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MCAT Review > Kaplan — Biochemistry > Flashcards

Kaplan — Biochemistry Flashcards

1
Q

Motif

A

Repetitive organization of secondary structural elements together

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2
Q

Collagen

A

Characteristic tri-helical fiber (three left-handed helices woven together to form a secondary right-handed helix) and makes up most of the ECM of connective tissue

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3
Q

Elastin

A

Component of ECM of connective tissue that can stretch and recoil like a spring

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4
Q

Keratins

A

Intermediate filament proteins found in epithelial cells

Contribute to the mechanical integrity of the cell and function as regulatory proteins

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5
Q

Actin

A

Protein that makes up microfilaments and thin filaments of the myofibrils

Have a positive and negative ends

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6
Q

Tubulin

A

Protein that makes up microtubules

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7
Q

Microtubules

A

Important for providing structure, chromosome separation in mitosis and meiosis, intracellular transport with lines in and dine in

Has a polarity

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8
Q

Microtubule polarity

A

Positive end usually in the periphery of the cell

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9
Q

Motor proteins

A

Display enzymatic activity (acting as ATPases) that power the conformational change necessary for motor function

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10
Q

Myosin

A

Primary motor protein that interacts with actin

Has a single head and neck

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11
Q

Kinesins

A

Motor proteins with two heads associated with microtubules

Key role in aligning of chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis

Moves toward positive end

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12
Q

Dyneins

A

Motor proteins with two heads that are associated with microtubules

Deal with sliding movement of cilia and flagella

Moves toward negative end

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13
Q

Binding proteins

A

Proteins that transport or sequester molecules by binding to them

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14
Q

Cell adhesion molecules (CAMs)

A

Proteins that are found on the surface of most cells and aid in the binding of the cell to the ECM and other cells

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15
Q

Cadherins

A

Group of glycoproteins that mediate calcium-dependent cell adhesion

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16
Q

Integrins

A

Group of proteins that all have two membrane-spanning chains called alpha and beta

Facilitate binding and communicating with the ECM

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17
Q

Selectins

A

Bind to carbohydrate molecules that project from other cell surfaces

Important role in host defense

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18
Q

Antibodies

A

Proteins produced by B-cells that function to neutralize targets in the body

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19
Q

Immunoglobulin (Ig)

A

Antibody

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20
Q

Antibody structure

A

Y-shaped proteins made of two identical heavy chains and two identical light chains that are held together by disulfide linkages and non-covalent interactions

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21
Q

Antigen

A

Target of antibodies

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22
Q

Opsonization

A

Marking the pathogen for destruction by white blood cells

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23
Q

Agglutinating

A

Clumping together the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages

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24
Q

Biosignaling

A

Process in which cells receive and act on signals

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25
Q

Ion channels

A

Proteins that create specific pathways for charged molecules, allowing for their facilitated diffusion

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26
Q

Undated channels

A

No gates preventing ion movement and are therefore unregulated

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27
Q

Voltage-gated channels

A

Regulated by membrane potential change near the channel

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28
Q

Ligand-gated channels

A

Binding of a specific molecule to the channel causes it to open or close

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29
Q

Enzyme-linked receptors

A

Three domains: membrane-spanning domain, ligand-binding domain, catalytic domain

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30
Q

Membrane-spanning domain

A

Anchors the enzyme-linked receptor in the cell membrane

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31
Q

Ligand-binding domain

A

Stimulated by the appropriate ligand and induces a conformation change in the enzyme-linked receptor

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32
Q

Catalytic domain

A

Activated by a conformational change in enzyme-linked receptors

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33
Q

Example of enzyme-linked receptors

A

Receptor tyrosine kinases (RTK)

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34
Q

G protein-coupled receptor

A

Large family of integral membrane proteins involved in signal transduction and have 7 membrane-spanning alpha-helices

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35
Q

Heterotrimeric G protein

A

Method of functionality that are connected to guanine nulceotides

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36
Q

G_s

A

Stimulates adenylate cyclase which increases levels of cAMP in the cell

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37
Q

G_i

A

Inhibits adenylate cyclase which decreases levels of cAMP

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38
Q

G_q

A

Activates phospholipase C which cleaves a phospholipid from membrane to form PIP2 which is cleaved to form DAG and IP3

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39
Q

IP3

A

Open calcium channels in the endoplasmic reticulum

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40
Q

Trimeric G protein cycle

A

Ligand binds the receptor and becomes activated (GDP → GTP)

Alpha subunit dissociates from beta and gamma subunits

Alpha subunit alters the activity of the adenylate cyclase and is dephosphorylated

It will then rebind the beta and gamma subunits

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41
Q

Homogenization

A

Crushing, grinding, or blending of tissue of interest into evenly mixed solution

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42
Q

Centrifugation

A

Isolate proteins from much smaller molecules before other isolation techniques must be employed

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43
Q

Electrophoresis

A

Subjecting compounds to an electric field which moves them according to their net charge and size

Negatively charged compounds will migrate to the positively charged anode

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44
Q

Electrophoresis formula

A

v = E * z / f

v → velocity of a molecule
E → electric field strength
z → charge on the molecule
f → frictional coefficient which depends on the mass and shape of the migrating molecules

45
Q

Polyacrylamide gel

A

Standard medium for protein electrophoresis

Slightly porous matrix mixture

46
Q

Native PAGE

A

Method for analyzing proteins in their native states

Limited by the varying mass-to-charge and mass-to-size ratios of cellular proteins because multiple different protein may experience the same level of migration

47
Q

SDS-PAGE

A

Separates proteins on the basis of relative molecular mass alone

48
Q

SDS

A

Detergent that disrupts all non-covalent interactions and neutralizes the protein’s original charge

49
Q

Isoelectric point

A

pH at which the protein or amino acid is electrically neutral

50
Q

Zwitterion

A

Electrically neutral form of an amino acid

51
Q

Isoelectric focusing

A

Electric field is generated across the gel

Negatively charged proteins will migrate towards the anode (acidic & positively charged)

52
Q

Chromatography

A

Variety of the cliques that requires the homogenized protein mixture to be fractionated through a porous matrix

53
Q

Stationary phase or adsorbent

A

Sodium medium through which the mobile phase runs through

54
Q

Elute

A

Run through the stationary phase

55
Q

Retention time

A

Amount of time a compound spends in the stationary phase

56
Q

Partitioning

A

Varying retention times of each compound in the solution results in the separation of components within the stationary phase

57
Q

Column chromatography

A

Filled with silica or alumina beads as an adsorbent

Less polar the compound → faster it can elute through the compound

58
Q

Ion-exchange chromatography

A

Beads in the column are coated with charged substances that can bind compounds that have an opposite charge

59
Q

Size-exclusion chromatography

A

Beads used in the column contain tiny pores of various sizes

Large compounds can’t fit in pores → move faster

60
Q

Affinity chromatography

A

Bind any protein of interest by creating a compound with a high affinity for that protein

Protein of interest will elute last

61
Q

X-ray crystallography

A

Provides information about protein structure

62
Q

Edman degradation

A

Uses cleavage of sequence proteins of up to 50-70 amino acids

Selectively and sequentially removes the N-terminal amino acid of the protein

Can be analyzed via mass spectroscopy

63
Q

Bradford protein assay

A

Mixes a protein in solution with Coomassie Brilliant Blue dye

Dye is protonated and green-brown in color prior to mixing with proteins → gives up protons, turning blue in the process

Standard curve is created for a protein

64
Q

Monosaccharides

A

Basic structural units of carbohydrates

65
Q

Triose

A

Monosaccharides made of 3 carbon atoms

66
Q

Tetrose

A

Monosaccharides made of 4 carbon atoms

67
Q

Pentose

A

Monosaccharides made of 5 carbon atoms

68
Q

Hexose

A

Monosaccharides made of 6 carbon atoms

69
Q

Aldose

A

Carbohydrates that contain an aldehyde group as their most oxidized functional group

70
Q

Ketose

A

Carbohydrates that contain a ketone group as their most oxidized functional group

71
Q

Carbonyl carbon in most ketoses

A

C-2

72
Q

Carbonyl carbon in aldoses

A

C-1

73
Q

Absolute configuration for biochemistry

A

D and L system (not based on direction of rotation)

74
Q

Fischer projection

A

Simple two-dimensional drawing of stereoisomers

75
Q

Epimer

A

Subtype of diastereomers that differ in configuration at exactly one chiral center

76
Q

Hemiacetals

A

Cyclic molecules formed from aldoses

77
Q

Hemiketals

A

Cyclic molecules formed from ketoses

78
Q

Anomeric carbon

A

Carbonyl carbon involved in the formation of the cyclic molecule that becomes chiral in the process

79
Q

Anomers

A

Ring forms that differ at the anomeric carbon

80
Q

α-anomer

A

-OH group is trans to the -CH2OH in glucose

81
Q

β-anomer

A

-OH group is cis to the -CH2OH in glucose

82
Q

Mutarotation

A

Spontaneous change of configuration about C-1 from α-anomer to β-anomer

83
Q

Reducing sugar

A

Any monosaccharide with a hemiacetal ring

84
Q

Aldonic acids

A

Aldoses that are oxidized where the aldehyde becomes the carboxylic acid

85
Q

Lactone

A

Cyclic ester with a carbonyl group

Formed where the aldose is in ring form and oxidation occurs

86
Q

Tollen’s reagent

A

Produced by mixing AgNO3 with NaOH to produce Ag2O and dissolving silver oxide in ammonia to produce [Ag(NH3)2]+

Will produce a silvery mirror when aldehydes are present

87
Q

Benedict’s reagent

A

Aldehyde group of aldose is readily oxidized, indicated by a red precipitate of Cu2O

88
Q

Tautomerization

A

Rearrangement of bonds in a compound, usually by moving a hydrogen and forming a double bond

89
Q

Enol

A

Ketone group will pick up a hydrogen and the double bond is moved between two adjacent carbons

90
Q

Alditol

A

Aldehyde group of an aldose is reduced to a sugar

91
Q

Deoxy sugar

A

Contains a hydrogen that replaces a hydroxyl group on the sugar

92
Q

Phosphorylation of glucose

A

Replacement of hydroxyl group with a phosphate group

93
Q

Glycosidic bonds

A

Formed when the hydroxyl groups are transformed into an alkoxy group

94
Q

Disaccharides

A

Formed between hydroxyl groups of two monosaccharides and linked by glycosidic bonds

95
Q

Sucrose

A

Glucose + fructose

96
Q

Lactose

A

Galactose + glucose

97
Q

Maltose

A

Glucose + glucose

98
Q

Polysaccharide

A

Long chain of monosaccharides linked together by glycosidic bonds

99
Q

Homopolysaccharide

A

Polysaccharide formed of the same type of monosaccharide

100
Q

Heteropolysaccharide

A

Polysaccharide formed of different types of monosaccharides

101
Q

Cellulose

A

Main structural component of plants

Chain β-D-glucose molecules linked by β-1,4 glycosidic bonds

102
Q

Starches

A

Made from α-D-glucose monomers

103
Q

Amylose

A

Linear glucose polymer linked via α-1,4 glycosidic bonds

Type of starch

104
Q

Amylopectin

A

Similar linkage to amylose

Contains branches via α-1,6 glycosidic bonds

105
Q

β-amylase

A

Cleaves amylose at the non-reducing end of the polymer (end with acetal)

Produces maltose

106
Q

α-amylase

A

Cleaves randomly along the chain to yield shorter polysaccharide chains

Produces maltose and glucose

107
Q

Glycogen

A

Carbohydrate storage unit in animals

Highly branched compound

108
Q

Glycogen phosphorylase

A

Cleaves glucose from the non-reducing end of a glycogen branch and phosphorylates it, producing glucose-1-phosphate

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