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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
Ion channels
Proteins that create specific pathways for charged molecules, allowing for their facilitated diffusion
26
Undated channels
No gates preventing ion movement and are therefore unregulated
27
Voltage-gated channels
Regulated by membrane potential change near the channel
28
Ligand-gated channels
Binding of a specific molecule to the channel causes it to open or close
29
Enzyme-linked receptors
Three domains: membrane-spanning domain, ligand-binding domain, catalytic domain
30
Membrane-spanning domain
Anchors the enzyme-linked receptor in the cell membrane
31
Ligand-binding domain
Stimulated by the appropriate ligand and induces a conformation change in the enzyme-linked receptor
32
Catalytic domain
Activated by a conformational change in enzyme-linked receptors
33
Example of enzyme-linked receptors
Receptor tyrosine kinases (RTK)
34
G protein-coupled receptor
Large family of integral membrane proteins involved in signal transduction and have 7 membrane-spanning alpha-helices
35
Heterotrimeric G protein
Method of functionality that are connected to guanine nulceotides
36
G_s
Stimulates adenylate cyclase which increases levels of cAMP in the cell
37
G_i
Inhibits adenylate cyclase which decreases levels of cAMP
38
G_q
Activates phospholipase C which cleaves a phospholipid from membrane to form PIP2 which is cleaved to form DAG and IP3
39
IP3
Open calcium channels in the endoplasmic reticulum
40
Trimeric G protein cycle
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
41
Homogenization
Crushing, grinding, or blending of tissue of interest into evenly mixed solution
42
Centrifugation
Isolate proteins from much smaller molecules before other isolation techniques must be employed
43
Electrophoresis
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
44
Electrophoresis formula
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
Polyacrylamide gel
Standard medium for protein electrophoresis Slightly porous matrix mixture
46
Native PAGE
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
SDS-PAGE
Separates proteins on the basis of relative molecular mass alone
48
SDS
Detergent that disrupts all non-covalent interactions and neutralizes the protein’s original charge
49
Isoelectric point
pH at which the protein or amino acid is electrically neutral
50
Zwitterion
Electrically neutral form of an amino acid
51
Isoelectric focusing
Electric field is generated across the gel Negatively charged proteins will migrate towards the anode (acidic & positively charged)
52
Chromatography
Variety of the cliques that requires the homogenized protein mixture to be fractionated through a porous matrix
53
Stationary phase or adsorbent
Sodium medium through which the mobile phase runs through
54
Elute
Run through the stationary phase
55
Retention time
Amount of time a compound spends in the stationary phase
56
Partitioning
Varying retention times of each compound in the solution results in the separation of components within the stationary phase
57
Column chromatography
Filled with silica or alumina beads as an adsorbent Less polar the compound → faster it can elute through the compound
58
Ion-exchange chromatography
Beads in the column are coated with charged substances that can bind compounds that have an opposite charge
59
Size-exclusion chromatography
Beads used in the column contain tiny pores of various sizes Large compounds can’t fit in pores → move faster
60
Affinity chromatography
Bind any protein of interest by creating a compound with a high affinity for that protein Protein of interest will elute last
61
X-ray crystallography
Provides information about protein structure
62
Edman degradation
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
Bradford protein assay
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
Monosaccharides
Basic structural units of carbohydrates
65
Triose
Monosaccharides made of 3 carbon atoms
66
Tetrose
Monosaccharides made of 4 carbon atoms
67
Pentose
Monosaccharides made of 5 carbon atoms
68
Hexose
Monosaccharides made of 6 carbon atoms
69
Aldose
Carbohydrates that contain an aldehyde group as their most oxidized functional group
70
Ketose
Carbohydrates that contain a ketone group as their most oxidized functional group
71
Carbonyl carbon in most ketoses
C-2
72
Carbonyl carbon in aldoses
C-1
73
Absolute configuration for biochemistry
D and L system (not based on direction of rotation)
74
Fischer projection
Simple two-dimensional drawing of stereoisomers
75
Epimer
Subtype of diastereomers that differ in configuration at exactly one chiral center
76
Hemiacetals
Cyclic molecules formed from aldoses
77
Hemiketals
Cyclic molecules formed from ketoses
78
Anomeric carbon
Carbonyl carbon involved in the formation of the cyclic molecule that becomes chiral in the process
79
Anomers
Ring forms that differ at the anomeric carbon
80
α-anomer
-OH group is trans to the -CH2OH in glucose
81
β-anomer
-OH group is cis to the -CH2OH in glucose
82
Mutarotation
Spontaneous change of configuration about C-1 from α-anomer to β-anomer
83
Reducing sugar
Any monosaccharide with a hemiacetal ring
84
Aldonic acids
Aldoses that are oxidized where the aldehyde becomes the carboxylic acid
85
Lactone
Cyclic ester with a carbonyl group Formed where the aldose is in ring form and oxidation occurs
86
Tollen’s reagent
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
Benedict’s reagent
Aldehyde group of aldose is readily oxidized, indicated by a red precipitate of Cu2O
88
Tautomerization
Rearrangement of bonds in a compound, usually by moving a hydrogen and forming a double bond
89
Enol
Ketone group will pick up a hydrogen and the double bond is moved between two adjacent carbons
90
Alditol
Aldehyde group of an aldose is reduced to a sugar
91
Deoxy sugar
Contains a hydrogen that replaces a hydroxyl group on the sugar
92
Phosphorylation of glucose
Replacement of hydroxyl group with a phosphate group
93
Glycosidic bonds
Formed when the hydroxyl groups are transformed into an alkoxy group
94
Disaccharides
Formed between hydroxyl groups of two monosaccharides and linked by glycosidic bonds
95
Sucrose
Glucose + fructose
96
Lactose
Galactose + glucose
97
Maltose
Glucose + glucose
98
Polysaccharide
Long chain of monosaccharides linked together by glycosidic bonds
99
Homopolysaccharide
Polysaccharide formed of the same type of monosaccharide
100
Heteropolysaccharide
Polysaccharide formed of different types of monosaccharides
101
Cellulose
Main structural component of plants Chain β-D-glucose molecules linked by β-1,4 glycosidic bonds
102
Starches
Made from α-D-glucose monomers
103
Amylose
Linear glucose polymer linked via α-1,4 glycosidic bonds Type of starch
104
Amylopectin
Similar linkage to amylose Contains branches via α-1,6 glycosidic bonds
105
β-amylase
Cleaves amylose at the non-reducing end of the polymer (end with acetal) Produces maltose
106
α-amylase
Cleaves randomly along the chain to yield shorter polysaccharide chains Produces maltose and glucose
107
Glycogen
Carbohydrate storage unit in animals Highly branched compound
108
Glycogen phosphorylase
Cleaves glucose from the non-reducing end of a glycogen branch and phosphorylates it, producing glucose-1-phosphate

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