BCHM Exam 2

What is the difference between channel proteins and carrier proteins?

Channel proteins have a fixed structure and a core

Carrier proteins change their structure and do not have a core

Carrier proteins grab and transport molecules in and out of the cell

There is a higher concentration of sodium __________ the cell

outside

Explain how voltage-gated sodium channels work:

• Voltage-gated sodium channels do not require activation energy, they are passive as they are activated by changes in membrane voltage (depolarization response)

• Na⁺ ions travel through the plasma membrane via protein channels

  • these protein channels are a pore with an inactivation gate and an activation gate towards the inside of the cell

• the inside of the cell has a resting potential with negative charge

• Na⁺ ions have an electrical attraction to this negative charge

• Depolarization will occur

  • the positive charge of the Na⁺ traveling through the pore of the membrane opens the activation gate (slow process)

  • transitions from resting potential to peak potential (positive charge)

• Re-polarization occurs next

  • the sodium travels back out of the cell through the channel

  • the ball-and-chain structure that’s the inactivation gate swings closed and plugs the pore, closing the gate and inactivating it

  • transitions from peak potential back to resting potential

Describe the structure of pores:

• pores have 4 subunits (labeled P) that surround a core

• each P subunit consists of 6 helices (labeled S)

• when a charge moves from the outside to the inside of the membrane through a pore, the 3D structure of helices S5 and S6 change (helices closest to the pore channel)

True or False:

Since Na⁺ and K⁺ both have a +1 charge, they travel through the same pore channels

False

• the geometries of the selectivity filters of Na⁺ channels are different than the selectivity filters of K⁺ channels

• K⁺ cannot pass through Na⁺ channels and vice versa

What distinguishes R groups from one another?

the R groups

__________ R groups are acidic

carboxylate

__________ R groups can covalently bond with each other

Sulfur

True or False:

Our cells contain little vesicles that store amino acids for when they are urgently needed

False

• Amino acids can not be stored

• we must consume outside protein from our nutrition

True or False:

Proteins can be broken down, and their amino acids recycled

True

List the essential amino acids

histidine

isoleucine

leucine

lysine

methionine

threonine

phenylalanine

valine

tryptophan

What is PDCAAS? What is it’s significance?

PDCAAS = Protein Digestibility Corrected Amino Acid Score

• gives us information on which type of foods supply us with which type of amino acids

• rates foods on how much amino acid variety they provide

• Ex. Egg whites have a PDCAAS of 1

  • this value is perfect

  • egg whites supply our bodies with all essential amino acids

What are the 4 categories that amino acids are listed under?

1) Non-polar, Aliphatic

2) Aromatic

3) Polar, Uncharged

4) Charged

There are ____ amino acids that serve as the building blocks of proteins in the human body

20

What is an example of a nutrition disorder involving protein?

Kwashiorkor

• Kwashiorkor is a nutrition disorder in which there is a disproportionate consumption of protein to other dietary needs

• there’s a lack of consumption of dietary protein

• negative Nitrogen balance

• a symptom of Kwashiorkor is ascites (accumulation of water that causes bloating of the abdomen)

• also negatively impacts the liver

What are zymogens? Give examples

• zymogens are the inactive form of an enzyme, protein, or hormone

• zymogens have to undergo a biochemical change to activate

• Ex. pancreatic hormones are formed as zymogens because they are proteolytic (protein-cleaving)

• they are formed as zymogens to prevent them from destroying the cells of the pancreas that produces them

• the pancreatic hormone zymogens are secreted by the pancreas and into the small intestine to be activated

• if these enzymes are activated too soon in the pancreas, an inflammatory condition called pancreatitis occurs

• Examples of zymogens: pancreatic hormones, pepsinogen, insulin

How does the consumption of amino acids impact the liver

• the liver needs an adequate amount of amino acids to function property

• a negative nitrogen balance and a positive nitrogen balance should both be avoided

negative Nitrogen balance

• not consuming enough protein

• albumin is the most abundant protein produced by the liver

• the amino acids that make up albumin must be consumed in our diet

• a low concentration of albumin in the blood causes fluid to leak from the blood vessels which leads to bodily edema

positive Nitrogen balance

• consuming too much protein

• the break down of amino acids occurs in the liver

• too high of a concentration of amino acids causes the liver to convert some to ammonia (NH₃) which is converted to urea

• someone with liver damage/dysfunction can not always convert this excess ammonia into urea, causing a buildup of ammonia in the bloodstream which becomes toxic

Describe the Sodium dependent cotransport of an amino acid into the cell in the intestines. Why does this occur?

• Sodium dependent cotransport can occur to move amino acids into the cell against their concentration gradient by coupling amino acid transport with sodium transport

• Sodium binds to the amino acid transporter (a passive process)

• this increases the carrier’s affinity for the amino acid, making the amino acid available to bind to the carrier → forms a sodium-amino acid cotransporter

• a 3D conformational change occurs in the complex, resulting in the delivery of the sodium and amino acid into the cytosol of the intestinal cell

• that sodium then gets pumped back out of the cell

Draw and describe the peptide bonds between two amino acids:

• two amino acids (in the trans configuration with steric rotation) are chained together by a peptide bond

• Peptide bond

  • the Nitrogen of one amino acid binds to the carbonyl Carbon of the next amino acid

  • this is a rigid bond that can NOT rotate

• Psi bond

  • bond that connects the carbonyl Carbon to the alpha Carbon (that is bonded to the R group)

  • can rotate

• Phi bond

  • bond that connects the Nitrogen atom to the alpha carbonyl Carbon that contains an R group

  • can rotate

Which bonds can rotate within a peptide bond?

• the psi and phi bonds rotate

• they rotate around around the peptide bond (they are the bonds that are the next atom over from the peptide bond)

• the stearic rotation impacts how proteins fold

How is the shape/rotation of polypeptides determined?

• the Levinthal Paradox applies to polypeptides

  • the folding of a protein happens very quickly and spontaneously, but it is not random, even though there are so many different conformations that are possible

  • proteins fold so that they are in the most stable, lowest energy conformation

• the Ramachandran plot shows how certain bond angles are more likely to be produced when polypeptides are folded because those angles are the most viable stearic rotations

  • most molecules default to these conformations

• certain conformations are eliminated as possibilities because they are physically impossible, have too much stearic hinderance, or they are just not thermodynamically-favorable

When do proteins have their highest energy? When do they have their lowest energy?

highest energy = unfolded states

lowest energy = folded states

Define: amorphous aggregates

proteins that have been incorrectly folded

Define: native state

state of properly-folded proteins

Define: chaperones

proteins that help fold other proteins into their lowest energy state

What are the enantiomers of amino acids? Which one(s) can be metabolize?

• there are L amino acid enantiomers and D amino acid enantiomers

• we can only metabolize the L amino acids

What is needed to insert an amino acid into a protein?

ATP is needed to insert an amino acid to a protein chain because the ATP molecule will “charge”/activate the amino acid beforehand

What are the different functions of proteins?

• function as enzymes 

• they are transporters (move ions or other proteins)

• they are receptors

• cell junctions

• provide structure (collagen, muscles, etc.)

• antibodies 

• antigens (trigger immune response)

a __________ is released in peptide bond formation

water molecule

the formation of a peptide bond creates __________ entropy

lower entropy when a peptide bond is created because it’s a rigid bond that provides structure/organization

What are the levels of protein structure?

1) Primary Structure

• what amino acids are present and in what order they are arranged in

• the sequence of amino acids

2) Secondary Structure

• the polypeptide backbones begin to fold into one of two structures: alpha helix or a beta-pleated sheet

• specifically, Hydrogen bonding occurs between the H and N of one peptide bind, and another Hydrogen bond occurs on the O of the Carbonyl group of the next peptide bond

• these hydrogen bonds hold the alpha helix structure or the beta-pleated sheet together

• Alpha helix

  • right-handed spiral structure

• Beta-pleated sheet

  • crimped like a sheet

  • can be parallel or antiparallel

    • antiparallel is more stable: there’s less bond angle strain because the bonds are lines up and not angled

  • two strands of beta sheets are connected by turns

    • Glycine and Proline are involved in turns

• there is no R-group involvement in secondary structures

3) Tertiary Structure

• tertiary structure is stabilized by R-groups

• the secondary structures fold based on the interactions between the R-groups that become involved

• types of R-group interactions:

  • electrostatic interactions

  • hydrogen bonds

  • hydrophobic interactions

  • disulfide bonds

4) Quaternary Structure

• two or more separate polypeptide chains (subunits) assemble and interact non-covalently to form a functional protein complex

• this is an allosteric change

• not all proteins reach quaternary structure

What causes proteins to denature? What causes proteins to renature?

• denaturation occurs under heated conditions

• renaturation can occur spontaneously in some proteins, where they refold back into their correct, original shape

Define Supersecondary structures:

• supersecondary structures are a combination of a few secondary structures: alpha helices and beta-pleated sheets (so not quite secondary but not quite tertiary structures)

• supersecondary structures can get added to proteins to fix it if it misfolds (and the cell won’t have to trash the entire protein)

• motifs and domains are supersecondary structures

• Motifs

  • play a structural role only

  • will fall apart if isolated from protein

  • types of motifs: beta-alpha-beta (a), meander (b), helix-turn-helix (c), barrel (d), greek key (e), EF hand, zinc finger, leucine zipper

• Domains

  • independent and won’t fall apart if isolated from the protein (higher level of organization than motifs)

Describe the Leucine Zipper:

• Leucine Zipper is a 7 amino acid sequence that repeats itself

• these 7 amino acids are labeled abcdefg

• the Leucine is located at the “d” position

• Leucine is hydrophobic, which makes it easier to unzip the helices of DNA

• the leucine zipper controls transcription (allows transcription-factor subunits to come together and bind to specified DNA sequences)

Define Microstate vs. Macrostate. Is the Macrostate or the Microstate of a protein consistent?

Macrostate is the arrangement of all the atoms in a protein (how the protein is folded as a whole)

• macrostate is consistent

• Ex. the entire folded protein

Microstate is the exact arrangement of atoms at a particular instant

• microstate is not consistent because proteins can vibrate

• Ex. the primary structure

Explain hemes and pyrrole rings

• heme groups are a part of myoglobin and hemoglobin proteins, that contain iron to help bond oxygen

• hydrophobic

• hemes are a linkage of four pyrrole rings (linked by methene bridges)

• has Iron in the center

• macrophages break down the heme, which gets converted to biliverdin, and then that gets converted to bilirubin

What structures contain hemes and pyrrole rings?

myoglobin and hemoglobin proteins are both contain a linkage of four pyrrole rings as part of their heme group

Describe the structure and function of myoglobin

• myoglobin is a storage protein that stores oxygen in the muscle cells

• myoglobin has a very high oxygen affinity

  • myoglobin’s oxygen affinity is NOT affected by pH or CO₂ fluctuations

  • has a hyperbolic oxygen-binding curve

• has a heme

• has 1 subunit made up of 8 alpha-helix structures

• contains two histidine (an amino acid) on opposite sides of the heme plane (one distal histidine and one proximal histidine)

• proximal histidine is directly bonded to (and anchors) the Iron at the center of the pyrrole ring heme structure

  • the proximal histidine pulls the iron into the plane of the heme when oxygen binds to the iron

• distal histidine forms a hydrogen bond with the bound O₂ molecule to stabilize it

  • distal histidine helps control access to the heme by other gases (it acts as a “gate” to the heme)

  • Ex. carbon monoxide should not be let in because it is toxic, even though it wants to bind to the heme’s iron

• 153 amino acids long

• myoglobin will release oxygen when the partial pressure of oxygen drops in the muscles (during muscle contraction, heavy exercise, or when blood flow is restricted)

Describe the structure and function of hemoglobin

• hemoglobin carries oxygen from the lungs and to the various tissues of the body

• has 4 subunits: 2 alpha helices and 2 beta sheets

  • so hemoglobin has 2 dimers: α₁β₁ dimer and α₂β₂ dimer

  • these dimers can rotate (they rotate 15 degreed after oxygen binds)

• the dimers surround a central solvent channel, which contains water and 2,3-bisphosphoglycerate

• exhibits the Bohr Effect

• hemoglobin will be in one of two states: deoxyhemoglobin or oxyhemoglobin

• deoxyhemoglobin is in a Taut state (T-state)

  • will release oxygen to tissues

  • stabilized by 2,3-bisphosphoglycerate (2,3-BPG), which prevents oxygen from rebinding (Ex. of negative allosterism: prevention)

  • central channel is wide

  • bound to little/no oxygen

  • low oxygen affinity

• oxyhemoglobin is in a Relaxed state (R-state)

  • central channel is narrowed

  • high oxygen affinity

  • oxygen binds

• positive cooperation occurs in hemoglobin as it transitions from Hb-deoxy state to HbO₂ state - this is when a 3D structural change occurs (allosteric change) and this process releases O₂

  • The iron (Fe) in the center of the heme must be in Fe²⁺ state to bind to oxygen

  • Oxygen binds to Fe²⁺ and makes it Fe³⁺ which pulls the Iron and the proximal histidine up into the same plane as the heme - structural 3D change - 15 degree rotation

  • Fe³⁺ gives its electron to oxygen, creating a superoxide ion which is a free radical (which are dangerous), so an extra electron binds to Fe³⁺ to make it Fe²⁺ as the oxygen is being released

Describe the gas exchange that occurs in red blood cells:

• CO₂ from tissues (about 20%) bind to the N-terminus of the hemoglobin molecule, creating HbCO₂

  • creates carbamino hemoglobin

  • CO₂ + Hb → HbCO₂

• the rest of the CO₂ from tissues gets added to water, then carbonic anhydrase reacts those molecules to form carbonic acid

  • CO₂ + H₂O —CA→ H₂CO₃

• the carbonic acid dissociates into a bicarbonate ion and a proton

• that bicarbonate ion leaves and at that same time Cl^- ion enters to balance the charge

• the proton binds to hemoglobin, causing an allosteric change

• Bohr Effect

• oxygen is taken out to be delivered to the tissues

Describe the Bohr Effect

Bohr Effect:

an increase in carbon dioxide concentration or an increase in acidity (decrease in pH) reduces hemoglobin’s affinity for oxygen, causing it to release more oxygen to body tissues by transitioning from deoxy state to oxy state which is an allosteric change

Describe the gas exchange that occurs in the alveoli in the lungs:

• CO₂ removed from carbamino hemoglobin, then that CO₂ gets released

  • HbCO₂ → Hb + CO₂

• oxygen that was delivered from the lungs displaces the proton on hemoglobin

  • O₂ + HbH⁺ → HbO₂ + H⁺

• bicarbonate ions and protons (released from binding with hemoglobin) are combined to form carbonic acid, which then is turned into water and CO₂ (with the help of carbonic anhydrase)

• HCO₃^- + H⁺ → H₂CO₃ —CA→ H2O + CO₂

• that CO₂ leaves the lungs

What are cross-bridges?

• protons coming out of tissues forms a cross-bridge

• cross bridges are formed in hemoglobin between the two parts of the beta subunit and between the beta subunit and the alpha subunit

An increase in partial pressure of oxygen in the tissues will cause a(n) __________ in the amount of oxygen to bind to hemoglobin

increase

What must occur when Oxygen binds to Fe³⁺?

• Fe³⁺ gives its electron to oxygen, creating a superoxide ion

• superoxide ions are free radicals (which are dangerous to our cells)

• oxygen is prevented being released in free radical form until an extra electron binds to Fe³⁺ to make it Fe²⁺ again as the oxygen is being released

What is the difference between the graphical representation of how readily hemoglobin and myoglobin binds to oxygen (at different partial pressures, which means at different amounts of oxygen availability)?

hemoglobin

• hemoglobin has a sigmoidal curve

• this is due to hemoglobin’s positive cooperativity

• hemoglobin is a quaternary protein with 4 subunits

• oxygen binds to the first subunit

  • a relatively slow process

  • first subunit’s oxygen affinity is low

  • when the oxygen binds and the Fe and proximal histidine of the F-helix are moved into the plane of the heme, that structural change is recognized by the second subunit

• the second subunit binds with oxygen after that signal, which signals the third subunit to bind, then that signals the fourth subunit to bind

• this binding sequentially gets faster each time

• this is called positive cooperativity

• positive allosteric changes are occuring

• the positive allosteric effector is Oxygen (that is the molecule that stimulates a response)

myoglobin

• myoglobin has a hyperbolic curve

• myoglobin is only made up one one subunit that has a tertiary structure

• myoglobin binds oxygen independently, without cooperative binding (only has one binding site, and one heme)

Which binds to oxygen more tightly: hemoglobin or myoglobin

myoglobin because it has a high affinity for oxygen

Which can carry more oxygen: hemoglobin or myoglobin?

hemoglobin can carry more oxygen because unlike myoglobin which only has one subunit (and therefore can only carry 1 oxygen molecule), hemoglobin can carry four oxygens as it has four subunits

makes hemoglobin ideal for transport and myoglobin ideal for storage

What protein structure level is myoglobin?

tertiary

What protein structure level is hemoglobin?

quaternary

Describe sickle-cell anemia:

• sickle-cell anemia is a recessive genetic defect within the Beta subunit of hemoglobin

• the 6th position amino acid in a healthy individual’s hemoglobin is glutamic acid, but the 6th position is mutated to valine in an individual with sickle cell anemia

• in the deoxyhemoglobin state, a hydrophobic protrusion in one Beta subunit finds a hydrophobic pocket a B subunit of another hemoglobin molecule

• this causes hemoglobins to clump together in the capillaries

• the shape of the red blood cells is impacted when the membrane collapses and loses its smooth disc shape

• electrophoresis is used to detect sickle-cell traits and diagnose sickle-cell disease

__________ proteins are more structural

Fibrous

__________ proteins are functional

globular

Which of these proteins are globular? Which are fibrous?

Hemoglobin

Insulin

Collagen

Antibodies

Hemoglobin = globular

Insulin = globular

Collagen = fibrous

Antibodies = globular

Describe the structure of antibodies:

• antibodies are in a Y-shape

• on the ends of the Y are variable regions (one heavy and one light)

  • Variable regions are what differentiate antibodies

  • these are the regions that antigens bind to

• towards the base of the Y are constant regions (heavy and light)

  • constant regions are the same in all antibodies

• shows structure/function coordination as this benefits the cell:

  • when a new antibody needs to be created, only the variable regions have to change - the constant regions always stay the same - so a whole entire new antibody doesn’t have to be made

Describe insulin

• Insulin has a globular structure

• Insulin is a hormone that’s created as a zymogen

• Insulin gets activated when the C-peptide is cut off the insulin

Describe collagen

• collagen is a fibrous protein

• each collagen molecule is made up of three polypeptide chains wound into a triple helix

• collagen molecules line up side-by-side and are cross-linked to form fibrils (that are strong)

  • the cross-linkages are created out of modifications from the enzyme lysyl oxidase

  • oxidizes lysine into allysine

• the amino acids that are prominent in collagen are:

  • Glycine: in alpha helices - allows tight packing

  • Proline: cyclical amino acid that helps maintain the helical structure

  • Hydroxyproline: helps stabilize the triple helix

  • Lysine

Describe the process of protein degradation?

• built into the amino acid sequences are pest sequences, which signal for degradation

• Ubiquitin is the protein that “tags” a misfolded protein to be degraded

• Ubiquitin recognizes the pest sequence, binds to it with the help of ATP

• That tagged protein gets sent to the proteasome, a large protein chamber where degradation occurs

  • the cap of the proteasome lets in the protein and unfolds it (this uses ATP)

  • the unfolded protein moves through the proteasome to the core, where it is chopped up and separated into amino acids that can get reused by the cell

Why must misfolded proteins be degraded or refolded?

• our bodies want to break down misfolded proteins to recycle those amino acids

• a large amount of misfolded proteins present can be pathological

• misfolded proteins can clump together - this can clog neurons and cause Alzheimer’s disease

Explain the process of protein folding:

• chaperone proteins help fold proteins properly

• Hsp 70 (heat-shock protein) is a chaperone

• Hsp 70 binds to the hydrophobic regions of unfolded proteins

• Hsp 70 then uses ATP to partially fold proteins (into a partially folded intermediate)

• Hsp 70 transfers the intermediate to the chaperonin (a large, barrel-like protein) to finish the folding of the protein using ATP

What are the 3 ways a protein can fold?

1) proteins can spontaneously fold by themselves without a chaperone

2) proteins can fold with the help of a chaperone only

3) proteins can fold with the help of a chaperone and a chaperonin