Biochem Exam 2

Alanine

Ala, A, Non-polar

Valine

Val, V, Non-polar

Phenylalanine

Phe, F, Non-polar

Tryptophan

Trp, W, Non-polar

Leucine

Leu, L, Non-polar

Isoleucine

Ile, I, Non-polar

Methionine

Met, M, Non-polar

Proline

Pro, P, Non-polar

Serine

Ser, S, Polar

Threonine

Thr, T, Polar

Tyrosine

Tyr, Y, Polar

Asparagine

Asn, N, Polar

Glutamine

Gln, Q, Polar

Cysteine

Cys, C, Polar (creates disulfide bonds with other cysteines

Histidine

His, H, Polar (can be charged)

Lysine

Lys, K, Basic (pos charge)

Arginine

Arg, R, Basic (pos charge)

Aspartate (aspartic acid)

Asp, D, Acidic (neg charge)

Glutamate (glutamic acid)

Glu, E, Acidic (neg charge)

Glycine

Gly, G, Not charged

Rank the following according to their strength as acids--rank from strongest (1) to weakest (5).

A - 4 B - 3 C - 5 D - 2 E - 1

Which of the following would NOT form a suitable buffer?

Hydrochloric acid/chloride

Under what conditions would a carboxyl group (COOH, pK 3.5) be mostly protonated?

pH < pK

Under what conditions would a carboxyl group (COOH, pK 3.5) be mostly deprotonated?

pH > pK

In aqueous solution, globules of up to several thousand amphiphilic molecules arranged with the hydrophilic groups on the surface and the hydrophobic groups buried in the center are called _____.

micelles

What term is used to describe the exclusion of nonpolar substances from an aqueous solution?

hydrophobic effect

Which of the following is an example of the hydrophobic effect?

all are examples of the hydrophobic effect

A molecule that has both a polar and nonpolar region is called _____________.

amphiphilic

If the pK value for acetic acid (CH3COOH) is 4.76 at what pH would one observe equal amounts of CH3COO- and CH3COOH?

4.76

During metabolic acidosis, ______ ventilation excretes acid in the form of _____ .

increased; CO2

The LOWER the pK value of an acid the STRONGER the acid.

True

Which of the following bond forces are important in tertiary structure:

Hydrophobic effect Hydrogen bonds Disulfide bonds

Which of the following amino acid substitutions would be most likely to effect protein function?

B

Select all the commonalities between alpha helices and b-pleated sheets. (i.e. select what is similar in both types of secondary structure)

prolines and glycines aren't suitable for the secondary structure hydrogen bonds between main chain CO and NH groups peptide bond is planar

The formation of a dipeptide from two amino acids involves A) side-chain complementarity. B) loss of water. C) oxidation of the alpha-carbon. D) reduction of the alpha-carbon. E) base catalysis.

B

The protein shown above is the human coronavirus protease. The structure contains 2 subunits, that have identical sequences. This protein can be classified as:

quaternary:homodimer

At what pH would an amino acid bear both a COOH and an NH2 group?

Never

All secondary structures in proteins involve helical forms.

False

Cys-Ala-Gly-Arg-Gln-Met In the above peptide, the amino-terminal amino acid is ____ and the carboxyl-terminal amino acid is ____

Cys; Met

For the amino acid structures shown above, the protonation state of structure A is shown at ______ pH, and the protonation state of structure B is shown at _______ pH.

low; high

Choose the amino acid that would be more likely to appear on the solvent-exposed (water facing) surface of a protein. Leu or Lys Ser or Ala Phe or Tyr Trp or Gln Asn or Ile

Lys Ser Tyr Gln Asn

Primary

The order in which the amino acids in a protein are linked by peptide bonds

Secondary

The arrangement of the backbone atoms in a polypeptide chain

Tertiary

The arrangement of all the atoms in a protein (interactions between the R groups, hydrophobic ones inside of the protein)

Quaternary

the interaction of several polypeptide chains in a multisubunit protein

Examine the four amino acids given below: Indicate which of these amino acids are associated with the following properties:

branched aliphatic sidechain - C basic sidechain - D aromatic R group - B cyclic (nonaromatic) R group - A

Which of the following amino acids carry a net positive charge at pH 7.0?

Arg, Lys

What is the net charge on the following peptide at pH 9.5? Lys-Ala-Glu-Gln-Cys-Ile

-2

What is the net charge of the pentapeptide Ala-Cys-Ser-Glu-Asn at pH 7?

-1

Any peptide which contains 2 sulfur-containing amino acids can form an internal disulfide bond.

False

The interactions that stabilize multisubunit complexes are different than those that stabilize tertiary structure.

False

Myoglobin is _____; hemoglobin is _____.

monomeric; tetrameric

The individual hemoglobin subunits and myoglobin share similar primary structure but have rather different secondary structure.

False

Which of the following fibers is correctly paired with the protein that forms the fiber?

extracellular support fibers: collagen microtubules: tubulin microfilaments: actin intermediate filaments: keratin (all are true)

Which amino acid is critical for crosslinking of keratin fibers?

Cys (disulfide bonds)

The idea that binding of one molecule of oxygen to hemoglobin enhances further binding of oxygen to hemoglobin is called _____.

cooperativity

What is the most prevalent secondary structure observed in the proteins of intermediate filaments?

alpha helices

Which of the following statements about actin are true?

Monomeric G-actin polymerizes to form F-actin. Actin filaments are polar (the ends can be distinguished).

Several oxygen dissociation curves are shown in the figure below. Assuming that curve 3 corresponds to isolated hemoglobin placed in a solution containing physiologic concentrations of CO2 and BPG at a pH of 7.0, indicate which of the curves reflects the following changes in conditions:

Increased BPG concentration 4 Increased pH 2 Dissociation of hemoglobin into subunits. 1

Match the feature of hemoglobin with the proper structural level.

Amino acid sequence in each of the alpha and beta polypeptide chains. Primary Structure 8 alpha helices in each of the subunits. Secondary Structure Spatial relationship between every atom in the individual subunits. Tertiary Structure Spatial relationship between the four polypeptide chains. Quaternary Structure

The presence of 2,3-BPG causes hemoglobin's affinity for oxygen to______.

decrease

Which amino acid is involved in heme coordination in both hemoglobin and myoglobin and is highly conserved?

Histidine

Calculate the fractional saturation for myoglobin when pO2 is a. 20 torr and b. 80 torr. Assume K=2.8.

a. 0.88 b. 0.97

Both myoglobin and hemoglobin exhibit cooperative binding to oxygen.

False

Conservative amino acid mutations (i.e. Val to Leu) are likely to affect stability or function of a protein.

False

Which of the following fatty acids have the lowest melting point?

Linoleate (18:2)

Which of the following types of lipids can be found in cell membranes?

glycerophospholipids cholesterol cerebrosides gangliosides

Select the statements the describe fatty acids:

can either be saturated or unsaturated. mostly found with an even number of carbons

In what way(s) do sphingolipids differ from glycerophospholipids?

Sphingolipids are not built on a glycerol backbone. Sphingolipids contain an acyl group attached via an amide bond on the serine potion of the sphingosine.

Show which are characteristics of peripheral membrane proteins and which are characteristics of integral membrane proteins.

peripheral bind to the surface of membranes integral have transmembrane domains

Which of the following is most likely to be an unnatural fatty acid?

17:3△t9,12,15 (uneven number of carbons)

Sphingosine is not a component of:

glycerophospholipids

Select the fatty acid in each pair that has the higher melting temperature.

16:1c9 or 16:2c9,12 - 16:1c9 18:0 or 18:1c9 - 18:0 18:0 or 20:0 - 20:0

Membranes are generally symmetrical, i.e., the outer face is composed of the same number and types of phospholipids as the inner face.

False

Phospholipids can freely diffuse from the interior leaflet of the plasma membrane to the exterior leaflet without the assistance of enzymes.

False

Triglycerides are fat storage molecules not typically found in membranes.

True

Match the description given with the correct lipid. (Answers may be used more than once)

Primary storage form of lipids. Triacylglycerols. Provides stability in the plasma membrane. Cholesterol Isoprene derivative Cholesterol Commonly found in nervous tissue Sphingomyelin Sphingosine backbone with several carbohydrates attached Ganglioside Glycerol backbone with two fatty acyl groups Glycerophospholipid

A membrane's fluidity is largely determined by the percentage of _____________.

unsaturated fats

The concentration of Ca2+ in the endoplasmic reticulum (outside) is 1 mM, and the concentration of Ca2+ in the cytosol (inside) is 0.1 μM. Calculate ΔG at 37°C when the membrane potential is −50 mV (cytosol negative)

-33,388.1

Which of the following is/are true regarding the glucose transporter?

it transports glucose down it's concentration gradient binding of glucose causes a conformational change so that the transporter is never open on both sides of the membrane

Match the transporter (A- blue, B- green, C- light purple) with it's description.

A - Symporter B - Uniporter C - Antiporter

Indicate whether the following compounds are likely to cross a membrane by simple diffusion or facilitated diffusion transport:

aspartic acid facilitated carbon dioxide simple glucose facilitated

Which of the following will cause the opening or closing of a gated ion channel?

voltage change

What substance will be transported through an aquaporin?

water

In the sodium-potassium pump:

sodium is transported out of the cell and potassium into the cell, both against concentration gradients

Active transport is uniquely characterized by:

the tight coupling of an input of energy, with the species going from a lesser concentration to a greater concentration.

Facilitated (Mediated) diffusion across a biological membrane:

is driven by a difference in solute concentration.

Energy requiring transport mechanisms include

Active transport

Inside a nerve cell at rest, [Na +] is ____ and [K+] _____ relative to the concentrations seen outside the cell.

low, high

The Hydrophobic Effect

The exclusion of nonpolar substances from an aqueous solution

Amphiphilic

experience both hydrophilic interactions and the hydrophobic effect. most lipids are amphiphilic.

the pH scale

The ionization of water can be described by a dissociation constant, K:

(products)/(reactants)

acid

substance that can donate a proton

base

a substance that can accept a proton

pK helps to

determine the strength of an acid (lower pK = stronger acid, higher pK = weaker acid)

Henderson-Hasselbalch Equation

*pK is the specific pH where there are equal concentrations of base and acid *log > 1 --> always positive, pH rises *log < 1 --> always negative, pH lowers

pH < pK

everything will be protonated

buffer

*weak acid/conj base system* aids in resisting changes in the pH of a system

Amino Acids (L and D groups)

L --> amino group to the left of the alpha carbon D --> amino group to the right of the alpha carbon L is the most common in nature

Amino acids are linked via a

condensation reaction

Amino acid residues

only the residual atoms remain.

Exopeptidases

enzymes that act from the end of the chain

Endopeptidases

enzymes that act from the middle of the chain

Oligo-

several amino acids linked together (8-20 usually)

Poly-

many amino acids together (20+)

Directionality of a protein

N-terminus to the C-terminus (N-terminus = the amino group, C-terminus = COOH)

The two types of secondary structures

- alpha helices (helix) - beta pleated sheets

The α helix

- Hydrogen bonds along the helical axis stabilize this structure - Right-handed (R groups face out) - HB only form between neighboring or very close carbons

Hydrogen Bonding β Sheets

- Parallel --> all amino groups run on the same end - Antiparallel --> amino groups run in opposite direction

Tertiary structures are heavily influenced by ...

the hydrophobic effect ... the interactions between R groups and whether they are polar or nonpolar plays an important part. nonpolar R groups will be folded inside of the protein and the polar R groups will face outward. (also impacted by HB, electrostatic, and Van Der Waals)

The only covalent bonds found in tertiary structures are ...

disulfide bonds formed between two cysteines.

Why do globular proteins have a hydrophobic core and hydrophilic surface?

because of the hydrophobic effect and its influence on the tertiary structure

Advantages of quaternary structures

Large proteins can be constructed incrementally Allows for some proteins to be assembled outside the cell Minimized impact of errors in transcription and translation Affords an opportunity for subunits to influence and regulate each other (cooperative behavior)

Nomenclature for quaternary structures

Monomer (no quaternary structure) Dimer Trimer Tetramer Pentamer Hexamer Homodimer - same subunits Heterodimer - different subunits

Fates of misfolded protein

Chromatography

the main way of isolating proteins - separating proteins based on a specific characteristic - Size Exclusion Chromatography - Ion Exchange Chromatography - Affinity Chromatography - High Performance Liquid Chromatography (HPLC)

Electrophoresis

a method in which charged molecules move through a gel-like matrix under the influence of an electric field

Mass Spectroscopy

a method for analyzing protein structure by measuring the size of peptide fragments.

when pI = pH

there is a 0 net charge

the pI is ...

the average of the pK values of all ionizable groups in a molecule

When calculating pI

1. order pK values 2. determine charge (is it protonated/deprotonated at that pH) 3. use those charges to determine what pH will get a net charge of 0 pI=(pK+pK)/2

Mass spec reveals ...

the amino acid/primary structure

NMR is good for ...

looking at small proteins

When identifying the amino acids on our exam ...

it will spell out a word

For amino acids with no other ionizable groups (other than the amino group and the COOH)

the pI will be equal to 6.75

Myoglobin

- globular structure - monomer (no quaternary structure) (1 alpha subunit or 1 beta subunit) - 8 alpha helices - contains a heme group which binds to the oxygen

Heme is a ____ group

prosthetic (covalently bonded organic molecule)

Structure of heme

Iron is coordinated by 6 different atoms

- 4 nitrogens - a histidine residue - and oxygen that bids to the top

K of Myoglobin

K=2.8 torr for human myoglobin (K values will be given on exam)

Fractional Saturation (Y)

the proportion of myoglobin molecules that have bound O2

Mb and Hb are similar in their ____ and ____ structures

secondary, tertiary

Hemoglobin

- tetramer - 2 alpha subunits, 2 beta subunits - binds 4 O2 molecules

Mb and Hb are only ~___% identical in primary sequence

18

Mb & Hb primary structures

- Invariant --> cannot change, must be the same in both - Conservative --> can change but must have similar properties (if nonpolar, the new one also needs to be nonpolar) - Variable --> can and will change, doesn't matter how different they may be

Hb _____ O2 in high concentrations

accepts

Hemoglobin structure changes when oxygen is bound to it

When binding occurs, it causes a shift so that the next heme group is open and receptive for binding until the fourth (last) oxygen binds to the molecule.

Bohr effect

In high pHs & areas of higher O2 concentration, the hemoglobin is more prone to being in the relaxed (oxy) state where it takes up oxygen (ie the lungs). In areas of low O2 concentration and low pH, the hemoglobin shifts to the tense (deoxy) state where it releases the oxygen it's carrying (ie tissues).

BPG binds only to the ___ conformation of Hb

tense (deoxy)

Myoglobin is ____ likely to give up its oxygen than hemoglobin

less

Three types of cytoskeletal filaments

- Actin filaments - Intermediate filaments - Microtubules

Actin is the ...

ATP binding protein

Actin has a globular subunit that

acts in a double chain to create a microfilament.

F-actin

- filamentous - long strings of multiple g-actins together - positive end --> quicker addition of the monomers - negative end --> slow addition of monomers

Dimers (tubulin)

composed of both alpha and beta tubulin dimers contain the GTP binding sites

Microtubules

- hollow fibers built from tubulin fibers - usually contain 13 protofilaments

Keratin

- intermediate filament - 2 alpha helices twist together: coiled-coil - left-handed twist - link together through covalent disulfide bonds

Collagen

- intermediate fiber - has hydroxyproline in it - triple helix (3 twisted together is a mature collagen fiber)

Fatty acids

- long-chain hydrocarbons - the even-numbered C16 and C18 species are most common in plants and animals - can be saturated with hydrogens ** saturated will not have a double bond - can be unsaturated or polyunsaturated ** unsaturated contains one or more double bonds ** double bonds are usually in the cis position

Delta and Omega Naming Systems

Delta: - start from the COOH carbon - Number of Carbons:Number of Double Bonds(superscript(Delta)Carbons where double bond starts) Omega: - Start from the Me carbon - Number of Carbons:Number of Double Bonds(omega)-Carbon where first double bond is seen

Only storage lipid we spoke about

triacylglycerols

Triacylglycerols

- the ester bond linking each acyl group is the result of a condensation reaction - 3 fatty acids linked to a glycerol backbone

Glycerophospholipids

2 fatty acids linked to a glycerol, with a phosphate group attached to the glycerol. (glycero --> from the glycerol, phospho --> phosphate group). has many different phosphate groups that it could be.

Phospholipases

cleave glycerophospholipids at specific sites

Sphignolipids: glycolipid

- some have CHOs as a head group ** cerebroside --> monosaccharide ** ganglioside --> polysaccharides/disaccharides (gang of sugars)

Sphingomyelin

has a phosphocholine or phophoethanolamine head group

Sphingosine

derived from palmitate and serine

Lipids that are isoprene derivatives

- cholesterol - fat soluble vitamins (A,D,E,K) are as well

Cholesterol

- RING STRUCTURE - amphiphilic isoprenoid - Important in membranes and steroids

A lipid bilayer

Forms spontaneously due to the hydrophobic effect - made up of: glycerophospholipids, sphingolipids, cholesterol, and proteins

The double bonds in a lipid ...

- kink the acyl change - account for the fluidity/fluid nature of some lipids - make it less efficient for packing together

The lipid membrane is ...

made up of both saturated and unsaturated fatty acids to help keep it fluid but not too fluid

Melting points of saturated vs unsaturated fats

Saturated fats with more carbons have the highest melting points. Saturated fats in general will have higher MPs. Unsaturated fats with one double bond will be higher than ones with more DBs, but still lower than saturated fats. Aka ... more carbons and no double bonds = high melting points, more double bonds = lower melting points.

Diffusion in membranes

Lateral --> favored Transverse --> not favored (the center of the membrane is hydrophobic, takes more energy to do this)

Protein associations with a membrane

- Integral membrane proteins - Peripheral membrane proteins - Lipid linked membrane proteins

Membrane proteins can span the bilayer

A membrane-spanning 𝛼 helix - Part of the protein bacteriorhodopsin - One can identify a transmembrane helix by its sequence (rich in highly hydrophobic amino acids) Beta Barrel - fully hydrogen-bonded where they span the width of the bilayer. hydrophobic side chains (green) on the barrel exterior face the bilayer core. aromatic residues (gold) are located mostly near the lipid head groups.

The fluid mosaic model

proteins can move laterally across a membrane but not transversely

Scramblase

switches to the inside side of a membrane or to the outside side of a membrane

Flippase

flips to the inside

Floppase

flips to the outside

Gibbs free energy, G

A measure of the free energy of a system based on H and S Units = J • mol

ΔG = ΔH – TΔS

ΔG = Gibbs free energy change ΔH = Enthalpy change ΔS = Entropy change

When ΔG <0

the reaction is spontaneous or exergonic. (generates energy)

When ΔG >0

the reaction is nonspontaneous or endergonic (requires energy)

Free Energy Changes in Coupled Chemical Reactions

The voltage across a membrane caused by

ion transport is the membrane potential **equation and other constants will be given on exam**

The equation reduces to the following when: monovalent ion (Z=1) at 20℃

An Action Potential

1. Depolarization --> membrane shifts from -70mV to +50mV --> caused by Na+ channels opening causing Na+ to enter the axon 2. Repolarization --> K+ channels open, K+ moves out of the cell

Propagation of a Nerve Impulse

Due to the hydrophobicity of the lipid bilayer, small ions like K+ are unable to leave the cell by simple diffusion.

True: charged ions are impermeable to the membrane

What is responsible for the extremely rapid propagation of axon potential?

Axons are insulated with a myelin sheath which prevents ion movement except at the nodes between myelinated segments.

Which of the following does occur when neurons are stimulated?

Neighboring Na+ channels open in response to the change in membrane potential, resulting in a wave of depolarization. Depolarization stimulates the opening of voltage-gated K+ channels, resulting in repolarization. Recovery involves the movement of Na+ out of the cell and K+ into the cell.

Porin

- always open - trimers - pores - high to low concentration - OmpF --> connects

Structure of the K+ Channel from S. lividans

4 subunits, alpha helices

K+ Channels ...

selectively filter

Operation of the Voltage-Gated K+ Channel

- open or close in response to the concentration gradient (or otherwise called the voltage differences across the membrane) - still a passive transport

Structure of an Aquaporin Subunit

- full aquaporin (not pictured) is made up of four subunits (single subunit pictured)

Operation of the Red Blood Cell Glucose Transporter

1. Glucose binds to a site on the transporter that faces the cell exterior 2. Glucose binding triggers a conformational change that exposes the glucose-binding site to the cell interior. 3. Glucose dissociates from the transporter. 4. The transporter reverts to its original conformation.

Types of Membrane Transport Systems

A pore that simultaneously transports two different molecules in different directions is called a(n)

antiporter

A pore that simultaneously transports two different molecules in the same direction is called a(n)

symporter