structure relationship function of proteins

Question 1

Explain 4 levels of protein structural organization and their significance for protein function

Answer 1

1. primary
   
   1. protein sequence
2. seconday
   
   1. main types
      
      1. alpha helices
      2. beta pleated sheets
      3. beta turns
      4. random coils
   2. super secondary structures- all involved with DNA binding domains
      
      1. HTH
      2. HLH
      3. LZ
         
         1. K is located at every 7th aa
      4. ZF
         
         1. stabalizes interactions
3. tertiary structure
   
   1. 3d structure creates specific pockets on the protein, which are essential for the function (structure=function)
   2. eg
      
      1. enzymes-have active(catalytic) sites that process biochemical reactions
      2. myglobin- has a pocket that binds heme and O2
      3. plasma membrane-receptors have binding sites for hormones, growth factors
   3. protein domains
      
      1. transmembrane-contains a helices of hydrophobic aa
      2. ligand binding-binds extracellular molecules (hormones)
      3. cytoplasmic-can bind molecules involved in intracellular signaling(kinases)
      4. atp binding pocket
4. quarternary structure- association of different protein chains
   
   1. examples
      
      1. type 2 collagen
         
         1. 3 identical proteins chains are held together by non-covalent interactions and covalent bonds (homotrimer)
      2. heterotrimeric G proteins
         
         1. 3 diff protein chains are held together by noncovalent interactions
      3. hemoglobin
         
         1. 2alph 2beta are held together by noncovalent interactions

Question 2

list three advantages to having quartenary structures

Answer 2

1. creates cooperativity between the protein subunits
   
   1. in Hb this increases O2 binding and realease
2. increases the stability of the protein
   
   1. collagens are incredibly stable due to disulfide linkages
3. regulates the activity of the protein
   
   1. heterotrimeric G proteins
      
      1. alpha subunit cannot perform its functino when it is bound to the beta and gamma subunits. once alpha dissociates the protein becomes active.

Question 3

describe protein folding; what determines protein folding?

What 4 changes can lead to change in function?

modifying a proteins can lead to what issues downstream in the process? CJD

do they need help?

Answer 3

correct protein folding is essential to the proper functioning of the protein.

The folding of a protein is determined by its primary structure, order of the amino acids

1. changes in structure change function
   
   1. mutations
   2. proteolytic cleavage
   3. oxidative damage
   4. altered environmental conditions
2. when the protein is modified it may not be recognized by other downstream processes. this mat lead to an aggregation with in the cell/precipitation which may have pathological consequences
   
   1. creutzfeld-jacob disease associated with abnormal denaturation of prion protein in brain
      
      1. familial:due to mutation(5-10%)
      2. sporadic form:uk cause.(85%)
      3. acquired form: mad cow, transfusions

some proteins require accesory proteins(chaperonins) t ofold into their native forms.

1. HSP70 binds to the growing protein chain during synthesis and prevents premature ptotein folding until protein synthesis is complete
2. hsp60 folds the protein by using energy from ATP. the nacent protein enters the cavity of hsp60 which provides a template for folding

other proteins can fold on their own and even refold after denaturation

Question 4

Differenciate some methods that lead to protein denaturation. Give clinical examples

1. mutation
2. disease
3. misfolding
4. oxidative damage
5. altered enviornment

Answer 4

1. mutation
   
   1. cjd
2. disease
   
   1. prion via madcow
3. misfolding
   
   1. amyloidosis
      
      1. aggregation/precipitation of various misfolded protein fragments produced by proteolytic cleavage.
      2. symptoms
         
         1. protein precipitation/deposits cause organ failure
         2. precipitated proteins have similar beta sheet-rich structures
      3. examples
         
         1. AA
            
            1. ​precipitation of serum amyloid A fragments
            2. associated with rhematoid arthiritis
         2. AL
            
            1. ​precipitation of Ig light chain fragmenst (bence-jones) proteins
            2. associated with multiple myeloma (cancer of antibody producing plasma cells)
         3. Aß
            
            1. ​precipitation of beta-amyloid proteins
            2. beta amyloid is a fragment of the amyloid precursor protein
            3. leads to brain degeneration
4. oxidative damage- from reactive oxygen species
   
   1. G6P dehydrogenase deficiency
      
      1. proteins in RBC are damaged by Oxygen radicals,
      2. proteins denature and precipitate generating: heinz bodies
5. altered environmental conditions as causes of protein denaturation
   
   1. pH
   2. temperature
   3. organic solvents

Question 5

what are the two types of globin and describe their structure and function

Answer 5

myoglobin

1. main oxygen storage molecule in skeletal and heart muscle
2. 8 alph helices fold into a globular(3) structure
3. folding of helices create pockets where a heme molecule (prosthetic group)
   
   1. Fe2+ binds

hemeglobin

1. oxygen transport molecule in RBC
2. 2alpha and 2beta(adult)
3. quartenery structure is held by noncovalent bonds

Question 6

define the states of Hb O2 binding

Answer 6

binding=cooperative

1. T(tight) state
   
   1. low O2 affinity
   2. No O2 is bound
2. R(relaxed)
   
   1. high O2 affinity
   2. O2 is bound

Question 7

Draw and explain the myoglobin and hemeglobin

Answer 7

1. myoglobin
   
   1. O2 sat curve is Hyperbolic
   2. bind O2 stronger than hemeglobin, due to being in O2 low enviornment
2. hemeglobin
   
   1. O2 sat is sigmoidal
   2. near muscle, O2 is released and picked up by myoglobin

Question 8

list regulators of O2 binding to hemoglobin

Answer 8

allosteric regulators-bind to Hb and changes the Oxygen binding affinity

Question 9

describe the effect of 2,3-BPG and explain its operation with O2 transfer

Answer 9

1. 2,3-BPG is a glycolysis byproduct abundantly present in RBCs
2. 2,3-BPG binds into a pocket between the Hb(beta) chains and stabalizes the Tstate
   
   1. this shifts the pO2 line to the right, making it easier to releaes O2

Question 10

An individual is training in a high altitude setting. What is changing with their hemglobin function?

Answer 10

high altitude is a form of hypoxemia

the 2,3-BPG levels increase to facilitate unloading O2 in the tissues shifting the curve further to the right.

Question 11

After eating working out, my lactic acid levels increase. What happens to O2 binding to Hb?

Answer 11

the Bohr effect describes the effect of pH on O2 binding of Hb.

1. H+ bind better to a stabilize the Tstate
   
   1. ​this facilitates the unloading of O2 in the tissues
2. lower pH shifts the graph to the right.

with more protons in metabolically active tissue, the capillaries there have a lower pH allowing O2 to travel to tissues that need it more

Question 12

what is the effect of CO2 on Oxygen binding of Hb

Answer 12

Its a dual role.

1. High Co2 leads ->more H+->lower pH
2. the CO2 binds directly to Hb and stabilizes the T state
   
   1. Co2 does NOT bind to the heme group, rather it reacts with the amino terminal carbaminohemaglobin

Question 13

summarize O2/Co2 transport in a person exercising

Answer 13

Question 14

The fire place door closed while Jerry was sleeping, leading to the house filling with smoke. What is Jerry susceptible to?

Answer 14

CO poisoning leads to sever tissue hypoxia

1. binds 220x’s more tightly to carboxyhemaglobin
2. this reduces O2 content of Hb
3. binding of one CO to a heme group causes other heme groups to bind O2with a higher affinity this means Hb cannot provide O2 effeciently to tissue, holds onto it when it should let go of O2 near tissues

Question 15

what are the types of Hb in adults?

Answer 15

Question 16

graph the O2 sat of different Hb and include the tissues

Answer 16

HbF

1. has higher O2 affinity than HbA
   
   1. lower affinity to 2,3-BPG
   2. ensure efficient transfer of O2 from the mother to the fetus
2. hereditary persistence of fetal hemoglobin(HPFH)
   
   1. certain individual have more HbF in adult life
   2. beneficial in hemeglobinopathies
      
      1. SCD
      2. beta-thalassemia

Question 17

list 6 common hemoglobinopathies and cause. 5 lead to what common disease

Answer 17

Question 18

Discuss methemoglobinemia and list causes and disease manifestation

Answer 18

1. causes
   
   1. acquired-excessive oxidative drugs and nitrates
   2. hereditary
      
      1. mutation in nadh-cytochrome b5 reductase ( or certain mutations in Hb that prevents the reduction of Fe+)
2. symptoms
   
   1. chocolate colored blood
   2. cyanic skin and mucous membrane
   3. shortness of breath, headache and seizure

Question 19

Discuss alpha thalassemias and list causes and disease manifestation

Answer 19

1. decreased amounts of absence of alpha-chain
   
   1. depending on how many of the 4 alpha globin genes are deficient
2. gamm and beta chain synthesis are unaffected
3. compensatory mechanism
   
   1. excess gamma and beta chains form homotetramers
      
      1. ​Hb Bart’s
         
         1. ​excess gamma
      2. HbH
         
         1. ​excess beta
4. the gamma and beta homotetramers bind O2 with high affinity
   
   1. leading to tissue hypoxia

Question 20

Discuss beta-thalassemia and list causes and disease manifestation

Answer 20

1. types
   
   1. B0 thalassemia(major)-complete lack of Beta chains
   2. B+thalassemia(minor) - greatly reduce levels of Beta chain
2. excess alpha chains precipitae in erythoid precursos
   
   1. causes inefficient RBC formation(no reticulocyte elevation).
      
      1. does the bone marrow keep trying to make reticulocytes?
3. reasons-
   
   1. decreased amounts
   2. absence of Beta-chain
   3. alpha chain unaffected
4. compensatory mech
   
   1. HbF and HbA2 increase.

Question 21

Answer 21

Question 22

An individual has rheumitoid arthritis and precipitation of serum amuloid A fragments. What is the disease and its manifetststion

Answer 22

AA amyloidosis

1. aggregation/precipitation of various misfolded protein fragments producted by proteolytic cleavage.
2. preciptate have a similar Beta sheet rich structure
3. if untreated may lead to organ failure

Question 23

A patient presents with Bence jones proteins during his treatment of multiple myeloma. what is the disease and exlain its manifestation.

Answer 23

AL amyloidosis

1. precipitation of antibody Light chain fragments
   
   1. Bence jones proteins
2. associated with multiple myeloma
   
   1. cancer of antibody producing plasma cells

Question 24

Jerry is experiencing brain degeneration from beta amyloid fragments precipitating. what is this associated with and how does it manifest?

Answer 24

alzheimer disease (A beta amylodosis)

1. precipitation of beta-amyloid proteins
2. beta-amyloid is a fragment of the amyloid precursor protein
3. brain degeneration

Question 25

these structures are seen on a blood sample from a person in the hospital. what is it associated with and resoning behind manifestation

Answer 25

Oxidative samage as a cause of protein denaturation/aggregarion

1. G6P dehydrogenase deficiency
   
   1. proteins (hemoglobin) in RBC are damaged by oxygen free radicals
   2. heinz bodies
      
      1. ​proetins are denatured and precipitate in the cells