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BioChem > Lecture 1 > Flashcards

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
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

26
Q

What is amyloid disease?

A

Accumulation of insoluble, spontaneously aggregating misfolded proteins, called amyloids consisting of B-pleated sheets

Examples include: Alzheimer disease and Parkinson disease

27
Q

What is prion disease?

A

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
Q

Different forms of hemoglobin

A

Oxygenated form = R (relaxed) state
Deoxygenated form = T (taut) state

29
Q

Myoglobin and hemoglobin dissociation curve shape

A

Myoglobin - Hyperbolic
Hemoglobin - sigmoidal

Myoglobin has higher affinity for oxygen

30
Q

Bohr effect and what the ligands do

A

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
Q

Carbon Monoxide on affinity for O2

A

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
Q

Hemoglobinopathies

A

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
Q

Fibrous proteins contain what and some examples

A

Contain regular secondary structural elements and examples include:
Collagen, Elastin, a-keratin

34
Q

Collagen

A

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
Q

Amino acid composition of collagen

A
  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
Q

Synthesis of collagen and collagen defects

A

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
Q

Where are elastin and keratin found?

A

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
Q

What are ribozymes?

A

RNAs with catalytic activity

39
Q

6 Major enzyme classes and additional classes

A
  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
Q

Enzymology Terms to know:
What are holoenzyme, apoenzyme, cofactor, and coenzyme?

A

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
Q

Difference between prosthetic group and cosubstrate?

A

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
Q

Michaelis-Menten equation

A

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
Q

First order and Zero order of the reaction

A

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
Q

What is the Lineweaver-Burk plot?

A

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
Q

Competitive vs noncompetitive Inhibition

A

Competitive: Km increases but Vmax does not change
Noncompetitive: Km does not change but Vmax decreases

46
Q

Difference between homotropic vs heterotropic effectors

A

Homotropic effectors: When the substrate itself serves as an effector
Heterotropic effectors: Effectors that are different from the substrate

47
Q

Regulation of enzymes by covalent modification

A

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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