Kaplan — Biochemistry Flashcards
Motif
Repetitive organization of secondary structural elements together
Collagen
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
Elastin
Component of ECM of connective tissue that can stretch and recoil like a spring
Keratins
Intermediate filament proteins found in epithelial cells
Contribute to the mechanical integrity of the cell and function as regulatory proteins
Actin
Protein that makes up microfilaments and thin filaments of the myofibrils
Have a positive and negative ends
Tubulin
Protein that makes up microtubules
Microtubules
Important for providing structure, chromosome separation in mitosis and meiosis, intracellular transport with lines in and dine in
Has a polarity
Microtubule polarity
Positive end usually in the periphery of the cell
Motor proteins
Display enzymatic activity (acting as ATPases) that power the conformational change necessary for motor function
Myosin
Primary motor protein that interacts with actin
Has a single head and neck
Kinesins
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
Dyneins
Motor proteins with two heads that are associated with microtubules
Deal with sliding movement of cilia and flagella
Moves toward negative end
Binding proteins
Proteins that transport or sequester molecules by binding to them
Cell adhesion molecules (CAMs)
Proteins that are found on the surface of most cells and aid in the binding of the cell to the ECM and other cells
Cadherins
Group of glycoproteins that mediate calcium-dependent cell adhesion
Integrins
Group of proteins that all have two membrane-spanning chains called alpha and beta
Facilitate binding and communicating with the ECM
Selectins
Bind to carbohydrate molecules that project from other cell surfaces
Important role in host defense
Antibodies
Proteins produced by B-cells that function to neutralize targets in the body
Immunoglobulin (Ig)
Antibody
Antibody structure
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
Antigen
Target of antibodies
Opsonization
Marking the pathogen for destruction by white blood cells
Agglutinating
Clumping together the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages
Biosignaling
Process in which cells receive and act on signals
Ion channels
Proteins that create specific pathways for charged molecules, allowing for their facilitated diffusion
Undated channels
No gates preventing ion movement and are therefore unregulated
Voltage-gated channels
Regulated by membrane potential change near the channel
Ligand-gated channels
Binding of a specific molecule to the channel causes it to open or close
Enzyme-linked receptors
Three domains: membrane-spanning domain, ligand-binding domain, catalytic domain
Membrane-spanning domain
Anchors the enzyme-linked receptor in the cell membrane
Ligand-binding domain
Stimulated by the appropriate ligand and induces a conformation change in the enzyme-linked receptor
Catalytic domain
Activated by a conformational change in enzyme-linked receptors
Example of enzyme-linked receptors
Receptor tyrosine kinases (RTK)
G protein-coupled receptor
Large family of integral membrane proteins involved in signal transduction and have 7 membrane-spanning alpha-helices
Heterotrimeric G protein
Method of functionality that are connected to guanine nulceotides
G_s
Stimulates adenylate cyclase which increases levels of cAMP in the cell
G_i
Inhibits adenylate cyclase which decreases levels of cAMP
G_q
Activates phospholipase C which cleaves a phospholipid from membrane to form PIP2 which is cleaved to form DAG and IP3
IP3
Open calcium channels in the endoplasmic reticulum
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
Homogenization
Crushing, grinding, or blending of tissue of interest into evenly mixed solution
Centrifugation
Isolate proteins from much smaller molecules before other isolation techniques must be employed
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
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
Polyacrylamide gel
Standard medium for protein electrophoresis
Slightly porous matrix mixture
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
SDS-PAGE
Separates proteins on the basis of relative molecular mass alone
SDS
Detergent that disrupts all non-covalent interactions and neutralizes the protein’s original charge
Isoelectric point
pH at which the protein or amino acid is electrically neutral
Zwitterion
Electrically neutral form of an amino acid
Isoelectric focusing
Electric field is generated across the gel
Negatively charged proteins will migrate towards the anode (acidic & positively charged)
Chromatography
Variety of the cliques that requires the homogenized protein mixture to be fractionated through a porous matrix
Stationary phase or adsorbent
Sodium medium through which the mobile phase runs through
Elute
Run through the stationary phase
Retention time
Amount of time a compound spends in the stationary phase
Partitioning
Varying retention times of each compound in the solution results in the separation of components within the stationary phase
Column chromatography
Filled with silica or alumina beads as an adsorbent
Less polar the compound → faster it can elute through the compound
Ion-exchange chromatography
Beads in the column are coated with charged substances that can bind compounds that have an opposite charge
Size-exclusion chromatography
Beads used in the column contain tiny pores of various sizes
Large compounds can’t fit in pores → move faster
Affinity chromatography
Bind any protein of interest by creating a compound with a high affinity for that protein
Protein of interest will elute last
X-ray crystallography
Provides information about protein structure
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
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
Monosaccharides
Basic structural units of carbohydrates
Triose
Monosaccharides made of 3 carbon atoms
Tetrose
Monosaccharides made of 4 carbon atoms
Pentose
Monosaccharides made of 5 carbon atoms
Hexose
Monosaccharides made of 6 carbon atoms
Aldose
Carbohydrates that contain an aldehyde group as their most oxidized functional group
Ketose
Carbohydrates that contain a ketone group as their most oxidized functional group
Carbonyl carbon in most ketoses
C-2
Carbonyl carbon in aldoses
C-1
Absolute configuration for biochemistry
D and L system (not based on direction of rotation)
Fischer projection
Simple two-dimensional drawing of stereoisomers
Epimer
Subtype of diastereomers that differ in configuration at exactly one chiral center
Hemiacetals
Cyclic molecules formed from aldoses
Hemiketals
Cyclic molecules formed from ketoses
Anomeric carbon
Carbonyl carbon involved in the formation of the cyclic molecule that becomes chiral in the process
Anomers
Ring forms that differ at the anomeric carbon
α-anomer
-OH group is trans to the -CH2OH in glucose
β-anomer
-OH group is cis to the -CH2OH in glucose
Mutarotation
Spontaneous change of configuration about C-1 from α-anomer to β-anomer
Reducing sugar
Any monosaccharide with a hemiacetal ring
Aldonic acids
Aldoses that are oxidized where the aldehyde becomes the carboxylic acid
Lactone
Cyclic ester with a carbonyl group
Formed where the aldose is in ring form and oxidation occurs
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
Benedict’s reagent
Aldehyde group of aldose is readily oxidized, indicated by a red precipitate of Cu2O
Tautomerization
Rearrangement of bonds in a compound, usually by moving a hydrogen and forming a double bond
Enol
Ketone group will pick up a hydrogen and the double bond is moved between two adjacent carbons
Alditol
Aldehyde group of an aldose is reduced to a sugar
Deoxy sugar
Contains a hydrogen that replaces a hydroxyl group on the sugar
Phosphorylation of glucose
Replacement of hydroxyl group with a phosphate group
Glycosidic bonds
Formed when the hydroxyl groups are transformed into an alkoxy group
Disaccharides
Formed between hydroxyl groups of two monosaccharides and linked by glycosidic bonds
Sucrose
Glucose + fructose
Lactose
Galactose + glucose
Maltose
Glucose + glucose
Polysaccharide
Long chain of monosaccharides linked together by glycosidic bonds
Homopolysaccharide
Polysaccharide formed of the same type of monosaccharide
Heteropolysaccharide
Polysaccharide formed of different types of monosaccharides
Cellulose
Main structural component of plants
Chain β-D-glucose molecules linked by β-1,4 glycosidic bonds
Starches
Made from α-D-glucose monomers
Amylose
Linear glucose polymer linked via α-1,4 glycosidic bonds
Type of starch
Amylopectin
Similar linkage to amylose
Contains branches via α-1,6 glycosidic bonds
β-amylase
Cleaves amylose at the non-reducing end of the polymer (end with acetal)
Produces maltose
α-amylase
Cleaves randomly along the chain to yield shorter polysaccharide chains
Produces maltose and glucose
Glycogen
Carbohydrate storage unit in animals
Highly branched compound
Glycogen phosphorylase
Cleaves glucose from the non-reducing end of a glycogen branch and phosphorylates it, producing glucose-1-phosphate
