Exam I Flashcards
Life is comprised of six elements. Name them.
Carbon, Hydrogen, Oxygen, Phosphorus, and Sulfur (CHONPS)
How many elements are necessary?
22
Why is carbon unique?
Carbon can form up to four stable covalent bonds. This enables long chains to be built.
Carbon has atomic orbitals that can hybridize. What are these orbitals, and what can they do?
s and p orbitals have very similar energies and can merge to form a new orbital.
Name the geometries and angles of sp3, sp2, and sp carbons.
sp3: 109º, tetrahedral
sp2: 120º, planar
sp: 180º, linear
What structures can carbon “skeletons” make?
Linear chains, branched chains, and cyclic structures
The major biomolecules in all known life forms are large macromolecules except for one. Name them and state which one isn’t a large macromolecule.
Proteins, carbohydrates, lipids (not a large macromolecule), and nucleic acids
Macromolecules consist of what?
Repeating units linked together by covalent bonds
Name three heteronuclear linkages found in living systems. (Know the chemical structures too!)
Amide linkage in proteins, phosphodiester linkages in nucleic acids, and ether linkages in carbohydrates
What is the most abundant class of biological molecules?
Carbohydrates
What is the basic unit of a carbohydrate?
A monosaccharide
What are the two most common monosaccharides?
Hexose (6 carbons) and pentose (5 carbons)
What are the two most common forms of sugars encountered biologically?
Pyranose (6-membered ring) and furanose (5-membered ring)
Carbohydrates are formed by what?
They are formed through dehydration (removal of H2O). Two monosaccharides are bonded together.
Carbohydrates form what two kinds of polymer shapes?
Branched and linear
What are the three functions of carbohydrates?
- They decorate the cell surface and are important in cell-cell recognition.
- They play important structural roles. (Ex. Cell walls and extracellular matrixes)
- They are important food storage molecules (Ex. Starch and glycogen)
What are the three components of a nucleic acid?
- Base
- Sugar
- Phosphate
What are the two kinds of aromatic bases in nucleic acids? Name them.
Purines:
1. Adenine
2. Guanine
Pyrimidines:
1. Cytosine
2. Thymine (DNA)
3. Uracil (RNA)
How are sugars connected in DNA/RNA?
Phosphate groups connect the 3’ and 5’ carbons of the sugar bases (phosphodiester bonds).
What is the difference between the sugars for DNA and RNA?
DNA has deoxyribose (no -OH group), and RNA has ribose.
Only DNA contains ___, and only RNA contains ___. (Which bases?)
Thymine, Uracil
What are the base pairings in nucleic acids?
C pairs with G, T pairs with A, and U pairs with A (in RNA only).
Lipids are composed of two parts? What are they?
Polar heads (hydrophilic) and non-polar tails (hydrophobic)
Why aren’t lipids considered macromolecules?
They’re not polymers.
Lipids include [3 things].
Fatty acids, phospholipids, and triglycerides
What are triglycerides?
They’re fat, a major food store in animals.
Oxidative metabolism of fat yields 2x the energy of an equivalent amount of protein or carbohydrate.
What does amphipathic refer to?
Molecules that have polar and non-polar regions. (Ex. phospholipids)
What are the bond energies of non-covalent and covalent bonds?
Non-covalent bonds are 4 - 75 kJ/mol, and covalent bonds are ~400 kJ/mol.
How are macromolecules stable in structure?
It’s due to the cumulative effects of many weak interactions/bonds.
Name the four types of non-covalent bonds.
- Hydrogen bonds
- Ionic interactions
- Hydrophobic interactions
- van der Waals interactions
Non-covalent bonds are continuously breaking and forming. This explains what?
The ability of biomolecules to bind/dissociate from other molecules, which is crucial to biomolecular function.
Ex. Enzymes, cell signaling
How do van der Waals interactions work?
Random variations in the positions of electrons around a nucleus may create a transient electric dipole, inducing an opposite transient dipole in a nearby atom.
True or false? Nitrogen is more electronegative than sulfur.
True
What geometry does a water molecule have?
Bent
A hydrogen bond is a combination of what two forces?
Electrostatic (90%) and covalent (10%)
The polar character of water makes it an excellent solvent for what substances?
Polar and ionic
What occurs during hydration?
Water molecules cluster around ions and polar groups, stabilizing them. This enables ions and molecules to separate/dissolve in water.
Biomolecule molecular masses are often referred to in what units?
Daltons (Da)
What’s the dissociation constant equation?
Ka = [H+][A-]/[HA]
What is Kw, the ion product of water?
1.0 x 10^-14 M^2
What is the equation to find pH?
pH = -log[H+]
What is the Henderson-Hasselbalch equation?
pH = pKa + log[A-]/[HA]
When pKa = pH…
The concentrations of an acid/base and its conjugate base/acid are equal.
A weak acid/base is a useful buffer when…
it’s 1 pH unit from its pKa.
Why is buffering important in biological environments?
Biomolecules are sensitive to pH. Cells and organisms must maintain a specific and constant pH.
What are stereoisomers?
Molecules with the same chemical bonds but with different configurations
Configuration is conferred by the presence of which two things?
Double bonds (no freedom of rotation) and chiral centers
Amino acids contain four groups attached to a carbon. What are they?
A hydrogen, an amino group, a carboxyl group, and a side chain/R group
What happens to the carboxyl and amino groups in an amino acid at a pH of 7?
They’re both ionized (zwitterion). The amino group gets protonated, and the carboxyl group gets deprotonated.
What’s the difference between a chiral and achiral molecule?
Chiral molecules CANNOT be superimposed on their mirror images, but achiral molecules can.
What can occur if the four covalent bonds on an sp3 carbon are chemically distinct?
Two chemically distinct configurations can occur. They cannot be interconverted without breaking/making chemical bonds.
What are stereoisomers?
Different configurations that can occur when a molecule has multiple chiral centers
Stereoisomer pairs that are mirror twins are called what?
Enantiomers
Proteins are made from what kind of amino acid?
L only
How are enantiomers distinguished?
They’re distinguished by how they interact with plane-polarized light (optically active).
L (left) and D (right)
What is the orientation of Fischer projections?
Vertical substituents are facing away from you, and horizontal substituents are facing towards you.
In Fischer projections, are the carbons vertical or horizontal?
Vertical
Where are the R groups in Fischer projections of amino acids?
Below the alpha/middle carbon
Where are D-amino acids found?
Bacterial cell walls
What are diastereomers?
Pairs of stereoisomers that aren’t mirror images of each other
How do amino acids polymerize?
They polymerize through the elimination of H2O (condensation). This results in a peptide bond.
What is the molecular weight to be considered a protein rather than an amino acid polymer?
> 10,000 MW
Where are peptide bonds formed?
Between the carboxyl acid group of one residue and the amino group of the next
What are the two ends of an amino acid polymer called?
Amino-terminal end and carboxyl-terminal end
What is the average mass of an amino acid as part of a protein?
110 Da
Nonpolar amino acids have side chains that are composed of what?
Carbons and hydrogens only
The R groups are hydrophobic.
The delocalization of pi-bonds in aromatic rings means that…
the bonds can’t freely rotate and maintain a planar structure.
True or false? The side chain of acidic amino acids can give up a proton (H+) to become negatively charged, and the side chain of basic amino acids can take up an extra proton to become positively charged.
True
True or false? Amino acids with nonpolar, uncharged side chains are the main acids and bases in proteins.
False. Amino acids with POLAR, CHARGED side chains are.
pKa isn’t absolute. It depends on what?
The chemical environment
What is primary protein structure?
The covalent structure of the protein or the amino acid sequence
In amino acids, disulfide bonds are formed between which residues?
Cys/Cysteine
Define interchain and intrachain
Interchain refers to linking two separate polypeptides, and intrachain refers to within the same polypeptide
What happens during oxidation and reduction?
Electrons are lost during oxidation, and electrons are gained during reduction.
What is it called when oxidation and reduction reactions happen simutaneously?
Redox
What does an oxidant do?
It brings about oxidation, being reduced in the process.
What does a reductant do?
It brings about reduction, being oxidized in the process.
The intracellular environment is primarily [reducing/oxidizing]. The extracellular environment is primarily [reducing/oxidizing].
reducing, oxidizing
Where are disulfide bonds found and why?
They’re found only in secreted/extracellular proteins because the formation of disulfides is an oxidation reaction.
The extracellular environment is mainly oxidizing.
Name some post-translational protein modifications.
Glycoslation, phosphorylation, acetylation, membrane anchors, glycosylphosphatidylinositol (GPI), and fatty acid chains or prenyl groups
Define phylogeny.
The relationship between all the organisms on Earth that have descended from a common ancestor
Define horizontal/lateral gene transfer.
Genes are transferred between species.
What are homologs?
Two proteins that possess similarities in sequences
What are paralogs and orthologs?
Paralogs are homologs that occur in the same species.
Orthologs are homologs that occur in different species.
Sequence positions that have no functional/structural role and are free to mutate are called…
hypervariable
When critical sequence positions required for function or structural maintenance are kept from changing, it’s called…
invariant
Some sequence positions can only change to residues with similar properties. They’re called…
conservative
How does protein sequence alignment work?
Alignments of protein sequences uses a scoring system at each residue position to rank the alignments.
Identical amino acids or conservative changes lead to high scores.
This method is used to compare protein sequences.
____ represents the last common ancestor from which all current life forms evolved.
LUCA
Name four ionic interactions in proteins.
- Between side-chains
- Involving N- and C- termini
- Involving post-translational modifications
- Hydration of the protein charges by water (H3O+ and OH-) stabilizes them.
Describe the hydrophobic interactions in a protein in an aqueous environment.
The protein folds up. The hydrophobic core region contains nonpolar side chains, and the polar side chains on the outside can form hydrogen bonds to water.
What is protein secondary structure?
It’s the stable and energetically favorable 3D conformations that a polypeptide can adopt as “building blocks.”
The peptide bond has double bond character. What does this mean?
It’s planar, and the C-N bond can’t be freely rotated around. This also introduces a slight electric dipole.
Most peptide bonds are [trans/cis].
trans
With which amino acid is the cis configuration is almost as energetically favorable as the trans?
Pro
Along the backbone of a protein, there are only two angles that allow rotations. What are they, and what are they called?
The N-Ca bond (phi) and the Ca-C(=O) bond (psi)
Which amino acid is constrained phi = -60º?
Pro
Which amino acid is much more flexible due to the lack of a side-chain?
Gly
For alpha helices, how many residues are there per turn?
3.6 residues/turn
Are alpha helices left or right-handed?
Right-handed
In alpha helices, where are all the side chains pointing to?
The N-terminus
What three things can destabilize an alpha helix?
- Like charges are adjacent to each other (Ex. Glu-Glu).
- Proline places a kink in the helix.
- Glycine’s flexibility can destabilize helices.
Because all the main-chain C=O’s point towards the C-terminus and the N-H’s point toward the N-terminus, alpha helices have a dipole moment.
Negatively charged amino acids stabilize the helix if they’re located at the _____.
Positively charged amino acids stabilize the helix if they’re located at the _____.
N-terminus; C-terminus
What does a helix being amphipathic mean?
One face of the helix is decorated in polar side-chains and the other by non-polar.
Name the two types of beta sheets.
Antiparallel and parallel
In anti-parallel beta sheets, the hydrogen bonds are _____ to the chain direction.
perpendicular
In parallel beta sheets, the hydrogen bonds are _____ to the chain direction.
70º
Beta sheets exhibit a ___-handed twist and can fold into barrels.
right
Turns and coils/loops are areas that alternate between what?
Alpha helices and beta sheets
These enable the connections between the very stable areas of alpha helices and beta sheets. Gly and Pro are commonly found in turns.
What is tertiary protein structure?
The 3D fold of a single polypeptide chain
What is a domain?
An element of overall structure within a protein that’s self-stabilizing and often folds independently from the rest of the protein chain
Different domains are often associated with different _____.
functions
What are some characteristics of intrinsically disordered proteins?
- They have no stable folded structure in solution.
- There are enriched with charged residues, which disrupts structure.
- They often interact with multiple protein partners.
- The part of the protein in contact with the protein partner becomes ordered.
- Some inhibit the activity of other proteins by wrapping around them.
What are integral membrane proteins?
They’re physically attached to the membrane and aren’t easily removed.
What are peripheral membrane proteins?
They’re either non-covalently associated with integral membrane proteins or associated via covalently bound lipid. They can be easily removed.
What are transmembrane proteins?
They traverse the membrane and have protein portions on both sides of the membrane.
What are the functions of integral transmembrane proteins?
They serve as cell signaling receptors and channels to transport ions, smal molecules, and proteins.
What two amino acids are often found at the solvent-lipid boundary in integral transmembrane proteins?
Trp and Tyr
What is the only kind of anchor that can target proteins to the outside of the membrane?
Glycosyl phosphatidylinositol (GPI) anchors
(All other lipid anchors associate proteins to the inner face of the membrane.)
Many domains have identical folds despite very low primary sequene homology. This probably evolved many times independently through _____.
convergent evolution
Some proteins are sequentially related, have similar 3D folds, and have evolved from a common ancestral protein through _____.
divergent evolution
What is a protein family?
Proteins of significant primary sequence similarity, similar structure, and usually similar function
What’s a protein superfamily?
Two or more proteins that have little primary sequence similarity but have similar structural domains
What are exons and introns?
Exons are protein coding regions, and introns are noncoding regions.
What is quaternary protein structure?
Functional protein assemblies that contain more than one polypeptide chain (multimeric)
What are oligomers?
Protein multimers with only a few subunits (individual chains)
If oligomers are composed of sequentially identical polypeptide chains, then the prefix ____ is used. If they’re composed of sequentially different polypeptide chains, then the prefix ____ is used.
homo, hetero
1 chain = ____
2 chains = ____
3 chains = ____
4 chains = ____
- Monomer
- Dimer
- Trimer
- Tetramer
Many multimers are made of repeating copies of a single/small group of polypeptides in a symmetrical arrangement. These repeating units are called ____.
protomer
What is a motif?
Stable arrangements of several connected secondary structure elements
What are some techniques to determine the 3D structure of proteins?
- X-ray crystallography: Highest resolution, can visualize huge structures like ribosomes and viruses
- NMR: Useful for smaller proteins, can measure molecular motion
- Cryoelectron microscopy: Mainly used for big structures, close to atomic resolution
List some examples of globular proteins.
Enzymes, transport and cell signaling molecules, receptors
True or false? Fibrous proteins are arranged in long strands/sheets and consists of a single secondary structure.
True
What are the functions of fibrous proteins?
They provide support, shape, and external protection in vertebrates.
a-keratin is the major component of what things?
Hair, nails, hooves, and horns
a-keratin consists of 2 a-helices wound around each other in a ____-handed coil.
left
a-keratin coils combine to form _____, which combine to form _____.
protofilaments; protofibrils
The strength of a-keratin depends on the number of what?
Intermolecular disulfide bonds
a-keratin belongs to what structual family?
Intermediate filaments
Where is collagen found?
Cartilage, bone, and tendons
What is the repeating sequence in collagen?
G-X-X
2nd position is often Pro, and 3rd position is 4-hydroxyproline
Collagen forms a ____-handed helix, which is coiled with 2 others to form a ____-handed triple helix.
left; right
What’s Gibbs free energy (G)?
The thermodynamic potential energy of a chemical for maximum or reversible work done at a constant temperature and pressure
It reflects the internal energy of the chemical and its inherent disorder at a particular temperature and pressure.
At constant pressure and temperature, the change Gibbs free energy (∆G) between reactants and products defines:
- The direction of the reaction
- The position of equilibrium
- The useful energy made available for work
What are the units of ∆G?
J/mol or cal/mol
When ∆G is negative, the reaction is _____. When ∆G is positive, the reaction is _____.
exergonic; endergonic
Non-spontaneous reactions have a [positive/negative] ∆G.
positive
How can non-spontaneous reactions be made to be favorable?
By coupling them to a highly exergonic reaction (Ex. Breaking the terminal phosphoanhydride bond of ATP)
Reaction coupling requires what?
A shared intermediate
Why does ATP hydrolysis have a large, negative ∆G?
- Charge separation relieves electrostatic repulsion between the 4 negative charges on the oxygen atoms on ATP.
- The product inorganic phosphate (Pi) is resonancce stabilized.
- ADP2- immediately ionizes, releasing H+ into a medium of low [H+].
- There’s a greater degree of solvation of the products relative to ATP.
What is ∆G’º?
The change in free energy under a set of biochemical standard conditions
There are three positions on ATP for attack by the nucleophile R18O. Name the three transfers.
- Phosphoryl transfer (Least negative ∆G’º)
- Pyrophosphoryl transfer
- Adenylyl transfer (Most negative ∆G’º)
Name some other phosphorylated compounds and thioesters.
PEP, Acetyl-CoA, Phosphocreatine
Concentrations of free ATP, ADP, and Pi can be lower due to what?
The tight binding of these molecules to some cellular proteins
ATP and ADP are always bound with what ion?
Mg2+
Define thermodynamics.
The study of the changes/transformations of energy which accompany physical and chemical changes in matter
Define bioenergetics.
The quantitative study of the energy transductions that occur in living cells
Define the system and universe.
The system is the chemical reactants, products, and their immediate environment within a defined space.
The universe is the system and everything that surrounds it.
Define open, closed, and isolated systems.
Open systems exchange matter/energy with surroundings (Ex. Living organisms).
Closed systems exchange only energy with surroundings.
Isolated systems exchange neither energy nor matter.
What is a dynamic steady state?
The constancy of concentration within a living system
What’s the first law of thermodynamics?
Energy can’t be created or destroyed.
What’s the second law of thermodynamics?
In all natural processes, the entropy of the universe increases (disorder increases).
What’s ∆H?
The change in enthalpy or heat content of a chemical system
What’s ∆S?
The change in entropy for a system; represents the change in disorder or randomness
Define equilibrium.
The point at which the rates of the forward and reverse reactions are equal
At equilibrium, there is no driving force and ∆G equals what?
0
What are the standard biochemical conditions?
- Soluable reactants and products at 1.0M initially
- Gases at a partial pressure of 101.3 kPa/1 atm
- Temperature at 298 K
Increasing the equilibrium constant leads to _____ being favored over _____.
products; reactants
Do enzymes have an effect on ∆G or the position of equilibrium?
No
An electromotive force is represented by what?
The transfer of electrons between chemical species with differing electron affinities
Electrons are transferred from one molecule to the other in 4 different ways. Name them.
- Directly as electrons
- As hydrogen atoms
- Directly as hydride ions (H-, 2 electrons)
- Through direct combination with oxygen
What is a reducing equivalent?
A single electron equivalent in redox reaction, whether as an electron, H atom, hydride ion, or oxygen
What’s reduction potential (E)?
A measure of the affinity of an electron acceptor for electrons in a conjugate redox pair
What’s E’º?
The biochemical standard reduction potential for a conjugate redox pair under standard conditions
Electrons flow from the half-cell with the ____ E’º to the half-cell with the ____ E’º.
lower; higher
Standard reaction conditions are pH __ with the concentrations of all participating species at __M initially.
7; 1
What are coenzymes? Name the two sets of universal coenzymes?
Low molecule weight compound required for catalytic activity
NAD+ and NADP+, FMN and FAD
NAD+ functions in [anabolism/catabolism], and NAD+/NADH are mainly located in _____.
catabolism; mitochondria
NADPH functions in [anabolism/catabolism], and NADP+/NADPH are mainly located in the _____.
anabolism; cytosol
Name the five steps to a functional protein.
- Folding
- Cofactor binding
- Covalent modification
- Translocation
- Assembly of multisubunit complex
Proteins will only spontaneously fold when ∆G is what?
Less than 0
Spontaneous folding of a protein generates disorder through what?
The release of water molecules that are ordered around hydrophobic parts of the protein. This adds disorder to the surrounding solvent.
During the spontaneous folding of a protein, ∆H is what?
Often close to zero
Describe the two models for protein folding.
- A hierarchical process in which local secondary structure forms first; these secondary structures interact to form supersecondary strucures, and ultimately the tertiary structure
- There’s a rapid collapse of the polypeptide (molten globule) to partition the hydrophobic groups from water, creating a hydrophobic core.
When proteins become “trapped” in a local free energy well, it doesn’t have the thermal energy needed to proceed to the native folded state. They need assistance from proteins called _____.
molecular chaperones
What kind of proteins are able to fold on their own?
Small, soluble, globular proteins
Most proteins require molecular chaperones to fold correctly.
What are the two major families of molecular chaperones in eukaryotic cells?
Hsp70 and Hsp60
(Heat shock proteins are upregulated when exposed to higher temperatures.)
How do Hsp70 molecular chaperones work?
It binds to hydropobic patches on proteins and blocks the folding of certain polypeptides until they’re translocated across membranes.
ATP hydrolysis leads to a conformational change that locks Hsp70 tighly to the polypeptide. Another ATP binding causes the conformational change to reverse, releasing the folded polypeptide.
Multiple cycles of binding and release occur at multiple sites during the folding process.
How do Hsp60 molecular chaperones work?
They act on fully synthesized polypeptides, which intially bind to hydrophobic regions around its rim.
7 ATP bind, causing a conformational change that opens up the mouth of the pocket, pulling the polypeptide inside.
The addition of a protein cap confines the polypeptide. After the ATPs are hydrolyzed, the cap dissociates, and the protein is released whether fully folded or not.
Repeated cycles may be required to complete folding.
What do protein disulfide isomerases (PDI) do?
They help many proteins form their correct disulfide bonds.
What do peptide prolyl cis-trans isomerases (PPI) do?
They catalyze the conversion between trans and cis prolines.
What do proteases cleave off?
- Signal sequences that target proteins to their cellular compartment
- Prosequences that prevent a protein from being active in the wrong cellular compartment
- Secretion signals that cause proteins to be secreted out of the cell
How does heat denature most proteins?
By affecting the non-covalent/weak interactions within the structure
The mid-point of the temperature range where denaturation occurs is known as what?
Melting temperature
Name some chemical denaturants.
Urea, detergents, alcohol, acetone (Disrupts hydrophobic core)
How does pH affect a protein?
It changes the net charge of a protein.
How does mercaptoethanol affect proteins?
It reduces the disulfide cross-links between Cys residues.
