Biochem Flashcards
Which are the tiny AA?
C.A.G.S
Cysteine, Alanine, Glycine, and Serine
What are the small AA?
D P N T
Aspartate, Proline, Asparagine, Threonine
What are the medium AA?
E, V, H, Q
Glutamic Acid, Valine, Histidine, Glutamine
What are the large AA?
K R I L M
Lysine, Arginine, Isoleucine, Leucine, Methionine
What are the extra-large AA?
F Y W
Phenylalanine, Tyrosine, Trytophan
What are the essential AA?
PVT TIM HALL
Phenylalanine
Valine
Tryptophan
Threonine
Isoleucine
Methionine
Histidine
Arginine
Lysine
Leucine
What are the three stop codons?
UAA
UGA
UAG
What does statin intolerance cause to a patient that is treated with statins?
Statin inhibits the Selenocystein-tRNA from producing selenoproteins
What does selenium deficiencies lead to?
Oxidative distress is inhibited
(Oxidative stress continues)
Muscle death and myopathies
Immune incompetence
What is pyrrolysine and where can it be found?
Two lysines put together (An amino acid)
Found within methanogen bacteria found in the human’s GI system
What are the 4 interactions that govern protein folding and stability?
Van der Waals Interactions
Hydrogen bonds
Electrostatic (Salt bridges/Charges)
Hydrophobic interactions
What are the 4 determinants of protein folding?
Secondary Structure
Hierarchical folding
Hydrophobic effect
Context-dependent
What are the bonds found in alpha-helices?
Intrachain Hydrogen bonds leaving 4AA residues
What are the bonds that are found in Beta-sheets?
Hydrogen bonds between peptide chains
What causes compact and globular shapes for polypeptide chains?
Reversal directions
(Reverse turn, beta turn, hairpin loop, omega loops)
Where can loops and turns of secondary structures be found?
They can be found on the surface of a protein
(Hydrophilic)
They are used in interactions with other molecules or proteins
What uses the superhelix structure?
Keratin, collagen, cytoskeleton, and muscle
(Structural proteins: Things that need to be strong)
AND
Regulators of gene expression
What kind of protein uses intra-sulfur bonds?
Extracellular proteins
i.e. Insulin
What are the events of the folding funnel?
- Rapid formation of secondary structure
- Formation of domains through cooperative aggregation
Concept of molten globule
Possible structure, but unstable - Adjustment of conformation
- Fine tuning of folding for native structure
What has a higher state of energy?
A higher state of entropy?
Denatured/unfolded proteins
They have a desire to be at a more stable state through protein folding into the native state
What does repeating motifs have in common? What is different?
Their final protein domains bind the same thing
i.e. calmodulin binds calciums
Their amino acid sequences are different
What kind of protein has the following characteristics
- Native-like
- Absence of specific tertiary structure
- Compact, but larger than native
- The loosely packed hydrophobic core
- Not specific
Molten globule proteins
How are molten globule proteins stabilized?
nonspecific hydrophobic interactions
Function of PDI
Protein Disulfide Isomerase
Fix misfolded proteins’ disulfide bonds
(Assists in refolding proteins so that correct disulfide bonds are created)
What is the purpose of accessory proteins
To fine-tune protein folding
Function of PPI
Peptidyl Prolyl Cis-Trans Isomerases
Changes the functional groups of a protein from trans to cis
T/F folding and unfolding is not an all or none process. It can be both
False.
All or none
It is either folded, or it is not
What are the methods of analysis of protein folding?
Turbidity: Proteins will create a clear semi-clear solution
Circular dichroism: Left and Right proteins bend light differently
Fluorescence: Aromatic structures absorb and emit light
Biological activity
What is the function of the 19s subunit of the proteosome?
Recognizes the ubiquitinated protein and allows entry into the degradation site (20s core)
What is the function of the 20s core in the proteosome?
A sealed barrel that contains proteolytic enzymes and a low pH for the degradation of proteins
What is the function of HSP 70
Coordinates cellular function by directing substrates for unfolding, disaggregation, and refolding or degradation
Works together with HSP 40
What is the function of HSP 40
HSP 40 is used to refold proteins
Does it on its own with soluble
Needs assistance from HSP 70 for insoluble
HSP 90
Helps fold signal transduction proteins
Inserts signaling functions at late folding stages
What are the functions of HSP 60 and HSP 10
They are chaperonins that have the barrel like structures
They create a hydrophobic microenviroment for folding of proteins
What are the three components of the cellular quality control system
Proteasomes: Protein degradation
Autophagy: Cellular digestion
ERAD: ER-Associated degradation (Sends useless proteins directly to proteasome)
What can improper degradation lead to?
Cystic Fibrosis
Good and bad proteins constantly being removed can lead to a build-up of half-assed proteins that were made too quickly to keep up
What can improper localization lead to?
Dual Toxicity
Improper folds cannot be sent to their respective site. Therefore there is a build-up of toxic proteins at one site and a loss of function at the other
Nucleophilic substitution
Swap functional groups
Nucleophilic Addition
Add functional group
Carbonyl condensation
Change the number of carbons
Elimination
Change the bond order
Oxidation/Reduction
Move electrons
Oxidoreductases
Oxidation-Reduction rxn
Transferases
Group Transfer
Hydrolases
Breaking of a bond using water
Lysases
Breaking of a bond without using water
May lead to double bonds
Isomerases
Intramolecular group transfers
Ligases
Ligation of two substrates at the expense of ATP hydrolysis
Putting things together
NAD+
Coenzyme Made of vitamin B and Adenine
Used by dehydrogenases in catabolic reactions to OXIDIZE into NADH
(Oxidation is the loss of a proton/Hydrogen)
NADPH
Coenzyme Made of Vitamin B3 and Adenine
Used by reductases in anabolic reactions to make NADP+
(Reduction is the addition of a proton/Hydrogen)
FADH2
Coenzyme Made of vitamin B6 and adenine
Found in oxidation reactions using FAD
FMNH2
Coenzyme Made of vitamin B6 and adenine
Used in reduction reactions with FMN
ATP
Coenzyme to transfer a phosphate group
Usually, gamma is moved
Pyridoxal phosphate
Coenzyme that transfers phosphates
Made of Vitamin B6
SAM
Conenzyme: S-Adenosylmethionine
A primary transferase that transfers a methyl group
Tetrahydrofolate
A coenzyme in a transferase process of a methyl group
Made of Vitamin B9
5’deoxyadenoxylcobalamin
A coenzyme in methyl transferases
Contains Vitamin B12 and cobalt
TPP
Coenzyme in ligase reactions
Thiamine pryophosphate
Made of Vitamin B1 and 2 phosphates
Adds Aldehyde gropus
CoASH and Lipoamide
Coenzymes that add Acyl groups (-COR)
Both have sulfurs
Biotin
Coenzyme that adds Adds CO2
Vitamin B7
Incomplete Enzymes that are inactive and require a cofactor or coenzyme
Apoenzyme
A whole enzyme that is active. Contains the cofactor/coenzyme
Holoenzyme
In terms of cooperativity on the hill plot:
A slop of 1 is interpreted as
No cooperativity
In terms of cooperativity on the hill plot:
A slope greater than 1 has
Positive cooperativity
In terms of cooperativity on the hill plot:
A slope that is less than 1 has
Negative cooperativity
What are the subunits of embryonic Hb
Fetal hemoglobin is made of 2 zeta and 2 gamma
What are the subunits for HbF
Fetal Hb = 2 alpha and 2 gamma
What are the subunits of HbA
2 alpha 2 beta
What are the subunits for HbA2
2 alpha 2 delta
What hemoglobins are found in an adult?
HbA, HbA2, and HbF
When does HbA reach dominancy as the main type of Hb
After 1 year after birth/ Gestational age
What subunits are Alpha chains of Hb
Found on chromosome 16, alpha and zeta
What subunits are beta chains in Hb
Found on chromosome 11, epsilon, gamma, delta, and beta
What causes the formation of HbS
In Sickle Cell hemoglobin, valine is substituted in place of glutamic acid in the 6th position of beta globulins
This causes polymerization of the Hb
What is the proximal histidine and what is it bound to?
F8 histidine and is bound to the heme group
(6th segment; 8th AA)
What is the distal histidine
E7
(5th segment; 7th AA)
Where does oxygen bind to in Hb
On the distal histidine and the heme group
What happens to the iron atom when oxygen binds
It moves from out of the plane to into the plane
This will pull the proximal histidine
T/F binding of oxygen is a cooperative process in myoglobin
False it is cooperative in hemoglobin
T/F When oxygen dissociates from hemoglobin, it makes it easier for other oxygens to dissociate
True: Reversibility of cooperativity
2,3 BPG induces what form of Hb?
The tense form which lowers the affinity
Absence of 2,3-BPG will do what to Hb?
It will increase affinity and keep Hb in the relaxed form
What correlation does pH have with Hb affinity?
As pH decreases so does the affinity
(more acidic)
What is HbA1c
Post-modification of the N-terminus in ß globulins
Low at normal glucose levels
High in diabetic patients that abuse glucose
What is Thalassemias
Reduced synthesis of a globulin that reduces the functionality of Hb
HbH
Excess beta globulins that will become tetramers
Alpha plus Thalasemia
Silent carrier: Deletion of 1/4 alpha genes
Alpha - Thalassemia
2/4 alpha genes are deleted
Microcytosis
Low mean cell volume
Found in alpha thalassemia
Hypochromia
Low mean cell hemoglobin
Found in alpha thalassemia
HbH Disease
3 alpha genes are affected
Severe Anemia, hypochromic hemolytic anemia, hepatosplenomegaly, mild jaundice
Hydrops Fetalis
All (4/4) alpha genes are silenced
Only gamma 4 Hb (Bart’s Hb)
Creates fetal onset of edema and anemia
Kills newborns
ß Thalassemia
Not enough ß chains are being made compared to alpha chains
This leads to alpha chains precipitating out and cause oxidative stress and hemolysis and destruction of immature erythroblasts in bone marrow
They do NOT form a tetramer
Covalent Catalysis
Binds covalently to transition state and stabilizes transition state
Acid-Base Catalysis
Partial proton transfer
(Hydrogens: Think of what amino acids can participate)
Approximation
Spatial orientation and close contact so that electrons and protons can be exchanged
Electrostatic Catalysis
Stabilization of unfavorable charges on the transition state
Chymotrypsin
A serine protease (Hydrolase)
What is the active site of chymotrypsin?
The catalytic triad
(Serine: Nucleophile
Histidine: Base
Aspartic Acid: Acid)
AND
Oxyanion Hole
(Serine and glycine)
Specificity of Chymotrypsin
Hydrophobic specificity pocket
Carbonic Anhydrase
Hydrolase that assists in the removal of carbon dioxide
Carbonic anhydrase active site
zinc ion that coordinates to 3 histidines and a water
Water facilitates the transition state
Reaction mechanism to what enzyme:
- Water binds to zinc and lowers its pKa (water then loses a hydrogen)
- Approximation as substrates enters active site
- Nucleophilic addition (adds hydroxyl group)
- Release of product and regeneration of enzyme
Carbonic anhydrase
Temporal control of gene expression
Protein degradation
Enzyme Compartmentalization
Substrate availability
Regulation of the amount or availability
(On/Off switch)
Myristolyation or Farnesylation
Post-translational modifications: addition of lipids
ADP ribosylation
Post-translational modifications: addition of nucleic acids
Ubiquination
Post-translational modifications: addition of proteins
Glycosylation
Post-translational modifications: addition of carbohydrates
Addition onto side chain oxygen or nitrogen
y-Carboxylation
Post-translational modifications: addition of small molecules
Adds onto gamma carbon
Acetylation or Methylation
Post-translational modifications: addition of acetyl or methyl group
Adds onto nitrogen side groups (arginine and lysine)
Phosphorylation
Post-translational modifications: addition of phosphate
kinases and phosphatases
Isozymes and Isoforms
Covalent Modifications
Allostery
Regulate the activity of the enzyme (volume control)
Isozyme and Isoforms
Catalyze the same reactions, but with different efficiencies
LDH is an example of ______ because it is made by _______.
Isozymes and Isoforms
Chooses the first 4 available isoform units: It isn’t picky
Zymgogens
Need to be proteolytically cleaved in order to activate
Proteases: Digestive enzymes, collagenase, and caspases
Examples of zymogens: collagen, blood clotting factors, Insulin/hormones, chymotrypsin
In ATCase, what activates and inactivates the enzyme
Binding of CTP induces the T form
(tense: Inactive)
Binding of ATP prefers the R form
(relaxed: active)
