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Lecture 1 Flashcards

1
Q

Which amino acid has a secondary amino group?

A

Proline (R group interacts with amino group to make secondary amino group)

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2
Q

pH > pKa = ?
pH < pKa = ?

A

pH > pKa = deprotonated
pH < pKa = Protonated

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3
Q

What is amphoteric property and zwitterions?

A

Amphoteric property - act as an acid or base
Zwitterions - Equal number of positive and negative charges

Amino acid is a zwitterion along with having amphoteric properties

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4
Q

Nonpolar Amino Acids to memorize

A

Glycine (H as R group)
Proline (CH2-CH2-CH2 as R group) (Causes steric hinderance)
Methionine (CH2-CH2-S-CH3) (Has sulfur in R group)

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5
Q

In Sickle cell anemia, what amino acids are substituted and at what position and subunit?

A

Substitution of polar glutamate with nonpolar valine at the 6th position of the Beta subunit of hemoglobin. Valine causes hemoglobin to aggregate to cause sickle cell shape.

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6
Q

Phosphates love to bond to what group?

A

OH group in Serine, Threonine, Tyrosine (Uncharged polar AA)

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7
Q

Memorize these uncharged polar amino acids

A

Serine - (CH2-OH)
Threonine - (CH3-CH-OH)
Tyrosine - (CH2-Aromatic Ring-OH)

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8
Q

Know hydroxyl, amide, and sulfhydryl structure and why they are important

A

Hydroxyl - (OH) Attach Phosphate group and oligosaccharide chains
Amide - (O=C-NH2) Attach oligosaccharide chains
Sulfhydryl - (SH) Important component of the active site of enzymes

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9
Q

Acidic amino acids to memorize

A

Aspartate - (CH2-Carboxyl group)
Glutamate - (CH2-CH2-Carboxyl group)
Side chains are proton donors

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10
Q

Basic amino acids to memorize

A

Lysine - (NH3+ at end)
Arginine - (Contains NH2+ and NH2 at end)
Histidine - (Has pentane ring structure at end) (Weakly basic)
Side chains are proton acceptors

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11
Q

Nonessential amino acids

A

Alanine, Arginine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Proline, Serine, Tyrosine
Nonessential amino acids are produced by the body.

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12
Q

What is an enantiomer?

A

Mirror images (cannot be superimposed on each other)
All AAs found in mammalian proteins are L-configuration

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13
Q

Why can Amino Acids act as buffers?

A

They contain weakly acidic a-carboxyl groups and weakly basic a-amino groups.

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14
Q

Bronsted-Lowry acid and bases

A

Acid - Proton donor
Base - Proton acceptor

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15
Q

Relationship between Ka, pKa, and pH and what is the Henderson-Hasselbalch Equation?

A

pka=-log(Ka) and pH = -log(H+)
Larger the Ka = smaller the pKa = stronger the acid
Smaller the Ka = larger the pKa = weaker the acid

pH = pKa + log((A-)/(HA))

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16
Q

pH of buffer should be within what pH unit range of the acid’s pKa value?

When does max buffering capacity occur?

A

+/- 1 pH unit of the acid’s pKa

When pH = pKa

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17
Q

What is isoelectric point and formula for it?

A

pH at which a molecule possesses no net charge
pI = (pKa1 + pKa2)/2

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18
Q

Naming polypeptides

A

All AA residues have their suffixed changed to -yl with the exception of the C-terminal AA

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19
Q

What are the Start and Stop codons?

A

Start: AUG (Methionine)
Stop: UGA, UAA, UAG

20
Q

a-helix properties and proteins containing them

A

Right hand spiral with side chains extending outwards to avoid steric hinderance with 3.6 AA per turn

Keratins contain a-helices along with myoglobin

21
Q

What are chaperons

A

Specialized group of proteins required for the proper folding of many species of proteins

22
Q

Denaturing Agents Include:

A

-Heat
-Organic solvents
-Mechanical mixing
-Strong acids or bases
-Detergents
-Ions of heavy metals such as lead and mercury

23
Q

Quaternary structure subunits are held together by what interactions

A

Noncovalent interactions (Hydrophobic interactions, H-bonds, and ionic bonds)

24
Q

What are isoforms and isozymes?

A

Isoforms - proteins that perform the same function but have different primary structures
Isozymes - Protein isoforms that function as enzymes

25
What are isoforms and isozymes?
Isoforms - proteins that perform the same function but have different primary structures Isozymes - Protein isoforms that function as enzymes
26
What is amyloid disease?
Accumulation of insoluble, spontaneously aggregating misfolded proteins, called amyloids consisting of B-pleated sheets Examples include: Alzheimer disease and Parkinson disease
27
What is prion disease?
Disease caused by the prion protein (PrP) Infections PrP is highly resistant to proteolytic degradation and tends to form insoluble aggregates of fibrils in the BRAIN Causative agent of transmissible spongiform encephalopathies (TSE) including: Creutzfeldt-Jakob disease in humans Scrapie in sheeps Bovine spongiform encephalopathy in cattle (mad cow disease)
28
Different forms of hemoglobin
Oxygenated form = R (relaxed) state Deoxygenated form = T (taut) state
29
Myoglobin and hemoglobin dissociation curve shape
Myoglobin - Hyperbolic Hemoglobin - sigmoidal Myoglobin has higher affinity for oxygen
30
Bohr effect and what the ligands do
Effect of a change in the O2 binding affinity of Hb, due to the binding of other ligands to Hb Ligands: H+ (pH) 2,3 - bisphosphoglycerate (In glycolysis pathway) CO2 Increase in all these ligands cause decrease in affinity for O2 These ligands stabilize the Taut (deoxygenated) state
31
Carbon Monoxide on affinity for O2
CO binding causes hemoglobin to shift to R state causing the other heme sites to bind O2 tightly Extreme increase in affinity for O2 causing Hb to not be able to release O2 to the tissue
32
Hemoglobinopathies
Sickle cell anemia (Hb S) - glutamate is substituted with valine Hemoglobin C (Hb C) disease - glutamate is substituted with lysine Hemoglobin SC disease - (Hb S + Hb C) Thallassemia syndromes - decreased production of normal hemoglobin
33
Fibrous proteins contain what and some examples
Contain regular secondary structural elements and examples include: Collagen, Elastin, a-keratin
34
Collagen
Most abundant protein in human body 3 Polypeptide helices that are twisted around each other to form a right handed triple helix 90% of collagen in humans is type I Type I collagen is found in teeth, bone, skin, and tendons
35
Amino acid composition of collagen
1. Glycine - approximately 1/3 of the AA residues 2. Proline and 4-Hydroxyproline - as much as 30% 3. 3-Hydroxyproline and 5-hydroxylysine (small amounts) also occur Hydroxyproline and hydroxylysine are not present in most other proteins so can be used as marker for collagen
36
Synthesis of collagen and collagen defects
Procollagen is made first in RER and enters the golgi and secreted into ECM to form tropocollagen which then forms collagen Ehlers-Danlos syndrome - results in fragile stretchy skin and loose joints (Genetic mutation) Osteogenesis imperfecta (OI) - results in bones that easily bend and fracture
37
Where are elastin and keratin found?
Elastin is a connective tissue protein with rubber-like properties so found in lungs, walls of large arteries, elastic ligaments Keratin found in hair, wool, skin, horns, and fingernails - composed of a-helical polypeptides
38
What are ribozymes?
RNAs with catalytic activity
39
6 Major enzyme classes and additional classes
1. Oxidoreductase - redox reactions 2. Transferase - transfers molecules 3. Hydrolase - Use water to break bonds 4. Lyase - Cleaves bonds 5. Isomerase - Converts D and L configuration 6. Ligase - Joins together molecules using ATP Synthetase - requires ATP Synthase - does not require ATP Phosphatase - Removes phosphate group Phosphorylase - Breaks bond using inorganic phosphate (Pi) Kinase - adds a phosphate group from a high energy molecule like ATP Oxidase - catalyze oxidation-reduction reactions using O2 as the electron acceptor but oxygen atoms are not added into substrate Oxygenase - oxidize a substrate by transferring oxygen atoms to it
40
Enzymology Terms to know: What are holoenzyme, apoenzyme, cofactor, and coenzyme?
Holoenzyme - enzyme with its nonprotein component (active) (Whole enzyme) Apoenzyme - enzyme without its nonprotein component (inactive) Cofactor - nonprotein moeity (inorganic like metal atoms or organic) of the enzyme Coenzyme - Nonprotein moeity (small organic molecule). Frequently derived from vitamins
41
Difference between prosthetic group and cosubstrate?
Prosthetic group refers to coenzymes that are permanently associated with the enzyme Cosubstrate refers to coenzymes that only transiently associate with the enzyme Allosteric enzyme refers to enzymes that change their conformation when bound by an effector at a site other than the active site.
42
Michaelis-Menten equation
Vo = (Vmax[S]) / (Km + [S]) Vo = initial velocity Vmax = maximum velocity Km = Michaelis constant = (K-1 + K2)/K1 [S] = Substrate concentration Higher Km = Lower the affinity for substrate
43
First order and Zero order of the reaction
First order with respect to substrate: - When [S] is much less than Km - V is proportional to [S] Zero order with respect to substrate: - When [S] is greater than Km - V is constant and independent of [S]
44
What is the Lineweaver-Burk plot?
Double reciprocal plot in which X axis is 1/[S] and Y axis is 1/Vo Y intersect shows 1/Vmax while x intersect shows 1/-Km Increases towards the intersect 1/Vo = (Km/Vmax[S]) + 1/Vmax
45
Competitive vs noncompetitive Inhibition
Competitive: Km increases but Vmax does not change Noncompetitive: Km does not change but Vmax decreases
46
Difference between homotropic vs heterotropic effectors
Homotropic effectors: When the substrate itself serves as an effector Heterotropic effectors: Effectors that are different from the substrate
47
Regulation of enzymes by covalent modification
Most frequently done by addition or removal of phosphate groups from serine, threonine, or tyrosine residues Phosphorylation by protein kinases Dephosphorylation by phosphoprotein phosphatases Increase (induction) or decrease (repression) of enzyme synthesis can regular enzyme activity as well

BioChem (4 decks)

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