Midterm 1 (Chapters 1-4) Flashcards
Cell theory
- All living things are composed of cells,
- All cells come from pre-existing cells,
- Cells are the structural unit of life
Model organisms
relatively simple, fast generation time, large number of offspring, easy to manipulate in lab, inexpensive to breed. E. coli, yeast, nematodes, mustard plant, zebra fish, mouse, fruit fly
Size
viruses are smaller than cells, proteins are smaller than viruses
Covalent bonds
pairs of electrons are shared between pairs of atoms. Strong bonds are not super useful in proteins since it takes a lot of energy to break
Nonpolar covalent bonds
equal sharing of electrons
Polar covalent bonds
unequal sharing of electrons
Ionic bonds
electrostatic attraction between two oppositely charged ions
Hydrogen bonding
weak attractive interaction between an electronegative atom and a hydrogen atom that is covalently linked to a second electronegative atom
Electronegativity
an indication of an atom’s ability to attract an electron (they are electron deficient). The more electronegative, the greater the ability of an atom to attract an electron.
Properties of water as a solvent
molecules that contain polar bonds and that can form hydrogen bonds with water dissolve readily in water
Hydrophobic effect
nonpolar molecules and nonpolar portions of molecules tend to aggregate in water. Nonpolar molecules are forced into aggregates to reduce exposure to water.
Functional groups
often behave as a unit and give organic molecules their physical properties, chemical reactivity, and solubility in aqueous solution.
Amphipathic
a molecule or protein having both hydrophobic and hydrophilic components
Macromolecules
large, highly organized molecules that form the structure and carry out the activities of the cell. 4 major categories: proteins, nucleic acids, polysaccharides, lipids
Building blocks of the cell -> larger units of the cell
Sugars -> polysaccharides.
Fatty acids -> fats, lipids, membranes.
Amino acids -> proteins.
Nucleotides -> nucleic acids
Glucose
forms a ring structure in our bodies. Double bonded O is found at C1, with CH2OH group at C6.
Anomeric carbon
carbon derived from the carbonyl carbon (the ketone or aldehyde group) of the open chain form of the carbohydrate molecule. Numbered as C1. can open and mutarotate in solution. When the anomeric carbon of a monosaccharide participates in a glycosidic bond it can no longer mutarotate and is in a fixed position
Identifying anomeric carbon
draw a line through the plane. If the OH group is above the plane it is in the beta position. Below the plane, it is alpha position.
Glycosidic bonds
monosaccharides that are linked together by covalent bonds. Formed between two OH groups on two separate monosaccharides, or a monosaccharide and another molecule. Always involve the hydroxyl of an anomeric carbon. Always generates a beta glycosidic linkage when it happens in the cell.
Disaccharide
2 monosaccharides linked by a glycosidic bond
N-glycosidic bond
when an anomeric carbon reacts with a nitrogen, always beta
O-glycosidic bond
when an anomeric carbon reacts with a hydroxyl - can be alpha or beta
Polysaccharides
polymers of sugars joined by glycosidic bonds.
Amylose
linear polymer, with alpha(1 -> 4) links between glucose monomers
Amylopectin and glycogen
branched polymer alpha(1 -> 4) linkages plus alpha (1 -> 6) linkages. Branched starches.
Glycoproteins
one or more oligosaccharides covalently joined to a protein. O-linked - oligosaccharide in a glycosidic bond with a serine or threonine hydroxyl. N-linked - oligosaccharide in an N-glycosidic bond to the amide nitrogen of an Asparagine residue
Cellular lipids
fats (triacylglycerols - TAGs), steroids, phospholipids. Amphipathic, long, unbranched hydrocarbon chains with a single carboxyl group at one end.
Fats (Triacylglycerols)
glycerol linked by ester bonds to three fatty acids
Fatty acids
differ in their length and presence of double bonds. Cis double bonds insert a bend into a hydrocarbon chain which reduces Van Der Waal interactions, thereby decreasing melting point.
Phospholipids
two fatty acid chains attached to a glycerol backbone which is bonded to a phosphate group (polar head group). Have two different properties: one end with a phosphate group (hydrophilic), the other end has two fatty acid tails (hydrophobic)
Peptide bond formation
carboxyl group + amino group in a dehydration reaction
Hydropathy index
the more negative the index = less soluble = more hydrophilic, will not be happy in the hydrophobic core. More positive = more soluble = more happy in the hydrophobic core. Polar charged will likely be on the surface, otherwise will likely be found inside the protein.
Protein structure
Primary - describes the unique order in which amino acids are linked together to form a protein.
Secondary - coiling or folding of a polypeptide chain that gives the protein its 3D shape (alpha helix, beta sheets).
Tertiary - comprehensive 3D structure of the polypeptide chain of a protein.
Quaternary - refers to the structure of a protein macromolecule formed by interactions between multiple polypeptide chains (assembled subunits)
Domain
a substructure produced by any part of a polypeptide chain that can fold independently into a stable structure that generally has a specific function.
Quaternary structure in a table
proteins that have more than 1 polypeptide chain has a quaternary structure. Largest protein is the one with the largest molecular weight.
Molecular chaperones
class of proteins that help other intracellular proteins fold. Proteins that bind and stabilize unfolded or partially folded polypeptides thereby preventing these proteins from aggregating and degrading.
Chaperonins
directly facilitate the folding of the proteins
Biomembranes
composed of lipids, proteins, carbohydrates arranged in a bilayer, but in different proportions and different specific lipids, proteins, carbs.
3 major lipids in cell membranes
phosphoglycerides, sphingolipids, cholesterol
Phosphoglycerides
glycerol backbone, phosphate group, head group, 2 fatty acids
Sphingolipids
instead of glycerol backbone, there is a sphingosine backbone and a fatty acid chain.
Sphingomyelin
is the only one with a phosphate
Cerebroside
sphingolipid with one sugar
Ganglioside
sphingolipid with multiple sugars
Cholesterol
complex molecule with OH group, rings. Amphipathic
Ceramide
building block of sphingolipids
Phospholipids
lipids with a phosphate group
Phosphoglycerides
phospholipids built on a glycerol backbone. Phosphatidylserine has a net negative charge.
Membrane biosynthesis
Step 1 - acyl transferases add two fatty acids to glycerol - 3 phosphate to produce phosphatidic acid.
Step 2 - a phosphatase removes the phosphate leaving DAG (diacylglycerol).
Step 3 - the addition of a head group
Membrane lipids (sphingolipids)
sphingosine, ceramide, sphingomyelin
Sphingosine:
an amino alcohol that contains a long hydrocarbon chain
Ceramide
sphingosine linked to a fatty acid
Sphingomyelin
phosphorylcholine added to a ceramide. The only sphingolipid that that is a phospholipid and a sphingolipid.
Glycolipid
a carbohydrate added instead of a phosphorylcholine
Glycoprotein and glycolipid orientation
found in the exoplasmic face of the plasma membrane. Sugar groups added in the lumen of the golgi
Membrane proteins
integral proteins, peripheral proteins, lipid-anchored membrane proteins
Integral proteins
penetrate and pass through lipid bilayer. Are amphipathic.
Peripheral proteins
located entirely outside of bilayer on either the extracellular or cytoplasmic side
Lipid-anchored membrane proteins
Proteins are covalently bound to a membrane anchored lipid.
Types of lipid-anchored membrane proteins
acylation, prenylation
Prenylation
lipid anchor is built from 5 carbon isoprene units attached to a carboxyl terminal cysteine. On the cytosol side of the membrane. Always faces interior of cell.
Acylation
generally attached to an internal cysteine, serine, or an amino terminal glycine. protein is covalently attached to a fatty acyl group.
GPI
attached to C-terminus of a protein during post-translational modification. Always faces outside of the cell. Attaches to a phosphatidylinositol which is attached to sugar units and an ethanolamine phosphate which attaches to the protein.
Transmembrane domain
a string of about 20 mostly nonpolar amino acids that span the lipid bilayer as a helix.
Hydropathy plot
anything above the 0 point is hydrophobic and will be found in the membrane. Below 0 is hydrophilic and will be outside of the membrane.
Fluidity
membranes function only in the fluid state. HOT: don’t want kinks in the membrane, want straight chained fatty acids, decrease fluidity. COLD: want more fluidity, more kinks in the membrane, adding double bonds = more fluid
Factors affecting fluidity
phospholipid content, length of and degree of saturation of fatty acyl chains, temperature, sterol content.
Lipid rafts
cholesterol and sphingolipids pack together to form lipid rafts that float within the more fluid and disordered environment (or may be anchored). They provide a favourable environment for cell-surface receptors and GPI-anchored proteins and sequester proteins involved in cell signalling
Bilayer thickness
bilayers with sphingomyelin and sphingomyelin and cholesterol are similar thickness, and are thicker than bilayers composed of phosphatidylcholine and phosphatidylcholine and cholesterol. Phosphatidylcholine and cholesterol are thicker than just phosphatidylcholine.
Protein mobility
proteins can move. When 2 different membrane proteins are coloured and combined, they begin to mix. They will fully mix after a period of time, a result of protein movement.
Lipid mobility
lipids can move. Phospholipid can move laterally within the same leaflet. To flip-flop, the hydrophilic head must pass through the hydrophobic centre.
FRAP
fluorescence recovery after photobleaching. Can measure the diffusion rates of proteins. Label proteins with fluorescent dye, photobleach a spot with a laser, watch the protein recovery (proteins fill spot that was bleached)
Passive transport
spontaneous movement down concentration gradient. No energy expended. Contains simple diffusion and facilitated diffusion.
Active transport
against concentration gradient, requires an input of free energy (pumps)
Simple diffusion
small molecules such as oxygen, CO2, ethanol. Have to be small and nonpolar enough to cross membrane without the aid of transport proteins. Movement of a solute from a region of higher concentration to lower concentration.
Facilitated diffusion
requires a protein to get the molecule across the membrane.
Membrane potential:
will influence charged molecules. Cytoplasmic side of membrane is usually negative relative to outside. Draws positive molecules in and drives negative molecules out.
Glucose uptake graph
high Km/Kt is more able to bring glucose levels in the body down. Calcium is important in signal transduction. low Kt = transports less glucose but picks up glucose more readily. high Kt = transports more glucose but requires more glucose to be present as it has a lower affinity
Carrier proteins
transport either one or two solutes. One solute = facilitated transport, 2 solutes = indirect active transport
Uniport
transports a single molecule at a time down its concentration gradient
Coupled transport
two solutes are transported at the same time. Either antiport or symport.
Antiporter
simultaneously transports two molecules in opposite directions. One molecule moves down its concentration, and the other moves up.
Symporter
simultaneously transports two different molecules in the same direction. One molecule moving down its concentration gradient and one molecule moves up.
P class pumps
two identical catalytic alpha subunits that contain an ATP binding site. perform active ion transport across biological membranes
P class pumps: Na+/K+ ATPase (pump)
Na+ concentration in the cytosol is much lower than extracellular fluid. K+ concentration in the cytosol is much higher than extracellular fluid. Na+ is always pumped out of the cell, K+ always pumped into the cell. Maintains intracellular sodium and potassium concentrations in animal cells which maintains osmotic balance and stabilizes cell volume.
Ca2+pumps
P class pump that keeps intracellular Ca2+ concentrations low. Unidirectional pump from cytosol to lumen of SR.
Glucose-Na+ symporter and glucose uniporter
work together to get glucose from the digestive system into the body. Sodium goes with its concentration gradient, glucose goes against its concentration gradient. The two types of transporters are kept segregated in the plasma membrane by tight junctions.
Voltage-gated channels
conformational state depends on the difference in ionic charge on the two sides of the membrane
Ligand-gated channels
conformational state depends on the binding of a specific molecule and can be either open or closed after ligand binding
Mechano-gated (stress gated) channels
conformational state depends on mechanical forces that are applied to the membrane (ie. stretch tension)
