Unit 2 Flashcards
The 3-D conformation is able to fulfill a specific ________
Biologic function
The 3-D structure is also known as the _______ ______ that has a large number of favorable interactions within the protein
Native fold
There is a cost in _________ ________ of folding the protein into one specific native fold
Cost in conformational entropy
What are the favorable interactions in proteins?
Hydropphobic effect
Hydrogen bonds
London dispersion (Van der Waals)
Electrostatic interactions
The resonance causes the peptide bonds
- to be _______ reactive compared to esters
- to be quite ______ and nearly ______
- to exhibit a large ________ _____ in the favored trans configuration
Less reactive
Rigid and nearly planar
Dipole moment
What type of linkages are seen in primary structures?
Covalent
Secondary structures contain what linkages and structures?
H-bonds
Alpha helices, beta sheets and beta turns
In the tertiary structure, what linkages are involved? And what are the linkages between?
Covalent
H-bond
Van der Waals
And hydrophobic
Linkages between the R groups
What is a peptide bond?
A bond formed by the carbonyl group and the amide group of another molecule
Quaternary structures contain all types of linkages except _______
Covalent
Where are the molecules bonded in quaternary structure?
Between subunits (mostly using R groups)
Virtually all peptide bonds in proteins occur in ______ configuration
Trans
What constitutes the polypeptide backbone?
The bond between the N and carbonyl carbon
The alpha helix is stabilized by H bonds between ________
Nearby residues
The beta sheet is stabilized by H-bonds between ________
Adjacent segments that may not be nearby
Irregular arrangement of the polypeptide chain is called the ________ _____
Random coil
Where does trypsin cleave at?
Lysine and arginine
Cyanogen bromide cleaves at ______
Methionine
Is the alpha helix right handed or left handed?
Right handed with 3.6 residues per turn
Peptide bonds are aligned roughly ______ with the helical axis
Side chains point out and are roughly_____ with the helical axis
Parallel
Perpendicular
What are strong helix formers? And what are some examples?
Small hydrophobic residues such as Alanine and Leucine are strong helix formers
What acts as a helix breaker and why?
Proline acts as a helix breaker because the rotation around the N-Ca bond is impossible
Glycine acts as a helix breaker because the R-group supports of conformations
What affects the formation of a helix?
Attractive or repulsive interactions etween side chains 3-4 amino acids apart
What is the functional insulin part?
C-peptide
In ______ ____, release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy
Hydrophobic effect
What are the favorable interactions in proteins?
Hydrophobic effect
H bonds
London dispersion
Electrostatic interactions
What are the hallmark features of primary structure of proteins?
Covalent bonds (peptide bonds) Made up of amino acid chains
What are the characteristics of secondary structures of proteins
H-bonds between peptide bonds
Types: alpha helix, beta sheets, beta turn
What is characteristic of tertiary proteins in terms of linkages
Covalent, H-bond, ionic, van der Waals and hydrophobic
Stability and linkages are formed based on the R groups
What are the types of tertiary structure?
Super-secondary structures such as motifs and domains
What is characteristic of quaternary structure?
All types of linkages except covalent
And interactions that form a quaternary structure is between subunits
What are types of quaternary structure?
Dimers and tetramers etc.
Structure of the protein is partially dictated by the properties of the ______ ______
Peptide bond
The ____ ______ is a resonance hybrid of two canonical structures
Peptide bond
The resonance causes the peptide bonds to be what 3 things?
Less reactive compared to esters
Rigid and nearly planar
Exhibit a large dipole moment in the favored trans configuration
What bond constitutes the polypeptide backbone?
N and alpha carbon carbonyl
What are the 5 functions of globular proteins?
Storage of ions and molecules Transport of ions and molecules Defense against pathogens Muscle contraction Biological catalysis
What globular proteins function in storage of ions and molecules?
Myoglobin and ferritin
What globular proteins function to transport ions and molecules?
Hemoglobin and serotonin transporter
What globular proteins funciton in defense against pathogens
Abs and cytokines
What are examples of globular proteins that function in muscle contraction?
Actin and myosin
What are some examples of globular proteins that function in biological catalysis?
Chymotrypsin and lysozyme
A molecule that binds to a protein is called a _______
Ligand
A region in the protein where the ligand binds is called the _______ _____
Binding site
Ligand binds via same ________ forces that dictate protein structure
Noncovalent
What allows the interactions of globular proteins with other molecules to be transient?
Ligands binds via noncovalent forces
What is the kinetics process?
The association rate constant Ka or the dissociation constant Kd
How do you know the Ligand and protein binding have reached equillibrium?
When the association and dissociation rates are equal
The ______ _______ is characterized by the equillibrium constant Ka
Equillibrium constant
What does Kd equal?
The concentration of ligand at which half of the available ligand-binding sites are occupied
If Kd is low, the binding affinity is _______
Tight
The lower the binding constant, the ________ the affinity
Higher
______ is the main oxygen storage protein
Myoglobin
______ is a circulating oxygen binding protein
Hemoglobin
The lower the affinity, the ______ the Kd value
Higher
Some transition metals bind O2 well but would generate _____ _______ if free in solution
Free radicals
Only _________ of Fe can be bound to myoglobin
Fe2+
_________ is free heme that is not bound to myoglobin
Fe3+
What are the components of heme?
Organic component: Protoporphyrin IX
Inorganic component: Iron (Fe2+)
How many coordination bonding sites are on the Heme-Fe?
4 bonded to the nitrogen atoms of the protoporphyrinIX and 2 perpendicular to the plane of the ring
The perpendicular sites on the heme are made up of what?
His residue on the proximal side
Oxygen binding site on the distal side
_________, ___, is the typical globular protein with most nonpolar a.a. Inside (except for the 2 Histidines which bind ______ and ______
Myoglobin, Mb,
Fe and O2
Where is myoglobin typically located?
Heart, muscle and liver
Binding to O2 is _______, it only depends on the [Mb] and on the pO2
Simple
Myoglobin has _____ helices terminate by _____ or Beta turns and loops
8
Proline
Fe3+ or the ferric state is also known as _________, and Oxygen cannot bind to it
Metmoglobin
The iron ion in the ferric state (or metmoglobin) _________ bind to oxygen
Doesn’t
______ blocks funciton of myoglobin, hemoglobin and mitochondrial cytochromes that are involved with oxidative phosphorylation
Carbon monoxide
Which has a higher affinity for hemeoglobin, oxygen or carbon monoxide?
Carbon monoxide
Why cant myoglobin transport O2?
Because it would not release the oxygen to the tissues because of its high affinity
______ is a tetrameric protein of 2 identical globin subunits
Hemoglobin
What makes up hemoglobin?
2 alpha globins and 2 beta globins and each globin molecules is structurally similar and folds like myoglobin
In hemoglobin, each globin molecule has a ______ group
Heme
Interactions in hemoglobin between the alpha and beta globins is _____ than interactions between the 2alphabbeta dimers
Stronger
What is the difference between myoglobin and hemoglobin’s oxygen saturation curve?
Myoglobin saturation curve is more hyperbolic meaning it has a higher affinity for myoglobin.
Hemoglobin saturation curve is more S shaped to where it has high affinity but not as strong as myoglobin
_______ binds too tightly to be useful in O2 transport
Mb
______ binds O2 cooperatively
Hb
Binding of O2 at heme-Hb site ________ the likelihood that O2 binds ar the remaining unoccupied sites and vice versa
Increases
What is the make up of hemoglobin?
2 alpha globulins and 2 beta globulins
Each has a heme group and behaves like a protein made of 2 identical dimers (alphaBeta)2
The interaction between the alpha and beta globins is mostly _________. The interaction between the alphabeta dimers is mostly ________
Hydrophobic
Ionic
Hb is mainly a transporter protein for ____ but it also binds and transports ______
O2
CO2
Adult Hb is identified as ______
Fetal Hb is identified as __________
HbA (alphabeta)2
HbF (alphagamma)2
Hb__ binds with greater affinity to O2 than Hb___ does
HbF; HbA
What are the two states of Hb?
Relaxed and tense state
O2 binding triggers a conformational change from the _____ state to the _____ state
T-state-> R state
Conformational change from the T state to the R state involves what?
Breaking ion pairs between the alpha1-Beta-2 interface
What triggers the conformational change from T to R state?
The binding of O2 to the histidine residue
Slide 28
Conformation change from the T state to the R state involves breaking what?
Breaking ion pairs between the alpha1 and beta 2 interface
The pH difference between the lungs and metabolic tissues _______ efficiency of the O2 transport
Increases
What is the Bohr effect?
The pH difference between lungs and metabolic tissues increases efficiency of the O2 transport
H+ binds to Hb and stabilizes the _____ state of Hb
T state
Explain how H+ binding to Hb stabilizes the T state
Protonates His146 which then forms a sal bridge with Asp94 -> leads to the release of O2 in the tissues
At a higher pH O2 has a _______ affinity for Hb
At a lower pH O2 has a ______ affinity for Hb
Higher
Lower
_______ forms additional salt bridges stabilizing the T state
Carbamate
CO2 is exported out of the peripheral tissues as what 3 forms?
Carbamate on the amino terminal residues of each polypeptide subunits
Bound to Heme as CO2
Exported as dissolved bicarbonate
CO2 conversion to bicarbonate produces _____ leading to a ______ in pH
Proton; decrease
What promotes the release of O2 from Hb in peripheral tissues?
Protons and CO2
What form of Hb does lower pH and higher CO2 stabilize?
The T state of Hb facilitating the release of bound oxygen
What is another name for the R form of Hb?
Oxyhemoglobin
Oxyhemoglobin (R form) prevails in the ______
Lungs
The R form or oxyhemoglobin form prevails when (high or low): PO2 \_\_\_\_\_\_ PCO2\_\_\_\_\_\_ [H+] \_\_\_\_\_ pH \_\_\_\_\_\_ [BPG] \_\_\_\_\_\_
pO2 high pCO2 low [H+] low pH high [BPG] low
What is another name for the T form of Hb?
Deoxyhemoglobin
Where does the Deoxyhemoglobin (T form) prevail at in the body?
The peripheral tissues
The deoxyhemoglobin (T-form) prevails when the following are high or low? pO2 \_\_\_\_\_\_ pCO2 \_\_\_\_ [H+]\_\_\_\_\_ pH \_\_\_\_\_ [BPG] \_\_\_\_\_
pO2 low pCO2 high [H+] high pH low [BPG] high
What is an example fo a negative heterotropic regulator of Hb function
2,3 Bisphosphoglycerate (2,3 BPG)
What Small negatively charged molecule binds to the positively charge central cavity of Hb and stabilizes the T state?
2,3 BPG
Why is 2,3 BPG important in erythrocytes?
Without 2,3 BPG Hb would be extremely inefficient in transporting O2 releasing only 8% of its cargo in the tissues
2,3 BPG is a(n) ________ ______ because biding to Hb affects its binding to O2
Allosteric regulator
2,3 BPG binds mostly to ______ amino acids in the Bet globins in the center of the tetramer of Hb. This pocket is only present in the ____ form of Hb
Basic
T form
On the T-to-R transition what happens to 2,3 BPG
The pocket where 2,3 BPG binds collapses and 2,3BPG is released
In order for the structural transition from T to R to take place what must happen to the bonds between Hb and 2,3 BPG?
They must be broken
What has a higher oxygen-binding affinity, HbF (fetal Hb) or HbA (adult Hb)?
HbF
What amino acid exchange goes on leading to the sickle cell shape of RBCs in sickle cell anemia?
Valine replaces glutamic acid
How does the exchange of glutamic acid for valine in th beta chain of Hb result in sickle cell?
Glutamic acid is a hydrophilic amino acid while valine is a hydrophobic branched chain amino acid. The different properties of these amino acids results in a change from the biconcave disc to a sickled cell shape
Imbalance in production of Hb chains results in ________
Thalassemias
What happens in alpha-thalassemia?
Alpha globins are not produced in sufficient amounts
Some Hb contains only the beta globins that bind to O2 highly with very poor release of O2
What happens in beta thalassemia?
Beta globins are not produced in sufficient amounts
Alpha globins form aggregates that precipitate inside immature RBC producing anemia
What small protein is found in RBC that binds to alpha chains and keeps them properly folded and in solution?
AHSP (alpha-hemoglobin stabilizing protein)
Muscle contraction occurs through a series of conformational changes to protein structure due to what 3 things?
Binding
Hydrolysis
Release of ATP and ADP
What are the four steps to the actomyosin cycle?
1) ATP binds to myosin -> myosin dissociates from actin
2) ATP is hydrolyzed -> conformational change of myosin
3) myosin reconnects tot he actin filament at a different location -> release of Pi
4) release of Pi-> power stroke where myosin returns to initial state; shifting actin filament relative to the myosin tail -> release of ADP
What regulates the availability of Myosin-binding sites on actin?
Tropomyosin and troponin
____ causes conformation changes to tropomyosin-troponin complex exposing myosin binding sites
Ca2+
The ______ is stabilized by H bonds between nearby residues
Alpha helix
The ______ stabilized by H bonds between adjacent segments that may not be nearby
Beta sheet
Irregular arrangement of the polypeptide chain is called the ________
Random coil
What amino acids are examples of strong helix formers?
Alanine and Leucine
What amino acids act as Helix breakers?
Proline and Glycine
What affects formation of helix and its stability?
Attractive or repulsive interactions between side chains 3-4 amino acids apart
What 5 amino acids are common in beta sheets?
Valine Isoleucine Tyrosine Cysteine Tryptophan
In _____ beta sheets the H-bonded strands run in the same direction
Parallel
In ______ beta sheets the H bonded strands run in opposite directions
Antiparallel
_______ beta sheets results in bent H bonds
Parallel
________ beta sheets result in linear H bonds
Antiparallel
________ beta sheets are stronger than ______ beta sheets
Antiparallel; parallel
What 3 amino acids are common in beta turns?
Proline
Glycine
Asparagine
What amino acid is common in type 1 beta turns?
Proline
What amino acid is common in type 2 beta turn?
Glycine
What does the tertiary structure refer to?
The overall spatial arrangement fo atoms in a protein
What are the two major classes of tertiary structure?
Fibrous and globular ( water or lipid soluble)
______ proteins always have combination of secondary structures and turns are always present
______ protein mostly one type of secondary structure
Globular
Fibrous
_______ proteins are practically insoluble
_____ proteins are fully soluble or membrane bound
Fibrous
Globular
The main function of ______ proteins are mostly dynamic roles
The main function of ____ proteins are mostly structural roles
Globular
Fibrous
______ proteins are located mostly intracellularly while ______ proteins are located mostly extracellualrly
Globular
Fibrous
What are examples of globular proteins?
Hemoglobin
Myoglobin
Enzymes
What are examples of fibrous proteins?
Collagen
Keratin
Elastin
_______ proteins are mostly primary and secondary structures while ______ proteins all have tertiary structures (simple) and many complex have quaternary structure
Fibrous; Globular
_____ proteins provide support for cells and tissues
Fibrous
______ is an important constituent of CT
Collagen
What is each collagen chain made of?
Long glycine and proline rich left handed helix
Three collagen chains intertwine into what?
A right handed superhelical triple helix
Many ________ assemble into a collagen fibril
Triple helicies
Type 1 collagen is present in what 5 tissues?
Skin Bone Tendon Blood vessels Cornea
Type 2 collagen is present in what 3 tissues?
Cartilage
Intervertebral disk
Vitreous body
Type 3 collagen is present in what 3 tissues?
Blood vessels skin and muscle
What types of collagen are fibril forming?
Type 1, 2 and 3
What types of collagen are network forming?
Type 4 and type 8
What types of collagen are fibril associated?
Type 9 and type 12
In the synthesis and processing of collagen what occurs inside the cells?
- Synthesis of pro-alpha-chains on ribosome ER to facilitate secretion
- Hydroxylation of selected Pro and Lys residues catalyzed by Pro and Lys hydroxylases
- Glycosylation of selected OH-Lys residues via an enzyme catalyzed process
- Spontaneous process of triple helix formation of Pro-collagen molecule
- Secretion of procollagen molecule
In synthesis and processing of collagen, what processes occur outside cells?
- Cleavage of extension peptides (may take place before secretion)
- Assembly into micro fibril
- Crosslink formation
- Assembly into mature collagen fibril
- Aggregation of collage fibrils to form a collagen fiber
Cleavage of extension peptides occurs ________ cells and is catalyzed by what?
Outside cells
Catalyzed by procollagen peptidases
What are the spontaneous processes that occur outside the cell in the synthesis and processing of collagen?
Assembly into micro fibril
Assembly into mature collagen fibril
Aggregation of collagen fibrils to form a collagen fiber
What causes cross-link formation in synthesis and processing of collagen?
Lysyl oxidase
What collagen genetic disease is associated with type 1 collagen?
Osteogenesis imperfecta
-weak bones that fracture easily
What collagen genetic disease is associated with type 2?
Chondriodysplasias
-abnormal cartilage, bone and joint deformities
What collagen genetic diseases are associated with type III and type V
Ehlers- Danlos syndrome
Fragile skin and blood vessels (type III aorta rupture) and hyper- mobile joints (type V)
What are motifs (folds)?
Specific arrangement of several secondary structure elements
___________ structure is formed by the assembly of individual polypeptides into a larger functional cluster
Quaternary
What are intrinsically disorder proteins composed of (amino acids)?
Composed of amino acids whose higher concentration forces less defined structure
Lys, Arg, Glu, and Pro
_________ _______ proteins facilitate interaction with numerous different partner proteins
Intrinsically disordered proteins
A proteins function depends on what?
It’s 3D structure
Loss of structural integrity with accompanying loss of activity is called __________
Denaturation
What denatures proteins?
Heat or cold pH extremes Detergents Reducing agents: DTT and Mercaptoethanol Chaotropic agents: urea
What reduces disulfide bonds?
Beta-Mercaptoethanol
Adding a chaotropic agent will _____ the protein but when the chaotropic agent is removed it causes the ______ of the protein and that protein is now catalytically active
Denature
Renature
What are 4 examples of protein misfolding and neurodiseases?
Alzheimer’s disease
Parkinson’s disease
Huntington’s disease
Prion disease
Alzheimer’s, Parkinson’s, Huntington and creutzfeldt- Jakob diseases result in deposition of protein aggregates called ______
Amyloid fibrils or plaques
Alzheimer’s, Parkinson’s, Huntington’s and creutzfeldt Jakob’s disease are called ______
Amyloidoses
What is a common feature of amyloidoses?
Normally soluble proteins are converted into insoluble fibrils rich in beta sheets
What is the major proteopathy in Parkinson’s disease?
Alpha-synuclein
Alpha-synuclein can form insoluble aggregates or ______________ that are a major part of Parkinson’s disease
Lewy bodies
Where is the site of synthesis of pepsinogen?
Stomach
What is the site of synthesis for chymotrypsinogen, trypsinogen, procarboxypeptidase and proeleastase?
Pancreas
What activates trypsinogen into trypsin?
Enteropeptidase
What activates chymotrypsinogen, proelastase and procarboxypeptidase?
Trypsin
What activates pepsinogen, what is its source, and what is its target?
[H+]/ pepsin activates
Source is the stomach
Target is Phe
What activates trypsinogen, what is its source and what is its target?
Enteropeptidase and trypsin activates it
Source is pancreas
Target is lys and arginine residues
What activates chymotrypsin, what is its source and what’s its target?
Trypsin and chymotrypsin activates it
Source is the pancreas
Targets aromatic and bulky amino acids
Different carriers transport the families of amino acids based on what?
The nature of the R groups
In protein digestion and absorption, free amino acids use secondary active transport using what type of gradient?
Sodium concentraiton gradient
What are enzymes?
Catalysts that increase reaction rates without being used up
What are examples of oxidoreductases?
Dehydrogenases
Reductases
Oxidase
What are examples of transferase?
Kinase and transaminases
What are examples of hydrolases?
Lipase and proteases
What are examples of lyases?
Anhydrases
Dehydratases
Hydratases
What are examples of isomerases?
Isomerase
Mutase
Epimerases
What are examples of ligases?
Carboxylases and synthetase
_______ are required by inactive app-enzymes to convert them into active holo-enzymes
Cofactors
What activated carriers carry electrons?
NADH, NADPH
FADH2
FMNH2
What activated carrier carries phosphoryl group?
ATP
What activated carrier carries an aldehyde?
Thiamine pyrophosphate
What activated carrier carries CO2?
Biotin
What activated carrier carries one carbon units?
THF (tetrahydrofolate)
What activated carrier carries glucose?
UDP- glucose (uridine diphophate glucose)
Enzymes alter only the ________ and not the _________
Reaction rate
Not the equilibrium
Enzyme ________ ______. Are complimentary to the transition state of the reaction
Active sites
Enzymes bind to __________ better than substrates
Transition states
The ________ of enzymes is a 3D cleft or crevice that takes up a small part of the total volume of an enzyme
Active site
How do substrates bind to the enzyme?
By multiple weak interactions depending on the precisely defined arrangement of atoms in an active site
Define Vmax
Maximal velocity when the enzyme is saturated with substrate
Nonlinear michaelis-menten plot should be used to calculate what?
Km and Vmax
Linearized double-reciprocal plot is good for what?
Analysis of two-substrate data or inhibition
What processes take place in the mitochondria?
TCA cycle
FA oxidation
Oxidation of pyruvate
What cellular processes occur in the cytosol?
Glycolysis
Pentose phosphate pathway
FA synthesis
What cellular processes occur in the nucleus?
DNA and RNA synthesis
What cellular processes occur in the lysosome?
Degradation of complex macromolecules
What are the factors that affect reaction velocity?
Substrate concentration
Temperature
pH
Large Km = ______ affinity of enzyme for substrate
Small Km = ______ affinity of enzyme for substrate
High Km= low affinity
Low Km= high affinity
At low concentration of substrate, the velocity of the reaction is what?
Proportional to the substrate concentration
First order
What high concentration of substrate, the velocity of the reaction is what?
constant and independent of substrate concentration
Zero order
T/F: allosteric enzymes do obey Michaelis-Menten kinetics
False; they do not obey Michaelis-Menten kinetics
Kinetics of allosteric enzymes display _______
Cooperativity
What is cooperativity?
Binding of substrate to one active site faciliatates the binding of the substrate to the other active sites
In competitive inhibition, what does the inhibitor bind to and how does it effect the Km and Vmax
Inhibitor binds to Enzyme only
Raises Km
Vmax unchanged
In uncompetitive inhibition, what does the inhibitor bind to and what is its effect on Km and Vmax?
Inhibitor binds to enzyme substrate ONLY
Lowers both Km and Vmax
Ratio Km/Vmax remains unchanged
In noncompetitive inhibition, what does the inhibitor bind to? And what its its effect on Km and Vmax?
Inhibitor binds to enzyme OR enzyme substrate complex
Lowers Vmax
Km remains unchanged
Describe feedback inhibition
The products of one pathway will inhibit further production of that product
What are examples of regulation of enzyme activity?
Feedback inhibition
Covalent modification
What are examples of covalent modification?
The addition and removal of phosphate groups
Zymogen activation and the blood coagulation cascade use what?
Irreversible covalent modification
What are the two most common types of cofactors?
Inorganic ions (metal) and coenzymes
Apoenzyme = ______
Holoenzyme= _______
Apoenzyme + cofactor -> _________
Inactive
Active
Holoenzyme
What is the cofactor for pyruvate dehydrogenase?
Thiamine pyrophosphate
What is the cofactor for pyruvate carboxylase?
Biotin
What is the cofactor for Lactate dehydrogenase?
Nicotinamide adenine nucleotide
What is the cofactor for methylamlonyl mutase?
5’ deoxyadenosyl cobalamin
What is the cofactor for thymidylate synthase?
Tetrahydrofolate (THF)
What is the cofactor for carbonic anhydrase?
Zn2+
What is the cofactor for hexokinase?
Mg2+
What is the cofactor for glutathione peroxidase?
Se
What is the cofactor for superoxide dismutase?
Mn
