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148 Cards in this Set
- Front
- Back
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most abundant elements
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C,H,O,N
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2nd tier elements
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Ca, P, K, S, Cl, Na, Mg
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3rd and 4th tier elements
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trace
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What allows carbohydrate to open and close to form a ring?
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aldehyde at the end of sugar
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What are the polar parts of nucleotides?
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phosphate
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---- are amphipathic, but most of surface area is hydrophobic
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Lipids
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How to look for polarity?
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1. Charge
2. EWG such as Oxygen |
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Building polymers from monomers requires a --- reaction
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condensation (loss of water)
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What are monomers in polymers called?
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residues
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Nucleic acids form what type of bond?
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phosphodiester bond
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Carbohydrates form what type of bond?
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glycosydic linkage
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Lipids --- instead of forming chains like carbohydrates and protein
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aggregate
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At equilibrium deltaG=
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0
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Living systems are never at ---
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equilibrium
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Metabolic reactions are all --- reactions
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redox
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What is an atomic orbital?
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illustration of where you are likely to find electrons in an atom
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covalent bonds must be in 1) --- to share valence electrons and also 2) --- correctly
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1) close proximity
2) oriented |
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All ionic bonds have some degree of ---
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covalency
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Elements on the LEFT of the periodic table 1) --- electrons and elements on the RIGHT of the periodic table 2)--- electrons in ionic bonds
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1) give up
2) take |
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Atoms that do no share a bond have no ---
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overlap
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What is the van der Waal's radius in atoms?
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distance between nucleus of one atom electron surface of the other atom
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Which has a shorter bond distance- hydrogen bond or covalent bond?
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covalent bond
*shorter bonds are stronger |
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We are --- % water.
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60
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What arrangement of hydrogen bond allows for maximum overlap and sharing of electron?
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linear
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Are molecules in constant motion or static?
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constant motion
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What are the 3 main properties of water?
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1) highly cohesive
2) high surface tension 3) liquid at room temperature |
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Why is water cohesive?
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hydrogen bonding
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What makes the molecules on the surface of water stronger?
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linear attachment
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What makes solid water less dense than liquid water?
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Hydrogen bonding
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What are H-bond donors?
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electronegative atom that has a H to donate
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What are H bond acceptors?
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electronegative atoms such as a carbonyl that does not have a H bond to share
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What kind of bond is most of the cell's architecture held together by?
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weaker interactions
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Why is most of the cell's architecture held together by weak bonds?
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Longer, weaker bonds are easily broken and reformed
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What is a non-permanent dipole called in which there is a small, transient dipole?
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London dispersion forces
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What does it mean when you say water has a dielectric constant?
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prevents attractions of solutes
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What is one good measure of polarity that is also a property of water?
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Dielectric constant
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The higher the dielectric constant, the greater its ability to --- charges
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insulate
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Solvation done by water is known as ---
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hydration
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Even though the water's environment is 1)--- it is not 2) ---
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1) aqueous
2) watery |
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Describe the hydrophobic effect
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If a non-polar substance is placed in water, a layer of the non-polar substance forms
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The hydrophobic effect represents a --- in entropy
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decrease (negative)
*less freedom of movement |
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When lipids are placed in water, and form a cluster, does entropy increase or decrease, comparatively
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increases (less order)
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The aggregation of non-polar substances spontaneous or non-spontaneous
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sponatenous
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Amphiphillic molecules can arrange in what ways?
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1) micelle- one hydrophobic tail
2) lipid bilayer- 2 hydrophobic tail |
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What generally closes up to form vesicles?
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lipid bilayers
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If free floating protons do not exist, what does H+ mean?
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H+ is the shorter version of H3O hydronium ions that are already present in water
a network of water molecules forms (H+) + (OH-) --> H2O |
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What is the difference between a strong acid and a weak acid?
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stronger acids have a greater tendency to donate protons
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What equation relates pH to pK?
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Henderson-Hasselbach equation
*pH= pK + log (WB/SA) |
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At what point does pH=pK?
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1/2 the Ionization point
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What molecules can act as both acids and bases?
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amino acids
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What are the 3 cytoskeleton proteins?
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microtubules
intermediate filaments microfilaments |
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What are microfilaments composed of?
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actin
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Keratin makes up which cytoskeleton protein?
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intermediate filaments
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Microtubules are composed of what?
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tubulin
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What is the largest cytoskeleton protein?
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microtubule
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What is the smallest cytoskeleton protein?
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microfilament
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What are the two forms if actin microfilament?
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1) G-Actin
2) F-Actin |
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Which form of actin filament is globular protein with ATP binding site?
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G-protein
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Which form of actin has:
- double chain of subunits - negative end has ATP site - positive at opposite end |
actin-microfilament
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Where in the cell does energy come from?
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It comes from bonds!
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What is the reversible process in actin known in which the rate of subtraction=rate of addition?
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treadmilling
+) growing -) falling off |
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What are 2 differences between tubulin and actin?
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1) tubulin:
-dimer -hollow cylinder 2) actin: -monomer -single filament |
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What microtubules makes them stronger than microfilaments?
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hollow cylinder
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Actin binds ---
Tubulin binds |
1) ATP
2) GTP |
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Hydrolysis of GTP to form microtubule, breaks which subunit?
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B subunit
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1 ATP per monomer
- GTP per dimer |
1
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What is used to construct to cillia and flagella?
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microtubule
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In tubulin, disassembly is faster at what end?
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+
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Which protein filament(s) are static?
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intermediate filaments
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Which protein filament(s) have/has a dimer as the basic subunit?
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tubulin and intermediate filament
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What holds intermediate filaments together?
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hydrophobic interaction (van der Waal's)
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What is a dimer (coiled coil)?
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monomer + monomer
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dimer + dimer =
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tetramer
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What protein filament makes up hair, skin, and nails?
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intermediate filament --> keratin
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What is the most abundant protein in our body?
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collagen --> intermediate filament
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What is the common triplet for collagen?
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Gly-Pro-Hyp
*every third is Gly |
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What if Glycine was not the main residue in collagen?
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The new residue would not fit because glycine is the only amino acid that does not have a side chain.
(H is the R group) |
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What stabilizes the triple helix in collagen?
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hydrogen bonding
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What are the steps for secreting collagen?
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1) proteases trim collagen
2) align side by side to form large fiber 3) oxidate lys chains to form strong cross links |
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Myosin and Kinesin have similar 1) --- but different 2) ---
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1) structure
2) function |
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What binds on the two independent heads of myosin?
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actin and ATP
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The neck or the --- allow for movement of myosin head
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light chains
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Which protein(s) hydrolyze ATP for energy?
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actin and myosin
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What part of the myosin is in contact with the thin (actin) filament?
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head
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When myosin rebinds to actin: PICK ONE
a) ATP is hydrolyzed b) ADP+Pi combines to form ATP) |
B
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When ATP is hydrolyzed, myosin:
a) attaches to actin b) detaches from actin |
B
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Why is the neck shorter in kinesin when compared to myosin?
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Necks don't strengthen and support movement
Located at other end of molecule |
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Kinesin moves by ---
Myosin moves by --- |
stepping
grabbing |
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How do motor proteins move?
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ATP hydrolysis
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How do the heads work in kinesin in compared to myosin?
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kinesin heads work together
myosin heads work separately |
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How is the binding of ATP different in myosin when compared to kinesin?
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myosin + ATP = myosin lets go of actin
kinesin + ATP = kinesin grabs tighter to tubulin |
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Myosin and Kinesin are part of what family?
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P-loop (family name) NTPases- hydrolyze ATP in order to move head
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What is the function of kinesin?
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move proteins between the cell body and axon ends of neurons
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The complexity of an organism is BEST measured by 1) --- but can also be measured by 2) ----
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1) genome size
2) gene expression |
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As complexity of an organism increases, the number of noncoding DNA ---
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increases
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1) How much of eukaryotic DNA is noncoding?
2) What is non coding DNA? |
1) 98%
2) DNA that is not expressed as protein |
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What are transposable elements?
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They are jumping genes that are copied and pasted multiple times to form repetitive sequences
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What are some ways to identify genes?
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1) open reading frame- look at longest amino acid chain
overestimation of gene sequence not sure if gene is expressed 2) compare sequence with other organisms underestimate gene sequence requires an organism with gene already present |
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What are the benefits of genomics?
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1) use model organisms to compare genes in humans
number of genes = metabolic toolbox mutate gene to determine function 2) identify disease markers multiple genes involved DNA different among individuals --> SNP Look for patterns in SNP |
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The more surface area an R group takes up, the more ---
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nonpolar
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Which AA is not chiral?
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Glycine (H=R group)
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Which amino acids side chain loops back on its backbone?
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Proline
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Most proteins have at lease one ---
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Trp
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When distinguishing polar amino acids, what groups should you look for?
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electron withdrawing groups (O, N, S)
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Why are polar amino acids are found in enzymes active site?
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used for catalysis
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Which amino acid forms disulfide bonds?
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cystine
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What is the significance of OH in Ser and Thr?
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1) OH serves as nucleophile
2) other chemicals can covalently bond via OH groups |
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Which amino acids are precursors of neurotransmitters?
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Tyr and Phe
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What makes Asn and Gln polar?
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amides in R group
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Which amino acid has an imidazole ring?
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His
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What are some examples of basic amino acid?
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His, Lys, Arg
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Which amino acid can be charged at certain pH values?
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His
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Which amino acids have positively charged side groups?
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Lys and Arg
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Which amino acids contain carboxyl groups (acidic amino acid) ?
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Asp and Glu
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1) When pH < pK
2) Whe pH > pK |
1) group is more protonated (acid)
2) group is less protonated (base) |
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When does pH=pI
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When the net charge on the molecule is 0
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What is the significance of pI?
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influences separation based on charge
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1) Define pH
2) Define pI |
1) charge state of single group
2) charge state of entire molecule |
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Ionizable side chains have ---
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pK3
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1) Amino acid sequence is held together by what type of bonds?
2) Tertiary structure of protein is held together by what types of interactions? 3) Quaternary structure of protein is held by what type of bonds? |
1) covalent
2) disulfide bonds, hydrogen bonds, ionic bonds, van der Waals 3) ionic, van der Waals, and disulfide bonds |
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What are the constraints in the primary structure of amino acids?
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1) no free rotation around polar C-N group
2) steric hinderence in residues |
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--- formation of hydrogen bond in alpha helix and beta helix stronger
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Linear
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Which beta sheet formation is more stable?
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antiparallel
N --> C -->N |
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Amino acids fold --- (spontaneously or nonspontaneously)
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spontaneously
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What is the hydrophobic effect and what does it impact?
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Protein's surface is largely hydrophilic
Proteins core is largely hydrophobic This impacts protein folding |
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Proteins fold into distinct ---
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domains
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Ion pairs contribute to protein stability (True or False)
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FALSE
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Where are covalent disulfide bonds NOT found?
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Intracellular proteins= reducing environment
prefer oxidizing environment |
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Disulfide bonds function in ---
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maintain conformation of polypeptide
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How can you denature a protein?
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1) temperature
2) pH 3) ion concentration Lose 3 --> 2 --> NOT 1 |
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How do you lose 1 structure?
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hydrolysis, enzymatic reactions
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Name the 6 classes of enzymes and the reactions involved
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1) Oxidoreductase - redox
2) Transferase- transfer of functional group 3) Hydrolase- hydrolysis 4) Lyase- elimination --> double bond 5) Isomerase- isomerization 6) Ligase- bond formation + ATP hydrolysis |
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Enzymes can not change ---
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equilibrium constant
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What is the energy barrier when 2 molecules combine?
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repulsive forces
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Enzymes do all of the following:
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- make it easier to reach transition state
- provide different rxn pathway - help stabilize transition state intermediate - can NOT change equilibrium constant - can NOT make non-spontaneous rxn --> spontaneous |
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Co-factors help enzyme function better. What are examples of co-factors?
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1) inorgranic metal ions
2) organic coenzymes |
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* What are inorganic metal ions able to do and why is it important?
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have multiple oxidation states
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What are the types of coenzymes?
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1) cosubstrates- enter and exit active site
2) prosthetic groups- remain associated with protein |
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What are the 3 catalytic mechanisms?
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1) acid- base catalysis
2) covalent catalysis 3) metal ion catalysis |
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How many energy hills are involved in covalent catalysis?
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2- one for schiff base and one for decomposing
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What represents the covalent bond formation in covalent catalysis?
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intermediate between 2 hills
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What can the metal ion do in catalysis?
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1) stabilize charge of transition state
2) interact directly with substrate 3) mediate redox rxn |
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Which family is chymotrypsin part of?
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Serine protease
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Chymotrypsin: covalent catalysis
1) Ser- 2) His- 3) Asp- |
1) provides nucleophile (O in 1st step and H2O in 2nd)
2) acts as base to activate Ser 3) stabilizes protonated His |
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What is the scissile bond in chymotripsin?
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The bond that must be cut (C-N)
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What are the limitations of lock and key model?
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1) doesn't explain how products are released
2) enzymes are dynamic- not rigid 3) doesn't explain enzymes effect on reaction rate |
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Pauling proposed a better explanation for how enzymes work. Describe his theory.
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Enzymes bind to substrate which stabilizes the transition state.
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How does chymotrypsin represent Pauling's theory?
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EXPLAIN
energy used to form H bonds primary- 3 H bonds secondary- low barrier H bonds |
