Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MCAT > Biochemistry Chapters 1-5 > Flashcards

Biochemistry Chapters 1-5 Flashcards

You may prefer our related Brainscape-certified flashcards:
MCAT flashcards
1
Q

What are the 4 groups attached to the central alpha carbon of a proteinogenic amino acid?

A
  1. R-group
  2. Carboxylic Group
  3. Amino Group
  4. Hydrgen Atom
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is the stereochemistry of the chiral amino acids that appear in eukaryotic proteins? And what is the exception?

A
  1. L
  2. S configuration
  3. Cysteine Exception
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Name the 7 nonpolar, nonaromatic amino acids

A
  1. Alanine (A)
  2. Isoleucine (I)
  3. Leucine (L)
  4. Glycine (G)
  5. Proline (P)
  6. Methionine (M)
  7. Valine (V)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Name the 3 aromatic amino acids

A
  1. Phenylalanine (F)
  2. Tryptophan (W)
  3. Tyrosine (Y)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Name the 5 polar amino acids

A
  1. Cysteine (C)
  2. Serine (S)
  3. Threonine (T)
  4. Asparagine (N)
  5. Glutamine (Q)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Name the 2 negatively charged, acidic amino acids

A
  1. Glutamic acid (E)
  2. Aspartic Acid (D)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Name the 3 positively charged, basic amino acids

A
  1. Arginine (R)
  2. Lysine (K)
  3. Histidine (H)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is the predominant form of NH2CRHCOOH at a pH of 1?

A

+NH3CRHCOOH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the predominant form of NH2CRHCOOH at a pH of 7?

A

+NH3CRHCOO-

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the predominant form of NH2CRHCOOH at a pH of 11?

A

NH2CRHCOO-

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the difference between an amino acid, a dipeptide, a tripeptide, an oligopeptide, and a polypeptide?

A

amino acid = 1
dipeptide = 2
tripeptide = 3
oligopeptide = “few” (<20)
polypeptide = “many” (>20)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What molecule is released during the formation of a peptide bond?

A

Water (H2O)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the definition, subtype, and stabilizing bonds of a primary structure?

A

Primary structure is a linear sequence of amino acids in a chain. There are no subtypes and they are stabilized by peptide amide bonds.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the definition, subtype, and stabilizing bonds of a secondary structure?

A

Secondary structures are local structures determined by nearby amino acids. alpha helix and beta pleated sheet subtypes. This structure is stabilized by hydrogen bonds.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What role does proline serve in secondary structure?

A

Proline’s rigid structure causes it to introduce kinks in alpha helices or create turns in beta pleated sheets.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Describe the key structure features of alpha helix secondary structure.

A

alpha helix is a rod-like structure, the peptide chain coils clockwise around a central axis.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Describe the key features of beta pleated sheet secondary structure.

A

peptide chains lie alongside each other forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is the definition, subtype, and stabilizing bonds of a tertiary structure?

A

Three dimensional protein shape. Subtypes include hydrophobic interactions, acid-base/ salt bridges, and disulfide links. Stabilizing bonds include Van der Waals forces, hydrogen bonds, ionic bonds, and covalent bonds.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the definition, subtype, and stabilizing bonds of a quaternary structure?

A

Interaction between separate subunits of a multisubunit protein. No subtype. Stabilizing bonds include Van der Waals forces, hydrogen bonds, ionic bonds, and covalent bonds.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

List three prosthetic groups that can be attached to a proteins and name the conjugated protein.

A

lipids, carbohydrates, and nucleic acids. Lipoproteins, glycoproteins, and nucleoproteins.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is the primary motivation for hydrophobic residues in a polypeptide to move to the interior of the protein?

A

Moving hydrophobic residues to the interior of a protein increases entropy by allowing water molecules on the surface of the protein to have more possible positions and configurations. Stabilizes proteins.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Why are proteins denatured by heat and solutes?

A

Heat increases average kinetic energy and disrupts hydrophobic interactions. Solutes disrupts elements of secondary, tertiary, and quaternary structures.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

How do enzymes function as biological catalysts?

A

Enzymes reduce the activation energy of a reaction (speeding up the reaction). They are not used up in the course of the reaction.

Enzymes improve the environment in which a particular reaction takes place which lowers its activation energy. They are also regenerated at the end of the reaction to their original form.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is enzyme specificity? Give an example.

A

A given enzyme will only catalyze a given reaction or type of reaction.
Ex: serine/threonine specific protein kinases will only place a phosphate group onto the hydroxyl group of a serine or threonine residue.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What are the names of the six different classes of enzymes?

A
  1. Ligase
  2. Isomerase
  3. Lyase
  4. Hydrolase
  5. Oxidoreductase
  6. Transferase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What is the function of Ligase?

A

Addition or synthesis of reactions (generally between large molecules and often requires ATP)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is the function of isomerase?

A

Rearrangement of bonds within a compound

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is the function of Lyase?

A

Cleavage of a single molecule into two products or synthesis of small organic molecules

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What is the function of Hydrolase?

A

Breaking of a compound into two molecules using the addition of water.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What is the function of Oxidoreductase?

A

Oxidation-reduction reactions (transferring electrons)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What is the function of Transferase?

A

Movement of a functional group from one molecule to another.

32
Q

In what ways do enzymes affect the thermodynamics vs the kinetics of a reaction?

A

Enzymes have NO EFFECT on the overall thermodynamics of the reaction. NO EFFECT of change in G or change in H.

Enzymes lower the energy of the transition state and thus the activation energy.

Enzymes have a profound effect on the kinetics of a reaction. Lowering the activation energy will achieve equilibrium faster (the equilibrium position does not change).

33
Q

How do the lock and key theory and induced fit model differ?

A

Lock and Key: The active site of an enzyme fits exactly around the substrate. There are no alterations to tertiary or quaternary structure of the enzyme. It is the LESS accurate model.

Induced Fit: Active site of enzyme molds itself around substrate only when substrate is present. Tertiary and quaternary structure is modified for enzyme function. MORE accurate model.

34
Q

What do cofactors and coenzymes do and how do they differ?

A

Cofactors and coenzymes are both activators of enzymes. Regulators induce a conformational change in enzyme which promotes its activity. Tightly bound cofactors or coenzymes that are NECESSARY for enzyme function are: prosthetic groups.

Cofactors tend to be inorganic (minerals)

Coenzymes tend to be small organic compounds (vitamins)

35
Q

What are the effects of increasing [S] on enzyme kinetics?

A

It depends on how much substrate was present to begin with.

If initial substrate concentration is low, increasing [S] will cause proportional increase in enzyme activity.

If initial substrate concentration is high, the enzyme is already saturated and increasing [S] will have no effect on activity because Vmax has already been attained.

36
Q

What are the effects of increasing [E] on enzyme kinetics?

A

Increasing [E] will always increase Vmax regardless of initial starting concentration of enzyme.

37
Q

How are the Michaelis-Menten and Lineweaver-Burk Plots similar and different?

A

Both relationships account for Km and Vmax under various conditions and provide simple graphical interpretations of these two variables.

Michaelis-Menten plot axis is v vs. [S]. Creates hyperbolic curve for monomeric enzymes.

Lineweaver-Burk plot axis is 1/v vs. 1/[S]. Creates a straight line.

38
Q

What does Km represent?

A

Km is a measure of an enzyme’s affinity for its substrate. Defined as the substrate concentration at which an enzyme is functioning at half its maximal velocity.

39
Q

What would an increase in Km signify?

A

An increase in Km would mean that the enzymes affinity for its substrate decreases.

40
Q

What does the x-axis in the Lineweaver-Burk plot represent?

A

X intercept represents -1/Km

41
Q

What does the y-axis in the Lineweaver-Burk plot represent?

A

y-intercept represents 1/Vmax.

42
Q

What is enzyme cooperativity?

A

Cooperativity refers to interactions between subunits in a multisubunit enzyme or protein.

Binding substrate to subunit induces change in other subunits from the T (tense) state to the R (relaxed) state. Relaxed state encourages binding of substrate to the other subunits.

In the reverse direction, the unbinding of substrate from subunit induces a change from R to T state in remaining subunits, promoting unbinding of substrate from remaining subunits.

43
Q

What are the effects of temperature, pH, and salinity on the function of enzymes?

A

Enzyme activity generally increases when temperature increases (Doubling for every 10 degrees). Above body temperature, enzyme denatures and activity drops off.

Enzymes maximally active within small pH range. Activity drops off quickly outside of pH range as ionization of active site changes and the protein is denatured.

Changes in salinity leads to loss of enzyme function. Disrupts bonds within an enzyme causing disruption of tertiary and quaternary structure.

44
Q

What is the ideal temperature for most enzymes in the body?

A

37 C = 98.6 F = 310 Kelvin

45
Q

What is the ideal pH for most enzymes?

A

7.4 for most enzymes

46
Q

What is the ideal pH for gastric enzymes?

A

2 for gastric enzymes

47
Q

What is the ideal pH for pancreatic enzymes?

A

8.5 for pancreatic enzymes

48
Q

What is feedback inhibition?

A

The product of the enzymatic pathways turns off enzymes further back in that same pathways.

Helps maintain homeostasis. As product levels rise, the pathway creating that product is appropriately down regulated.

49
Q

What is irreversible inhibition?

A

A competitive inhibitor increases Km because substrate concentration has to be higher to reach half maximum velocity in the presence of the inhibitor.

Mixed inhibitor will increase Km only if inhibitor preferentially binds to the enzyme over the enzyme-substrate complex.

50
Q

Of the 4 reversible inhibitors, which could potentially increase Km?

A

Irreversible inhibition (prolonged or permanent inactivation of an enzyme)

51
Q

What are some examples of transient and covalent enzyme modifications?

A

Transient enzyme modifications: Allosteric activation and allosteric inhibition.

Covalent enzyme modifications: phosphorylation and glycosylation.

52
Q

Why are some enzymes released as zymogens?

A

Zymogens are precursors of active enzymes and it is critical that certain enzymes remain inactive until arriving at their target site.

(Ex: digestive enzymes of the pancreas)

53
Q

How do cytoskeletal proteins differ from motor proteins?

A

Cytoskeleton proteins are fibrous with repeating domains.

Motor proteins have ATPase activity and binding heads.

Both proteins function in cellular motility.

54
Q

True or False: Motor proteins are not enzymes

A

False:
An enzyme is a protein or RNA molecule with catalytic activity, which motor proteins do have. Motor function is generally considered nonenzymatic, but the ATPase functionality of motor proteins indicates that these molecules do have catalytic activity.

55
Q

What could permit a binding protein involved in sequestration to have a low affinity for its substrate and still have a high percentage of substrate bound?

A

If the binding protein is present in sufficiently high quantities relative to the substrate, nearly all the substrate will be bound despite a low affinity.

56
Q

What are three main classes of cell adhesion molecules and what type of adhesion does each class form?

A

Cadherin: two cells of the same of similar type using calcium.

Integrin: One cell to proteins in the extracellular matrix.

Selectin: One cell to carbohydrates, usually on the surface of other cells.

57
Q

When an antibody binds to its antigen, what are the three possible outcomes of this interaction?

A
  1. Antibody-antibody interactions - result in neutralization of the pathogen or toxin.
  2. Opsonization - Marking the antigen for destruction.
  3. Insoluble antigen-antibody complexes that can be phagocytized and digested by macrophages (agglutination).
58
Q

Compare and contrast enzyme linked receptors with G protein-coupled receptors.

A

Enzyme-linked receptors - autoactivity and enzymatic activity.

G protein coupled receptors - two protein complex, dissociation upon activation, trimer.

Both - extracellular domain, transmembrane domain, and ligand binding.

59
Q

What type of ion channel is active at all times?

A

Ungated channels are always open

60
Q

How do transport kinetics differ from enzyme kinetics?

A

Transport kinetics display both Km and Vmax values. They can also be cooperative like some binding proteins.

Transporters do not have analogous Keq values for reactions because there is no catalysis.

61
Q

What separation methods can be used to isolate a protein on the basis of isoelectric point?

A

Isoelectric focusing and ion-exchange chromatography. Both separate proteins based on charge. The charge of a protein in any given environment is determined by its isoelectric point.

62
Q

What are the relative benefits of native PAGE compared to SDS PAGE?

A

Native PAGE allows a COMPLETE protein to be recovered after analysis and more accurately determines the relative globular size of proteins.

SDS PAGE can be used to eliminate conflation from mass-to-charge ratios.

63
Q

What are two potential drawbacks of affinity chromatography?

A

The protein of interest may not elute from the column because its affinity is too high or it may be permanently bound to the free receptors in the eluent.

64
Q

True or False: In size exclusion chromatography, the largest molecules elute first.

A

True. The small pores in in size exclusion chromatography trap smaller particles, retaining them in the column.

65
Q

Why are proteins analyzed after isolation?

A

Protein isolation is generally the first step in analysis. Protein identity must be confirmed by amino acid analysis or activity. With unknown proteins, classification of their features is generally desired.

66
Q

What factors would cause an activity assay to display lower activity than expected after concentration determination.

A

Contamination of the sample with detergent or SDS can yield an artificially increased protein level, leading to lower activity than expected because protein concentration was calculated as higher than its actual value.

Or enzyme was denatured during isolation and analysis.

67
Q

True or False: The Edman degradation proceeds from the carboxy (C-) terminus

A

False, Edman degradation proceeds from the amino N- terminus.

68
Q

What is the name for a five-carbon sugar with an aldehyde group?

A

Aldopentose

69
Q

What is the name of a six-carbon sugar with a ketone group?

A

Ketohexose

70
Q

What is the relationship between the carbonyl carbon, anomeric carbon, and the alpha and beta forms of a sugar molecule?

A

During hemiacetal or hemiketal formation, the carbonyl carbon becomes chiral and is termed anomeric carbon. The orientation of the -OH substituent on this carbon determines if the sugar molecule is the alpha or beta anomer.

71
Q

Explain the difference between esterification and glycoside formation.

A

Esterification is the reaction when a hydroxyl group reacts with either a carboxylic acid or carboxylic acid derivative to form an ester.

Glycoside formation is the reaction between an alcohol and a hemiacetal (or hemiketal) group on a sugar to yield an alkoxy group.

72
Q

What purpose do Tollens’ reagent and Benedict’s reagent serve? How do they differ from each other?

A

Tollens reagent and Benedict’s reagent are used to detect the presence of reducing sugars.

Tollens’ reagent is reduced to produce a silvery mirror when aldehydes are present whereas Benedict’s reagent is indicated by a reddish precipitate of Cu2O.

73
Q

From a metabolic standpoint, does it make sense for carbohydrates to get oxidized or reduced? What is the purpose of this process?

A

It makes sense for carbohydrates to become oxidized while reducing other groups. This is because aerobic metabolism required reduced forms of electron carriers to facilitate process such as oxidative phosphorylation.

Because carbohydrates are a primary energy source, they are oxidized.

74
Q

Which of the two forms of starch is more soluble in solution and why.

A

Amylopectin is more soluble in solution than amylose because of its branched structure. The highly branched structure of amylopectin decreases intermolecular bonding between polysaccharide polymers and increases interaction with the surrounding solution.

75
Q

Regarding glycogen and amylopectin, which of these two polymers should experience a higher rate of enzyme activity from enzymes that cleave side branches? Why?

A

Glycogen has a higher rate of enzymatic branch cleavage. This is because it contains significantly more branching than amylopectin.

MCAT (5 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions