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172 Cards in this Set

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What causes associations between water molecules?
dipole interactions (H bonds)
Why are the polar bonds in H2O linear?
The linear geometry leads to increased strength of the interaction
How many hydrogen bonds can H2O accept and give?
2 donors 2 acceptors
In liquid H2O how many Hydrogen bonds exist on average?
3.4 per molecule
When ions are solvated by H2O what happens?
Attraction or repulsion of the original ions is diminished substantially
What is a dielectric constant?
Factor by which attractive (or repulsive) force between charges is decreased by solvent (Vacuum: 1 H2O:80)
In aqueous solutions polars groups are likely to H bond with _____________.
In (aq) solution polar groups are unlikely to H bond with anything but H2O due to the hight H2O content
What is H2O's hydrophobic effect?
H2O excludes non-polar things due to its preference to interact with itself over other non-polar molecules
H2Os are more stable when they are near or far from each other?
Near
Why do H2Os like to huddle together?
If they huddle together less of the molecules are exposed to non-polar interactions => greater stability.
What is an amphiphile?
Molecules with both a hydrophilic and hydrophobic region.
What are (3) examples of amphiphilic molecules?
*Phospholipids (cell membrane) *Nucleic Acids *Proteins
Is the ionization of H2O fast?
Yes extremely fast?almost instantaneous
H2O ionizes extremely fast what is this reaction called?
rapid equilibrium reactions
What is the ionization of water reaction?
ionize water pic
None
What is the law of chemical equilibrium in water?
water equilibrium
None
At standard temperature does water ionize and to what extent does this have an effect on other molecules?
Only an extremely small amount of the H2O ionizes. This amount is not negligable and can have significant impact on other molecules in the area
Many biological reactions are regulated by something that is associated with the ionization of H2O. What is it?
Rates of many rxns are proportional to the [H+]
In pure water H and OH will be in what proportion to each other?
Equal proportion
How do you express [H+] in log form?
log
None
In pure H2O what is the concentration of the ions?
Equal @ 10^-7 M
What is the pH of various substances?
ph Scale
None
Given an acid base rxn what is the conjugate acid and conjugate base?
con acid
None
What is the rxn of dissocation of acetic acid?
acetic acid
None
What is the rxn of dissociation of ammonia?
ammonia
None
What is the derived Henderson-Hasselbalch equation?
HH
None
What is the significance of the Henderson-Hasselbalch equation?
If you know (2) of the variables you can solve for the 3rd
In the Henderson Haslbalch equation the pH varies as the ratio of the ____________/_____________.
pH varies as the ration of [basic]/[acidic]
Does a strong acid have a low or high pKa?
A strong acid has a low pKa. A strong base has a high pKa
What does a pKa indicate?
The pKa indicates which one of the acid/base pair has the higher concentration at a given pH.
What can the pKa tell you in regards to buffers?
The pKa can help decide if a given acid/base pair's buffering range is appropriate
Why is a buffer important?
Many biomolecules react with H+ and this changes their reactivity
What does a buffer do?
resists (minimizes) the pH changes
What is the effectiveness of a buffer based upon?
The concentration of the buffer. Relationship of the pKa and the pH of the solution.
What is the illustration that demonstrates buffers?
Titration Curve
At what pH is a given buffer effective?
pH ~ pKa +/- 1
What are the two types of interatomic interactions?
Covalent Bonds/Non-covalent Bones
Are covalent or non covalent bonds stronger?
Covalent bonds are stronger more stable and tend to last longer than non-covalent bonds
"From strongest to weakest, what are the main noncovalent interactions?"
Electrostatic dipolar (hydrogen bonds) van der waals (hydrophobic/philic)
What is the strength and shape of a NCI based upon?
Molecules size and shape Polarity of molecules covalent bonds
What are nonpolar noncovalent bonds?
Electrons are shared equally
What are polar noncovalent bonds?
Electrons are not shared equally and a polar molecule likely to result
"Within polar bonds, what is the unequal sharing of electrons due to?"
electronegativity/electronaffinity
What are the (6) most common atoms in biochemicals?
H C N O P S
What is the orbital shape in Hydrogen?
One sphere
"What is the orbital shape of C, N, O, P, S?"
Tetrahedral (4)
"Of the six most common atoms in biochemicals, rank them in order of decreasing electronegativity:"
O>N>S~P~C~H
"When sharing of electrons is unequal in a molecule, what is it called?"
A dipole
What functional groups have unpaired electrons?
Hydrides of O and N
Are C-H and C-C bonds polar?
"No, they are comparatively equally shared"
What determines chemical reactivity?
Polarity Most interactions occur at regions of polarity
"Compared to the hydrides near Oxygen (CH4, NH3, H2S), water has a relatively high _____________ & _____________."
High BP Large heat of vaporization
What does BP and Heat of Vaporization measure?
Measure of the energy required to overcome molecular interactions
Describe the orbitals of H2O:
(4) electron orbitals Tetrahedral (2) orbitals have e pairs (2) are empty
"Within water, how many dipoles are present?"
(3) Total (2) OH dipoles & (1) Overall molecule dipole
How many amino acids are there?
Just 20 are needed as precursors to everything
What kind of amino acids are used in proteins?
alpha AA (NH2 linked to alpha carbon)
In (aq) solution, the pKas of NH2 and COOH are such that at neutral pH _________________.
They are both in a charged state.
What form are most AA in at neutral pH?
zwitterion
At low pH, are the NH3 and COOH groups in acidic or basic form?
Both are in the acidic form
What is the isoelectric point?
pH at which net charge = zero
At high pH, are the NH3 and COOH groups in acidic or basic form?
Both are in the basic form
What is the typical pKa of COOH and NH3 groups on the Amino Acids?
COOH ~ 2.34
NH3 ~ 9.6
What is stereoisomerism?
aka: chirality, handedness
What are enantiomers?
Mirror images of each other (molecules) about the chiral carbon
L or D for proteins?
L

Proteins for life
Why is the specific chiral form of importance?
Active sites, receptors, etc react differently on the differing chiral forms
What specifically about an AA provides it its characteristics?
The R group side chains
Where is the R group attached to the AA?
alpha carbon
If a sidechain has lots of Cs and Hs, what behavior is likely to be displayed?
less polar

hydrophobic
If a sidechain has lots of Os and Ns, what behavior is likely to be displayed?
Polarity

Hydrophilic
In an acid base pair, what can be said of the polarity in comparing the ion and neutral form?
The ionized form is far more polar
What determines the biological activity of amino acids?
R side chain
What is an amide bond?
Carboxyl group of 1 amino acid linked to amino group of another
What is the potential H bond receptor in amino acids?
Carbonyl Group
What is the potential H bond donor in amino acids?
amide NH
What is the definition of protein in terms of amino acids?
polypeptides: > 50 amino acid units
What is the repeating units in proteins called?
Backbone

or

Main chain
At physiological pH, what can be said of the N-terminal and C-terminal?
charged
Are most peptide bonds cis or trans?
Most are trans and in linear form and allows for very little movement
Why does a peptide bond exhibit double bond character?
The proximity of carbonyl group draws the unshared e pair on N, giving Peptide bond partial double bond (non-rotation) character
Despite the lack of rotation around the peptide bond, rotation does exist at what bonds?
Phi: rotation around N-C(alpha)

Psi: rotation around C(alpha)-C=O
What interactions occur during primary structure?
peptide bond
What interactions occur during secondary structure?
H Bond
What interactions occur during tertiary structure?
H Bond, ionic, nonpolar, S-S bond
What interactions occur during quaternary structure?
H Bond, ionic, nonpolar, S-S Bond
Interactions of protein exteriors are likely to be:
Hydrophilic (polar)
Interactions of protein interiors are likely to be:
H bonding resulting in helix and sheets
What way does the alpha helix turn?
Right handed
Where do the R group side chains on the alpha helix point?
Outwards
Amino Acids ____ residues apart are proximate
3-4
What is the axial distance between AA on the alpha helix?
1.5 angstrum
Within the alpha helix, the C=O is H bonded with what amide residue?
C=O is H bonded to amide 4 residues down the chain
How much of a protein can be alpha helix?
0-70%
Are there specific number of residues in between H bonds on beta sheets?
No, all depends on actual arrangment and makeup of AAs
In what two forms can Beta sheets be found?
Parallel and antiparallel
How much of a protein can be beta sheet?
0-90%
In a beta turn, where does the H bond exist?
H bond on beta turns exist between groups 3 residues from each other

ex:
#1 NH <-> #4 C=O
#4 NH <-> #1 C=O
What do beta turns often connect?
They often connect antiparallel beta sheets
What are beta turns also called?
reverse turn, hairpin bend, hairpin loop
What is a beta loop relative to a beta turn?
A beta loop is significantly longer than a beta turn
Do beta loops have consistent structure?
Not necessarily.

They have no consistent:
regular structure
H bonds
Where do beta loops tend to be located?
on exterior surface of proteins
What purpose do beta loops often provide for the protein?
Beta loops are often part of external interactions with targets and other proteins
Thioredoxin:
a helix
b sheet (par and antipar)
b turn
What is this molecule and what characteristics are present?
Ribonuclease:
a helix
b sheet
b turn
loop
disulfide bond
What is this molecule and what characteristics are present?
How much energy is required to break an H-bond?
~5 kcal/mol
The presence of certain side chains can strengthen secondary structures, what are they?
*
What side chain destabalizes a-helix and b-sheet?
Proline
What is the cooperative effect?
The longer the polypeptide, the more H bonds and the more stable
Why are internal surfaces of proteins more stable?
H bonding of the protein does not have to compete with the destabalizing effects of water H bonding on the internal protein
What are the two protein classification types?
Fibrous
Globular
What is the usual function of fibrous proteins?
mechanical support
How are protein fibers usually arranged?
Into insoluble bundles

long and thin

resembles a rope, fiber, or rod
Describe connective tissue collagen:
Three intertwined polypeptide chains (triple helix)

H bonds between main chains

No tertiary structure (R groups point away from center, => no interactions)
Why does collagen fibers have no tertiary structure?
No tertiary structure R groups point away from center, => no interactions
Do globular proteins have tertiary structure?
Yes, unlike fibrous proteins, globular proteins do have R group interactions
What is the main structural feature of globular protien?
Highly folded and compact
In globular proteins, the structure is compact, why is this?
Tertiary: Mainly non-polar side chains are clustering

Secondary: In core are polar main chain peptide H bonds resulting in a-helix and b-sheets
Must a protein be folded to be active?
Yes, the protein must be folded in its 3D conformation in order to be active
What happens to misfolded proteins?
They can have little function and in some cases cause pathology

mad cow disease
alzhiemers
On a protein, there are specific regions that are involved with interactions with targets and other proteins called _________________.
Active sites
What are some features of active sites?
Structurally complement the ligand

The result of protein folding

Usually not composed of amino acid residues that are not proximate in the amino acid sequence
Active sites can have other names depending on function. Specifically: enzyme, antibodies, hormones. What are those names?
Enzyme: Catalytic site
Antibody: Combining (antigen binding) site
Hormone: receptor binding site
How does complementarity apply to tertiary structure?
Interacting side chains often complement each other in size, shape, and polarity.
There are (3) types of interactions between side chains at the tertiary level. What are they?
***interactions
What are the main factors favoring side chain-side chain interactions?
Proximity of potentially interaction side chain

Exlucion of H2O
Non polar side chains tend to be where within the molecule?
Embedded within
Polar-charged side chains tend to be where within the molecule?
Outside, interacting with H2O
Polar-uncharged side chains tend to be where within the molecule?
located both inside and outside of protein
Folding of a biologically active protein is based principally on:
Maximization of favorable interactions

Minimization of unfavorable interactions
Is a disulfide bond a primary, secondary, tertiary or quaternary interaction?
Tertiary
What is a disulfide bond?
Side chain-side chain interaction formed via a covalent bond between cysteine side chain sulfhydral group (SH) into a disulfide bridge.

Example of a post translational modification
What are some examples of post translational modification?
disulfide bridges
alkylation
hydroxylation
hydrolysis
phosphorylation
What is the oxidized and reduced form of cysteine? What form is the 'bridge'?
cysteine->cystine
Forward: oxidation
Forward: loss of 2H+ & 2e
Where are disulfide bonds most common?
Extracellular
What is the role of the S-S crosslink?
*impose constraints on polypeptide chain

*strengthen the functional structure

*more resistant to unfolding (denaturation)

*connect otherwise seperate chains (quaternary structure)
What is a motif?
A common protein structure seen in many proteins.

Some examples include:
beta-alpha-beta
alpha-beta barrel
What is a beta-alpha-beta motif?
2 beta strands are PARALLEL

(4) or more b-a-b motifs can form an alpha-beta barrel
What does it take to form an alpha-beta barrel?
(4) or more beta-alpha-beta units
beta-alpha-beta motif
What is this?
beta-alpha barrel

(4) beta-alpha-beta units
What is this?
How are alpha and beta motifs held in place?
Via side chain interactions

(tertiary structure)
What motif style does thioredoxin have?
beta-alpha-beta motif
The 4-helix motif is polar, nonpolar or amphiphilic?
Amphiphilic:
Polar groups face out
Non-Polar groups face in
Within the 4-helix motif, there are both polar and non-polar groups present. What are the details of each?
Polar side chains:
Face Outward
Interact with H2O and other polar groups

Nonpolar Groups:
Face Inward
Interact with one another
Hold helix together
Side chains fit in with other side chains (shape complementary)
What type of motif is often found in DNA binding proteins?
DNA-binding motifs

Examples:
helix-turn-helix
zinc finger
What is common to DNA binding motifs?
All contain a recognition helix: side chains which H bond to major groove of DNA double helix
What is a zinc finger?
Component of some DNA recognition motifs

his2-Zn-cys2 complex
What determines the tendancy of a protein to become a specific secondary structure?
The tendancy of a sequence to form a specific 3D structure is based upon the properties of the primary sequence
What is the sandwich structure?
(2) layers of beta layers
In a sandwich motif, where are the nonpolar and polar groups?
The nonpolar groups are within (meat) and the polar ones are exterior (outside bread side)
What is a globin fold?
Globin fold is a backbone folded into alpha helixes linked by loops

helix creates two layers

Folding provides binding site for cofactor (heme)
What are transmembrane proteins generally alpha helix?
The NH and C=O groups are polar, yet in an alpha helix form, they are paired.
How is quaternary structure held together?
Usually non-covalent interactions

occasionaly via disulfide bridges
In proteins with quaternary structure, are subunits the same?
No, they do not have to be the same
Within a quaternary structure, what are the individual units called?
monomer

or

protomer
What is an oligomer?
Monomer with finite number of units (unlike polymer, which implies unlimited number of units)
What is intersubunit communication?
Within quaternary structure, the behavior and conformation of one subunit effects the others.

The control of subunits is often key in mediating biological processes.
Within quaternary structures, what is key in regards to the shape and polarity of the subunits?
They must be complementary in shape and polarity.
What is a domain?
Two or more regions independantly folded, connected via a polypeptide chain.

Each domain usually has a descreet and specific function
Where do domains typically come from?
Domains are the product of discrete gene-coding regions called exons
What does lowering the pH do to proteins?
Protonates:

*carboxylates-->removes their (-) charge

*his side chains not already protonated

As a result, the (+) charges lead to repulsion and the protein tends to unfold
What is the MOA of thermal denaturation?
Be definition, increasing the temperature increases the kinetic energy of the system

This increases breakdown of weak interactions that keep the protein in functional shape.

Small proteins can sometimes be cooled and reformed by themselves
How do detergents work in denaturation?
Detergents are amphiphilic-->can interact with both polar and nonpolar regions of the protein

As a result, inner non-polar regions no longer need shielding from the water

Additionally, the detergent will repel each other once it has emulsified the protein, further pulling it apart
What is a surfactant called?
Detergent
What are some example detergents?
sodium lauryl sulfate
sodium dodecyl sulfate
chlorhexidine
Which AA has no chiral carbon?
Glycine

Has to hydrogens
Mb has _______ % made of alpha helix.
70%
In a beta sheet, what direction do the arrows point?
Arrows point toward C terminus
What is a subunit?
Different parts of the quaternary structure
What does lowering the pH do to proteins?
Protonates:

Carboxylates (removes - charge)

his side chains that are not already protonated