Exam 1 Flashcards
What are the four small, organic molecules that are contained in all living species?
Sugars, fatty acids, amino acids, and nucleotides
What bonds contribute to the ability of a molecule to be hydrophilic?
Polar covalent and hydrogen
What bonds contribute to preventability of a molecule to be hydrophobic?
Non polar covalent
What are acids?
Substances that release protons when they dissolve in water
What are bases?
Substances that accept protons when they dissolve in water
What combinations of atoms occur repeatedly in organic molecules?
Methyl (CH3), hydroxyl (OH), carboxyl (COOH), carbonyl (C=O), phosphoryl (PO3^2-), and amino (NH2)
What are the primary source of chemical energy for cells?
Sugars
What are monosaccharides?
The smallest sugars with the general formula (CH2O)n
What are oligosaccharides?
2-10 monosaccharides
How do monosaccharides join together?
By linking their covalent bonds called glycosidic bonds to form larger carbohydrates
What is a condensation reaction?
A bond is formed between OH groups between sugars and a water molecule is expelled
What is hydrolysis?
A bond is broken between OH groups and a water molecule is consumed
What are some polysaccharides?
Glycogen and starch (used as energy store), cellulose (used as support), and chitins (used as exoskeletons and fungal cell walls)
How can oligosaccharides be linked?
To proteins to form glycoproteins or to lipids to form glycolipids
What are an even richer (but not more prevalent) energy source for cells than sugars?
Fatty acids
What is the essential function of fatty acids?
To form lipid molecules that assemble into cell membranes
What are the two chemically distance parts of fatty acids and what are their characteristics?
Long hydrocarbon chain (hydrophobic, not reactive) and the carboxyl group that behaves as an acid because in aqueous solution it is (ionized, hydrophilic, and chemically reactive)
What are amphipathic molecules?
Molecules that have hydrophilic and hydrophobic regions
How are fatty acid molecules linked?
Covalently by their carboxyl regions
What is a saturated fat?
No double bonds between carbons and the maximum number of hydrogens
What is an unsaturated fat?
One or more double bonds that creates kinks in the hydrocarbon tails and interferes with its ability to pack together
What are lipids?
Found in the long hydrocarbon chains of fatty acids and multiple linked aromatic rings in steroids that are insoluble in water but soluble in fat and other organic solvents
What are phospholipids?
Type of fatty acid that forms a lipid bilayer due to its amphipathic nature
Which bonds are non polar?
C-H, C-C
What are the three non covalent bonds?
Ionic, hydrogen, and van der waals forces
What are sugars used for?
Energy, structure, component of nucleic acids, component of exterior plasma membrane
Which functional group found in fatty acids is most chemically reactive?
Carboxyl
What is the name of the reaction that takes place between two sugars to form polymers of sugars?
Condensation
Lipids include which of the following?
Fatty acids, steroids, and oils
Glycogen, starch and cellulose are formed from simple sugars. What are two general names for glycogen, starch and cellulose?
Polysaccharides and carbohydrates
Which of the following pairs of functional groups might form hydrogen bonds with one another in water?
Carbonyl and hydroxyl
Which of the following functional groups are present in all sugars (monosaccharides, not in aqueous solution)?
Hydroxyl and carbonyl
What is a sugar in general?
A chain of carbons (at least 3) that has OH groups on each carbon except one which has a C=O
What is a fatty acid?
A hydrocarbon chain with a carboxyl group on one end
How are phospholipids and triacylglycerides related to fatty acids?
They’re formed by binding 2 (phospholipid) or 3 (triacylglycerides) fatty acids to a glycerol molecule through reactions between the carboxyl group on the fatty acid and the hydroxyl group on the glycerol
What is the general name for phospholipids, triglycerides, and other molecules?
Lipids
What are saturated fats solid and unsaturated fats liquid at room temperature?
Saturated fats have straight fatty acid chains that allow them to fit together more closely and have more van der waals forces and greater affinity whereas unsaturated fats have kinks where there are double bonds that doesn’t create enough attraction between molecules to make it solid
What are amino acids?
Building blocks of proteins that have a carboxylic acid and an amino group; they are distinguishable by their side chains
What are the long chains that amino acids make up called?
Proteins or polypeptides
What is the bond between two amino acids and how is it formed?
Peptide bond; condensation reaction
What are nucleotides?
Subunits of DNA and RNA composed of a nitrogen-containing ring compound linked to a 5-carbon sugar where there are one or more phosphate groups attached
What are pyrimidine bases?
One six-membered ring (i.e. cytosine, thymine, and uracil)
What are purine bases?
One six-membered ring attached to a 5-membered ring (i.e. guanine and cytosine)
What do nucleotides do?
Serve as storage and retrieval of biological information and building blocks for the construction of nucleic acids
What are nucleic acids?
Long polymers in which nucleotide subunits are linked by the formation of covalent phosphodiester bonds by a condensation reaction between the phosphate group attached to the sugar of one nucleotide and a hydroxyl group on another
What is metabolism?
The sum total of all the chemical reactions it needs to carry out to survive, grow, and reproduce
What are catabolic pathways?
Break down foodstuffs into smaller molecules, thereby generating both a useful form of energy for the cell and some of the small molecules that the cell needs as building blocks
What are anabolic or biosynthetic pathways?
Use the energy harnessed by catabolism to drive the synthesis of the many molecules that form the cell
What is the second law of thermodynamics?
States that, in the universe or in any isolated system, the degree of disorder can only increase
What is the first law of thermodynamics?
Energy cannot be created or destroyed but it can be converted from one form to another
What is catalysis?
The acceleration of the specific chemical reactions needed to sustain life
What do enzymes do?
Increase activation energy so molecules can be converted to a lower energy state
What are substrates?
Where the enzyme binds
What is a catalyst?
Type of enzyme that lowers the activation energy of a reaction by increasing the rate of the chemical reactions (they allow a much larger proportion of the random collisions with surrounding molecules to kick the substrates over the energy barrier)
When does disorder increase?
When useful energy that can be harnessed is dissipated as heat
What do all amino acids contain?
Carboxyl and amino groups
What varies among different amino acids?
Side chains
As a strand of DNA is replicated, a polymer of nucleotides is made by forming covalent bonds between the phosphoryl group on one nucleotide and the _______________ group on the next.
Hydroxyl
What type of bond links the two antiparallel polynucleotide chains to each other in a double helix of DNA?
Hydrogen
What is the covalent linkage called between two adjacent amino acids in a protein?
Peptide bond
An enzyme facilitates a reaction by…
Lowering the activation energy of the reaction
Energetically favorable reactions are those that…
Decrease the free energy of a system
In thermodynamics, what does the term “free energy” refer to?
Energy that can be harnessed to do work or drive chemical reactions
Why do chemical reactions tend to speed up when the concentration of the reactants is increased?
The reactants collide more often
If the equilibrium constant (K) for the binding of molecule A to molecule B is K = 1000, and K for the binding of molecule A to C is K = 20000, which molecule has a stronger binding affinity to A?
C
Two molecules will bind to each other by means of noncovalent bonds if the ΔG° of the interaction is:
Negative (the free energy of the product is lower than the sum of the free energies of the unbound partners).
A common means of providing energy to an energetically unfavorable reaction in a cell is by
Coupling of ATP hydrolysis to the reaction
The KM of an enzyme-catalyzed reaction…
Describes the affinity of an enzyme for its substrate.
When an enzyme is functioning at Vmax, the rate of the reaction is limited by
The rate at which the enzyme can convert bound substrate to product and release the product.
Any reaction A ⇔ B is at equilibrium when
∆G = 0.
Suppose you have a favorable reaction A → B when the concentrations of A and B are equal. If you were to raise the concentration of B relative to A, what effect would this have on ΔG?
ΔG would increase
When will two molecules bind?
When the free-energy change of the resulting complex is lower than the sum of the free energies of the two partners when unbound
What is the equilibrium constant, K, directly proportional to and why?
Binding energy because the larger K is, the greater the drop in free energy between dissociated and associated states and the more tightly molecules will bind
What is binding energy?
The energy released in the binding interaction
How do enzymes catalyze reactions that are energetically unfavorable?
Directly coupling energetically unfavorable reactions with favorable ones via carrier molecules or by keeping the product at low concentration by converting it or by removing it from the cell
How is rapid binding of enzyme to substrate possible?
Molecular motions are extremely fast because heat energy allows them to be in constant motion and consequently will explore the cytosolic space efficiently by wandering randomly
How are molecules held together?
They form many weak bonds like van der Waals, hydrogen bonds, and electrostatic attraction that allow them to be held together long enough for a covalent bond to be formed or broken
Why do molecules dissociate?
The two colliding molecules with poorly matching surfaces yield few weak, non covalent bonds so their total energy is negligible compared to thermal motion so the two molecules dissociate rapidly
What is the process of catalysis?
Enzyme binds to substrate, substrate undergoes reaction to form product (which initially remains bound to enzyme), product released and diffuses away, and enzyme is free to bind to another substrate and catalyze another reaction
What is K?
concentration of product over concentration of reactant
What are activated carriers?
Molecules that carry their bond energy from the sites of energy generation to the sites where energy is used for biosynthesis
What does a coupled reaction do?
The amount of heat released by the oxidation reaction is reduced by exactly the amount of energy that is stored in the energy-rich covalent bonds of the activated carrier
What forces play roles in determining protein shape?
van der Waals, hydrogen bonds, ionic bonds, and hydrophobic interactions
Where do non polar hydrophobic molecules form?
The interior of the protein where they avoid the aqueous cytosol surrounding them inside the cell
Why are hydrophobic molecules forced together?
To minimize disruption of hydrogen bonds in the surrounding water molecules
Where do polar hydrophilic molecules form?
Arrange themselves inside near the outside of the folded protein where they form hydrogen bonds with water and other polar molecules
How does a protein fold?
Generally folds into the shape in which the free energy of the protein is minimized in order to make folding more energetically favorable as it releases heat and increases disorder
How can non covalent interactions be disrupted?
By treatment with solvents or heat that unfolds the protein in denaturation
What is renaturation?
Refolding when the solvent is removed to its original conformation
What do misfolded proteins do?
Often form aggregates that damage cells and tissues potentially causing neurodegenerative disorders
What are prions?
Infectious misfolded proteins that infects the brain and eats the tissue and spreads aggregates from cell to cell
What are chaperone proteins?
Help protein chains fold along the most energetically favorable conformation by binding to partly folded chains or forming isolation chambers in which the chains can fold without risk of forming aggregates
What are common folding patterns? Why?
Alpha helices and beta sheets; they form hydrogen bonds between the N-H and C=O groups in the polypeptide backbone
What is a primary protein?
Amino acid sequence
What is a secondary protein?
Alpha helices and beta sheets that form in segments of the chain
What is a tertiary protein?
Three-dimensional structures formed by the entire polypeptide chain
What is a quaternary protein?
Complex of more than one polypeptide chain
What is a protein domain?
Organizational unit where any segment of a chain that can fold independently into a compact, stable structure
What is an intrinsically disordered sequence?
Relatively unstructured lengths of chain linking domains lacking any structure, which bend and flex, allowing them to wrap around target proteins and increase frequency of encounters between domains
What is the equation for the chains?
Protein that is n amino acids long, then 20^n different chains are possible
What are protein families?
Proteins groups in which they have similar amino acid sequences and three-dimensional conformations
What primarily determines what the three dimensional structure of a protein in a cell will be?
The sequence of amino acids in the protein
A discrete, locally folded unit of tertiary structure usually having specific function best describes:
A domain
Which of the following contribute to the final stable structure of a folded protein? (there may be more than one correct answer)
Hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic interactions
Which of the following amino acids would you expect to find more often near the center of a folded globular protein, rather than at the surface?
Leucine because it’s nonpolar
β sheets and α helices are typically _________ structures in proteins, primarily due to ____________.
rigid; regular hydrogen bonds
Those portions of a transmembrane protein that cross the lipid bilayer usually consist of which structures?
An alpha helix with mostly nonpolar side chains
What does the primary structure of a protein refer to?
The amino acid sequence of the protein
If a protein is denatured, what happens to it?
It becomes unfolded
What is a binding site?
Any region on a protein’s surface that interacts with another molecule (ligand) through covalent bonds
What is a dimer?
Two polypeptide chains form this symmetrical complex from identical binding sites of each monomer
How are extracellular proteins like collagen and elastin stabilized?
By covalent cross-linkages in which two amino acids are joined together in the same polypeptide chain or several polypeptide chains are joined together in a protein complex
How are disulfide bonds formed to stabilize extracellular proteins?
Formed before the protein is secreted in the endoplasmic reticulum by linking two -SH groups from adjacent cysteine side chains
How do proteins show specificity?
The ligand for that protein needs to make many non covalent bonds simultaneously in order for the ligand to be held to its specific protein and this is only possible when the contours of the ligand’s surface match that of the proteins
What are antibodies?
Immunoglobulin proteins produced by the immune system in response to foreign molecules that recognizes its target molecules, antigens, with specificity and very tightly
How do enzymes work?
Bind to one or more ligands called substrates and convert them into chemically modified products
How do proteins use nonprotein molecules?
They use them to perform functions that would be impossible for amino acids alone
What is a classic example of proteins using nonprotein molecules?
Hemoglobin using heme groups to carry oxygen from the lungs to tissues via the iron in heme
What is a regulatory site?
Where other molecules besides the substrate bind
What is negative regulation?
Prevents an enzyme from acting
What is feedback inhibition?
An enzyme acting early is inhibited by a late product in the pathway
What is positive regulation?
Enzyme’s activity is stimulated by a regulatory molecules rather than being suppressed
What is allosteric?
Molecules can adopt two or more different conformations and their activity can be regulated by a shift from one to another by “communicating” binding sites
What is protein phosphorylation?
Kinase transfers a terminal phosphate group from ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain
What is dephosphorylation?
A protein phosphatase removes phosphate
What is a plasma membrane and what is its function?
A protein-studded, fatty film where the molecules of living cells are held; prevent the contents of the cell from escaping
Why is a lipid bilayer formed?
Hydrophobic molecules force adjacent water molecules to reorganize into a cavelike structure that is more highly ordered so it requires more free energy and when the hydrophobic molecules cluster together the energy cost is minimized due to limited contact with the surrounding water molecules
How is a bilayer self-sealing?
Any tear in the sheet will create an exposure to water which is energetically unfavorable so the bilayer will spontaneously rearrange to eliminate the free edge
How does an amphipathic sheet like the lipid bilayer avoid having free edges?
By forming a boundary around a closed space
What are the properties of the bilayer?
It’s two-dimensional (it prevents membrane lipids from escaping but the molecules can move about in the plane of the bilayer) and it’s flexible
What does the fluidity of the bilayer depend on?
Phospholipid composition and the hydrocarbon tails; closer and more regular packing of tail entails less fluidity
What does packing of the tails depend on?
Length and number of double bonds; the shorter and more double bonds present the more fluidity
How can fluidity be controlled in animal cells?
By cholesterol because the molecules fill the spaces between phospholipid tails that are left by kinks making it less fluid and less permeable
Why is membrane fluidity important?
Enables many membrane proteins to diffuse rapidly and to interact with one another, permits membrane lipids and proteins to diffuse from sites where they’re inserted into the bilayer after synthesis to other parts of the cell, ensures membrane molecules are distributed evenly when cells divide, and allows membranes to fuse and mix their molecules
Where are phospholipids made and how do they get to where they need to be?
They’re made by enzymes bound to the cytosolic surface of the ER that use free fatty acids as substrates and deposit the new phospholipids to the cytosolic half of the bilayer where scramblases will remove randomly selected phospholipids from one half to the other half of the bilayer
How does asymmetry arise in cell membranes?
The Golgi apparatus membrane contains flippases that remove specific phospholipids from the side of the bilayer facing the exterior space and flips them into the monolayer that faces the cytosol
What are the functions of membrane proteins?
Transporters, anchors, receptors, and enzymes
What are the types of associations of proteins with the bilayer?
Transmembrane that extend to either side of the membrane, monolayer located almost entirely in the cytosol by an alpha helix, lipid-linked that are entirely outside the bilayer attached to the membrane by one or more covalently attached lipid groups, and protein attached where they aren’t bound directly but are held in place by their interactions with other membrane proteins
What are integral membrane proteins?
Proteins directly attached to the bilayer that can only be removed by detergent interactions
What are peripheral membrane proteins?
Proteins not directly attached that can be removed by gentler extraction that leaves the membrane intact
What are single-pass transmembrane proteins?
Polypeptide chains that crosses the membrane once in an alpha helix that are receptors for extracellular signals
What are multipass transmembrane proteins?
Polypeptide chains that cross the membrane more than once as alpha helices that function more as channels
What are detergents?
Small, amphipathic, lipid-like molecules that have a hydrophilic head and a single hydrophobic tail that makes them aggregate into small clusters called micelles and when mixed with membranes the hydrophobic ends tend to interact with the membrane-spanning hydrophobic regions of the transmembrane proteins and the hydrophobic tails of phospholipids
The most abundant class of lipids in cell membranes are
Phospholipids
What is true of membrane phospholipids?
They are amphipathic. They can contain both saturated and unsaturated fatty acids. They have two fatty acids attached to a glycerol molecule, and a polar head group with an attached phosphate.
What characteristics generally are correlated with an increase in the fluidity of a lipid bilayer?
Fewer van der waals interactions among the lipids,
a decrease in the amount of cholesterol, and an increase in the percentage of unsaturated fatty acids
What statements regarding lipid membranes is/are TRUE?
Membrane lipids diffuse within the plane of the membrane and phospholipids will spontaneously form cell membrane-like lipid bilayers in a sphere in polar solvents.
What statement about cell membranes is TRUE?
The composition of lipids on the extracellular side of the lipid bilayer is typically different than that found on the intracellular side (the lipid distribution is asymmetric).
What describes a common property of detergents that can be used experimentally to solubilize phospholipids?
They are amphipathic
What are ways that proteins are associated with membranes?
Transmembrane protein through membrane as a β barrel,
covalently attached to lipids in membrane, bound to a transmembrane protein, and completely cross membrane as α helix
