
: The red area shows..?
the sterically allowed conformations of extended, β-strand-like structures (slide 49)
The β-strand is the other common secondary structure in proteins.
: Form because of hydrogen bonding between two almost ____ ______ protein chains called "β-strands."
: the side chains of adjacent amino acids points in same/opposite directions?
: fully extended
: opposite (slide 50)
(note the difference in distance btw adjacent amino acids compared to α helix)
Like the α-helix, the β-sheet works because it facilitates ____ between the _____ backbone functional groups.
H bonding, polar
: Adjacent β strands run in same/opposite direction?
: H-bonds between NH and CO groups connect each amino acid to a single amino acid on an ____
Parallel β sheet
: Adjacent β strands run in same/opposite direction?
: H-bonds connect each amino acid on one strand with ___ ____ amino acids on adjacent strand
: 2 different
Diagram of a mixed β sheet
arrows indicate directionality of each strand (slide 52)
In protein representations, β-pleated sheets are depicted as ...?
flat, broad arrows pointing in the direction of the carboxyl-terminal end to indicate the type of β sheet formed- parallel or antiparallel (slide 53)
Relative Frequencies of amino acid residues in secondary structures table
PP chains can change direction through ____ (also known as ___ or ____)
reverse turn, β turn, hairpin turn (44)
The coiled-coil "superfamily" is a common strategy for forming ______ in the cell.
fibrous material (slide 56)
α-helical coiled coil:
: Two right-handed helices wind around one another to form a _____ superhelix
: The two helices are cross-linked by ____ interactions and _____ bonds
: Structures are present in ____ in hair, quills, claws, horns
: weak, disulfide
Collagen (different type of helix than keratin-α helix )
: ___ chains twist around each other to form a ____
: Strands are linked by _____ bonds that form btw the peptide NH groups of ___ residues and the ___ groups of residues on ___ chains
: 3, superhelix
: hydrogen, glycine, CO, other
: Spatial arrangement of amino acids that are close/far apart in sequence (the overall, folded, 3-dimensional shape of a single polypeptide unit)
: Affected by many factors
far apart (slide 58)
Tendencies in Tertiary Structure
: Nonpolar residues tend to be in the interior/exterior of the protein, away from ____.
: Polar and/or charged side chains tend to be on the _____, where they can interact with ____. If they are in the interior of the protein, they are usually ____-bonded.
: ____ bonds between two ____ residues can affect the stability of the overall structure.
: Atoms ______ to fill most of the available space.
: α-helices and β-strands are typically "______." - this means..?
: interior, water
: surface, water, H
: disulfide, Cys
: pack together
: amphipathic, the α helix or β strand has a hydrophobic face which points into the protein interior, and a more polar face, which points into solution (47)
Tertiary Structure of Myoglobin
diagram (slide 60)
Exceptions to Tertiary Structure
: outside (which contacts hydrophobic groups in membranes) is covered largely with hydrophobic residues
: the center includes a water-filled channel lined with charged and polar amino acids (slide 63)
The β-barrel is a VERY common protein structure, particularly in ____
lipid bilayers (slide 64)
what are motifs/supersecondary structures?
certain combinations of secondary structure present in many proteins and frequently exhibit similar functions
(ex. helix-turn-helix pg 48)
Protein structures are often constructed by "_____", small, compact units of tertiary structure.
domains (slide 65)
: _____ arrangement of _____ protein subunits and the nature of their interactions
- Found only in proteins which consist of more than 1 polypeptide chain
: spatial, separate
: Multi-subunit proteins are named by the _____ of subunits and whether those subunits are ______ from each other
- 2 subunits: dimer
- 3 subunits: trimer
- 2 different subunits: heterodimer (αβ)
- 2 similar subunits: homodimer (α2)
: number, similar or different
: ex. This homo-dimeric protein structure from bacteriophage λ binds to DNA. (slide 67)
Hemoglobin: α2β2 hetero-tetramer diagram
diagram (slide 68)
So, why is the folded state more stabled than the unfolded one?
slide 69 listen to lecture/notes
Unfolded vs Folded State
: H Bonds
: van der Waals
: hydrophobic effect
...but don't forget, the folding of a protein into a single conformation will reduce/increase entropy of the system. However, the unfolded/folded state is already somewhat conformationally restricted due to the _____ of the peptide bond!
reduce, unfolded, partial double bond character
Insulin is a protein containing _____ residues that form intra- and inter-molecular ______
cysteine, disulfides (72)
The amino acid sequence of bovine ribonuclease
diagram (slide 73)
A simple experiment that tests the relationship between an amino acid sequence of a protein and its structure.
1. used urea to disrupt ____
2. used β-mercaptoethanol to cleave ____
: what happened when these two agents were removed?
: what did this experiment show?
1. non covalent bonds
2. disulfide bonds (reversible)- disulfides (cystines) converted into sulfhydryls (cysteines)
: the denatured protein regained enzymatic activity
: sulfhydryl groups became oxidized by air and enzyme spontaneously refolded into active form
: the information needed to specify the catalytically active structure of the protein is contained in its amino acid sequence (sequence specifies conformation) (50)
Why was the result different when reduced ribonuclease was reoxidized while it was still in urea?
the wrong disulfides formed pairs in urea (slide 78)
amino acids have different propensities forming α helices, β sheets and turns. Some observations include:
: branching at the β-carbon atoms , as in valine, threonine and isoleucine tends to destabilize α helices because of ____
: serine and asparagine tend to disrupt α helices because their side chains contain ___ in close proximity to the ____, where they compete for main-chain ___ and ___ groups
: Glycine readily fits into all structures but its ___ renders it well-suited to ____ turns
: steric clashes
: H bond donors or acceptors, main chain, NH, CO
: conformational flexibility, reverse
why is the order of addition of the β-mercaptoethanol is key?
by adding trace amounts of β-mercaptoethanol to scrambled ribonuclease, this catalyzed the rearrangements of disulfide pairings until the native structure was regained (slide 76) pg 50
The all-or-nothing paradox of protein folding
: results from ___
- the loss of interactions will destabilize...?
: cooperative transition
- the remainder of the structure
The essence of protein folding is the tendency to retain _____ rather than by _____
: this diagram represents the ____ model which suggests that...?
partly correct intermediates, random search
: nucleation-condensation, certain pathways may be preferred (slide 81)
: what is Levinthal's paradox?
: proteins do not fold by trying every possible conformation; instead they must follow at least a partly defined folding pathway consisting of intermediates btw fully denatured and its native structure (53)
-- think of monkey and typewriter
The folding pathway from an energy landscape model. diagram
: what does this show?
: wide rim represents all possible structures accessible to the ensemble of denatured protein molecules
: as the free energy decreases, the proteins move down into narrower parts and fewer conformations are available
: at the bottom of the funnel is the folded state with its well-defined conformation (54)(slide 82)
what are metamorphic proteins?
exists in an ensemble of structures of approximately equal energy that are in equilibrium
: diagram- Lymphotactin exists in 2 conformations which are in equilibrium (pg 55) (slide 83)
diagram of human prior protein amyloid
: some parts of the protein that had been in α helical or turn conformations have been converted into β strand conformations (slide 84)
protein-only model for prion-disease transmission
a nucleus consisting of proteins in an abnormal conformation grows by addition of proteins from the normal pool (slide 85)
many proteins are ____ modified through the attachment of groups other than ___ to augment their functions
covalently, amino acids (slide 86)
other special groups are generated by chemical ____ of ____ and sometimes the peptide backbone
rearrangements, side chains
: diagram depicts chemical rearrangement of GFP in jellyfish to produce fluorescence (87)