Biology/Biochemistry (Ours) Flashcards
1
Q
Mutation changes within the interior of a protein (ex) Arg change to Leu) and its influence on delta G BCR
A
Hydrophobic effect is a major driving force in protein folding as well as favorability of amino acid interactions. Look at whether residue is positive or negative and whether it is favored in the nonpolar or acidic protein interior. If favorable interactions, then more spontaneous/favorable reactions, lower delta G
2
Q
irreversible (comp/noncomp) vs. reversible noncompetitive inhibition affect on kinetics: V vs. [S] BCR
A
The kinetics seen under these conditions would be similar to both of these interactions because the net effect would be loss of active enzyme available for reaction. If enzyme concentration is effectively lowered, Vmax will be reduced. If Km were affected, it would increase, indicating that the substrate-enzyme interaction has been compromised in some way.
3
Q
Which category of enzymes will irreversibly modify their substrate? BCR
A
A protease Proteases are enzymes that cleave their substrates at specific sites, permanently removing a part of the protein. This is practically irreversible.
4
Q
Kinase BCR
A
Adds a phosphate to its substrate and this modification can be reversed by a phosphatase that will remove the phosphate.
5
Q
Acetylase BCR
A
Will add an acetyl group
6
Q
Phosphatase BCR
A
will remove the phosphate.
7
Q
What does increasing temp do to the ability of an enzyme to bind to its substrate? BCR
A
Increasing the temp of an enzyme’s surroundings may or may not affect the likelihood of an enzyme binding its substrate. Increasing temp = increase kinetic energy of sub = higher chance of entering active site of enzyme BUT be aware of “beyond temp of denaturation”
8
Q
Enzymes and changing pH BCR
A
Changing the pH of the solution to a non-optimal level will affect the change of the protein side chains and enzyme function
9
Q
Enzymes and mutating acidic residues to basic residues BCR
A
will change the charge of the active site substantially and likely affect the subs ability to bind to the active site
10
Q
Enzymes and altering shape/size of sub BCR
A
will decrease the sub’s ability to effectively bind to the active site
11
Q
For a given enzyme concentration at low sub concentration, how does the reaction rate change as the sub concentration increases? BCR
A
Linearly At low sub concentrations, the rxn rate increases linearly as the sub concentration increases. At or near saturation levels, the rxn rate begins to level off and does not change regardless of how much substrate it added. This is called the max velocity of the reaction rate or Vmax.
12
Q
Cooperativity - proteins BCR
A
- a protein must be composed of multiple protein subunits that are able to interact with one another, or less likely, should have multiple active sites within the same protein. - if no cooperativity, protein may have one subunit or multi non-cooperative subunits - cooperative enzymes usually exhibit sigmoidal curves - this involves changes in binding affinity when a sub is
13
Q
Lineweaver-Burk plot and competitive inhibitors BCR
A
-the y-intercept represents 1/Vmax and the x-intercept represents -1/Km. Bc competitive inhibitors do not change the Vmax and instead increase the Km, this plot with differing concentrations of comp inhib will show intersecting lines that share a common y-intercept.
14
Q
Lineweaver-Burk plot’s slope and competitive inhibitors BCR
A
Slope: dependent variable (y) is 1/v, the independent variable (x) is 1/s, they-intercept (b) is 1/Vmax, and the slope (m) is Km/Vmax. Comp inhib increases Km, while non-comp inhib reduces Vmax. As both Km and Vmax contribute to the slope, both modes of inhibition will produce a change in slope of the L-B plot
15
Q
Production of NADPH BCR
A
-by the pentose phosphate pathway - cells use it as the e- donor in reductive biosynthesis and in the process of detoxification of reactive oxygen species
16
Q
NADH+ BCR
A
is an e- acceptor in the oxidative metabolism of nutrients
17
Q
Lineweaver-Burk plot and non-competitive inhibitors BCR
A
a non-comp inhib binds to the allosteric site on the enzyme, effectively turning the enzyme off, but it doesn’t affect the ability of the enzyme to bind to substrate. Thus, Vmax will be decreased and Km will remain the same. A decrease in Vmax = an increase in the y-int (1/v) and Km is the x-int, which doesn’t change in this case.
18
Q
Enzymes alter the rate of chemical reactions by all of the following methods EXCEPT:
A
altering substrate primary structure The primary structure of a protein substrate is the amino acid sequence of the protein. Enzymes cannot alter primary structures of protein, but can co-localize substrates, alter local pH, and alter substrate shape.
19
Q
Ornithine is an amino acid that is found in cells, but not incorporated into proteins. Which of the following statements gives the most fundamental reason why ornithine is unlikely to be found in proteins synthesized in vivo? BCR
A
There is no codon for it in the standard genetic code. without a corresponding codon in the genetic code, an amino acid cannot take part in the process of protein translation from an mRNA transcript.
20
Q
What is a catalyst, cofactor, substrate, & activator? BCR
A
1) enzymes = catalysts = speed up reaction 2) is a non-protein chemical compound or metallic ion that is required for an enzyme’s activity as a catalyst; increases rate of reaction 2) the substance on which an enzyme acts 3) molecules that bind to enzymes and increase their activity. They are the opposite of enzyme inhibitors.
21
Q
The statement that the “XYZ” assay is highly specific means that it:
A
can distinguish “XYZ” activity from the many other enzymatic reactions in a cell enzymes such as “XYZ” are highly specific both in the reactions that they catalyze and in their choice of substrates and therefore catalyze only a single chemical reaction or occasionally a set of closely related reactions.
22
Q
acetyl coenzyme A is the main input where?
A
is the main input of the citric acid cycle
23
Q
protein levels relate most directly to _____ levels BCR/BR
A
mRNA
24
Q
Phases of Cell Cycle & the order BR
A
Interphase, metaphase anaphase, telophase
25
Do circulating erythrocytes do contain DNA? BR
mammalian erythrocytes (red blood cells) lose their nuclei during maturation. Therefore, circulating erythrocytes can't contain DNA that could affect endothelial cell growth, hypothetically.
26
The process of culturing bacteria often involves inoculation of cells on a noncellular, agar-based medium. Such a methodology would NOT result in growth of animal viruses because animal viruses: BR
are obligate parasites. viruses can only reproduce in a host cell, and are therefore obligate intracellular parasites.
27
How would the following nucleotides bond?
nucleotides are linked to one another by phosphodiester bonds between the **sugar** base of one nucleotide and the **phosphate group** of the adjacent nucleotide in a way that the **5' end bears a phosphate**, and the **3' end a hydroxyl group**.
28
During an action potential, the movement of sodium ions into a neuron causes the neuronal membrane to do which of the following?
Depolarize
the movement of sodium ions into a neuron during an action potential results in opening of more voltage-gated sodium channels, causing further depolarization
29
glucocorticoids
act on skeletal muscle causing the breakdown of muscle proteins
30
The most rapid rate of gluconeogenesis will most likely occur in the body when:
BCR
gluconeogenesis is the pathway for the synthesis of glucose from other metabolic compounds and thus it is activated when the body’s stores of carbohydrates are low.
31
A translated polypeptide is cleaved into the mature form and secreted from the cell. The cleavage most likely takes place in?
BR
Endomembrane system
secreted proteins, such as insulin, are cleaved into mature form within endomembrane system.
\*\*make sure to know role of endomembrane system in processing of secreted proteins.\*\*
32
Despite the effects of diabetes, the brains of diabetic patients still receive adequate nourishment. This is most likely because the brain uses:
BR
glucose is the main fuel for brain cells, and since the brains of diabetic patients receive an adequate amount of glucose, the brain must use an **insulin-independent mechanism** for glucose uptake.
33
A certain bacterium was cultured for several generations in medium containing 15N, transferred to medium containing 14N, and allowed to complete two rounds of cell division. Given that the bacterium’s genome mass is 5.4 fg when grown in 14N media and 5.5 fg when grown in 15N medium, individual bacteria with which of the following genome masses would most likely be isolated from this culture?
BR
5.4 fg and 5.45 fg
**DNA replication is semi-conservative.** Therefore, after the first round of cell division the genome mass in each bacterium will be 5.45 fg (one DNA strand will contain 15N and the other strand 14N). Following the second round of cell division, half of the bacteria will have a genome mass of 5.4 fg (14N exclusively) and the other half a mass genome of 5.45 fg (14N in one DNA strand and 15N in the other)
34
Know how to calculate the number of offspring with a particular phenotype from a parental cross
ex) Assume that K and M are two unlinked genes that affect hearing. The dominant K allele is necessary for hearing, and the dominant M allele causes deafness regardless of the other genes present. Given this, what fraction of the offspring of parents with the genotypes KkMm and Kkmm will most likely be deaf?
5/8
Based on the Punnett square analysis, 10 out of 16 or 5/8 of all offspring are likely to be deaf.
35
An RNA molecule has 1500 bases. What is the maximum number of amino acids it can encode?
500
each amino acid is encoded by three bases, so 1500/3 is 500, which is the maximum of amino acids the RNA molecule can encode.
36
thermodynamics
is the study of the energetics of chemical rxns
kinetic & potential energy
37
What is the most important potential energy storage molecule in all cells?
ATP, which stores energy in ester bonds between its phosphates
38
First law of thermodynamics / law of conservation of energy
energy of the universe is constant
if energy of system decreases, energy of rest of surroundings must increase
39
Second Law of Thermodynamics
disorder, or **entropy (s)** , of the universe tends to increase
Spontaneous rxns tend to increase the disorder of the universe
40
Gibbs Free Energy / free energy
delta G increases with increasing bond energy (delta H = enthalpy) and decreases with increasing entropy. Which one would be more favorable? One with decreasing free energy bc entropy increases.
determins whether a rxn is favorable (**spontaneous = neg delta G** or **nonspon = pos delta G**)
41
exergonic vs. endergonic
rxns with neg delta G = exergonic = energy exits the system
rxns with pos delta G = endergonic = energy is added
42
exothermic vs. endothermic
exothermic = neg delta H = liberate heat
endothermic = pos delta H = input of heat
43
How can delta G be negative if delta G naught (delta G\*` = in standard conditions) is positive, (which indicates that the reaction is unfavorable at standard conditions)?
rxn may be favorable if the ratio of the concentrations of reactants to products is sufficiently large to drive the reaction forward (so if delta G is *more* neg than delta G naught is pos), regardless of the sign of their delta G naught.
44
Does Keq indicate the rate at which a rxn will proceed?
BCR p. 42
Keq only indicates the relative concentrations of reagents once equilibrium is reached, not the rxn rate (how fast equilibrium is reached).
45
When Keq is large, which has a lower free energy: products or reactants?
A larger Keq means that more products are present at equilibrium. Equilibrium tends towards the lowest energy state. Hence, when Keq is large, products have a lower free enegy than reactants.
46
When Q is large, which has lower free energy: products or reactants?
The size of Q says nothing about the properties of reactants and products. Q (products/reactans concentrations) is calculated from whatever the intial concentrations happen to be. It is Keq that says something about the nature of reactions and products, since it describes their concentrations after equilibrium has been reached.
47
There are two factors that determine whether a reaction will occur spontaneoulsy (delta G = negative) in the cell:
1) the intrinsic properties of the rreactants and products (Keq)
2) the concentration of reactants and products (RT LnQ)
3) in the lab, ther eis a 3rd factor: temp; if Ln Q is negative and the temp is high enough, delta G will be neg, regadless of the value of delta G naught
48
What does "spontaneous" say about rate of reaction?
Spon. means that a reaction is energetically favorable, but it says **nothing** about the rate of rxn
49
chemical kinetics
transition state (TS)
Activiation Energy (Ea)
BCR p. 43
study of reaction rates
unstable, short, takes a lot of energy
energy required to produce the transition state
50
catalyst ____ Ea and without changing the \_\_\_\_\_. it ____ the transition state and is _____ with each reaction cycle. ____ are a biological catalysts.
lowers the **Ea** of a rxn without changing the **delta G;** they increase rate of rxn (have a kinetic role, NOT a thermodynamic one)
it **stabalizes** the transition state
**regenerated**
**Enzymes**
51
photosynthesis
photoautorophs
chemoheterotrophs
the process by which plants store energy from the sun in the bond energy of carbohydrates
plants are \_\_\_\_\_, bc they use energy from the light to make thier own food
we are \_\_\_\_\_, bc we use erngy of chemicals produced by other living things
52
Oxidation
loss of electrons
1) gain oxygen atoms
2) loss of H
3) loss of e-
53
reduction
the gain of e-
1) loss of Oxygen
2) gain of H
3) gain of e-
54
Will an enzyme alter the concentration fo reagents at equilibrium?
No. It will affect only the rate at which the reactnats and products reach equilibrium.
55
catabolism
anabolism
oxidative catabolism
is the process of breaking down molecules --\> "cata-strophe"
is "building-up" --\> "add-a"
the way we extract energy from glucose; we break down glucose by oxidizing it
56
redox pair
when one atom gets reduced, another myst be oxidized
ex) glucose oxidation
57
Bronsted-Lowry Acids & Bases
Acids: proton (H+) donors
Bases: proton (H+) acceptors
58
Lewis Acids & Bases
Acids: e-pair acceptors
Bases: e-pair donors
ex) AlCl3 + H2O
59
Conjugate Base
Conjugate Acid
when a Bronsted-Lowery acid donates a H+, the remaining thing is a con base
when a B-L base bonds with a H+, it becomes a con acid
60
strength of an acid
Ka = acid ionization (or acid-dissociation) constant
pKa
**strength of an acid** is direclty related to how much the products are favored over the reactants
**Ka = [products] / [reactants]** = equilibrium expression for an acid-dissociation reaction = the larger the Ka, the stronger the acid
the lower the **pKa**, the stronger the acid
**pKa = -logKa**
\*\*Kb & pKb exist\*\*
61
What acid would dissociate to the greatest extent in water?
the acid with the largest Ka value
62
polyprotic
has more than one proton to donate
63
amphoteric
What compounds are amphoteric?
substance that can act as either a base or an acid
**Amino Acids**
64
pH equations & pKa/b equations
pH = -log[H+]
pOH = -log [OH-]
pH + pOH = 14
pKa/b = -log Ka/b
\*\*the lower the pKa, the stronger the acid\*\*
65
What would contain the lowest concentration of H3O+ ions if you're given pH?
Since pH = -log [H3O+], we know that [H3O+] = 1/10 pH. This fraction is the smallest when the pH is the greatest.
So, look for the highest pH.
66
buffer solutions
a solution that resists pH when a small amount of acid or base is added
buffering capacity = presence of weak acid and conjugate base (vise versa)
most important buffer system = bicarbonate buffer system (H2CO3 -\> H+ + HCO3-
67
describe the function of enzymes
by decreasing the energy of the transition state, enzymes increase the amt of product formed per unit time
68
In general, know what get's reduced & oxidized in a reaction
BCR p. 45
do example probelms !
69
Acidic Glu has a pKa value of 2.3 and found near neutral Ile residue. What will be the effect on the pKa of the Glu reside if a nutation subsitutes a positively charged Lys residue for the Ile residue?
the pKa will decrease due to favorable ionic interactions b/w the deprotonatd Glu and Lys residues.
The sub of a pos charged lysine for a neautral isoleucine would help stabilize Glu in its deprotonated, neg-charged state. Bc it would be more stable, it is more likely to give up its proton (becomes more acidic) and the pKa would decrease.
70
proteins are biological macromolecules that act as...
enzymes, hormones, receptors, channels, transporters, anitbodies, support strucutres inside/outside cell
composed of 20 diff amino acid links
71
amino acid structure
72
side chains of amino acids
BCR p. 63
the unique feature of each amino acid is its **side chain (variable r-group),** which gives it the physical and chemical properties that distinguish it from the other nineteen
73
chemical properties to know of amino acids
shape, ability to hydrogen bond, and ability to act as acids or bases (which determines their charge at physiologial pH)
74
Aspartic Acid & Glutamic acid
Acidic amino acids; have a carboxylic acid functional group
could be seen as asparate and glutamate = anionic (deprotonated) form of each molecule
75
Lysine, Arginine, Histidine
basic amino acids
Lys: pKa = 10, cationic (protonated) at physiological pH,
Arg: pKa = 12, cationic (like Lys),
His: pKa = 6.5, protonated or deporotonated at pH 7.4 = "HIS goes both ways"
at 7.4 pH (physiological pH): -COOH or -NH2 (RCOO-) = anionic and RNH3+ = cationic
76
hydrophobic (nonpolar) amino acids
either have alkyl or aromatic side chains
found on interior of folded globular proteins, away from water
Glycine - aliphatic side chain
Alanine - aliphatic side chain
Valine - aliphatic side chain
Leucine - aliphatic side chain
Isoleucine - aliphatic side chain
Phenylalanine - aromatic side chain
Tryptophan - aromatic side chain
77
polar amino acids
r-group polar enough enough to from hydrogen bonds with h2o, but which doesn't act as an acid or base -\> hydrophilic
**serine** - hydroxyl groups residuews are often modified by the attachment of a phosphate group by a reg enzyme, a kinase = change in strucutre (protein regulation)
**threonine** - hydroxyl groups residuews are often modified by the attachment of a phosphate group by a reg enzyme, a kinase = chaneg in structure (protein regulation)
**tyrosine** - hydroxyl groups residuews are often modified by the attachment of a phosphate group by a reg enzyme, a kinase = change in structure (protein regulation)
**asparagine -** amide derivative of aspartic acid
**glutamine -** amide derivative of glutamine
78
sulfur-containing amino acids
**cysteine** - contains a thiol, polar
**methionine** - thioether, nonpolar
79
proline
amino group is covalently bound to its nonpolar side chain, creating a secondary alpha-amino group and ring structure
protien folding = important with this
80
general overview of acidic, basic, polar, and nonpolar amino acids
81
Amino acids are composed of an ___ group (the ______ acid) and a ____ group (the \_\_\_\_).
**carboxylic** acid, **basic** group, **amine**
82
83
Henderson-Hasselbalch equation
the mathematical formula that describes the relatinoship between pH, pKa, and the position of equilibrium in an acid-base reaction
84
When the ____ of a solution is ___ than the ___ of an acidic group, the acidic group will moslty be in its ____ form.
BCR p. 68
**pH**
**less**
**pKa**
**protonated**
85
When the pH of a solution is greater than the pKa of an acidic group, the acidic group will moslty be in its ____ form.
deprotonated
86
Which functional group of amino acids has a stronger tendency to donate protons: carboxyl groups (pKa = 2.0) or ammonium groups (pKa = 9)? Which group will donate protons at the lowest pH?
A high pKa = weak acid. Acids with a **low pKa tend to deprotonate easily.** Therefore, ammonium groups have stronger tendency to keep their protons, and carboxyl groups will donate protons at the lowest pH (highest [H+]).
87
ammonium group
amine - NH 4 +
88
Assuming a pKa of 2, will a carboxylate group be protonated or deprotonated at pH 1.0?
the pH is less than the pKa here, so protonation wins over dissociation, and the group will be protonated. The correct answer is -COOH.
89
zwitterion
Isoelectric Point of Amino Acids
a molecule with positive and negative charges that balance is referred to as a dipolar ion, or zwitterion
the pH at which a molecule is uncharged is reffered to as its iso point (pI)
average the pKas of two function groups on a molecule to calculate the pI of an amino acid
90
there are two common types of covalent bonds between amino acids in proteins:\_\_\_\_\_ AND \_\_\_\_\_
**peptide bonds** that link amino acids together into polypeptide chains and **disulfide bridges** between cystine R-groups
91
how is a peptide bond formed?
backbone
residue
a peptide bond is fromed between the carboxyl group of one amino acid and the alpha-amino group of another amino acid with the loss of h2o
in a polypeptide chain, the N-C-C-N-CC = backbone
an individual amino acid is a residue when it is part of a polypeptide chain
92
Hydrolysis of a protein by another protein is called _____ or _____ \_\_\_\_\_, and the protein that does the cutting is known as a ____ \_\_\_\_ or \_\_\_\_\_.
**proteolysis** or **proteolytic cleavage.** Proteolytic cleavage = specific means of cleaving peptide bonds
**proteolytic enzyme** or **protease**
93
disulfied bond
1) cysteine is an amino acid with a reactive thiol
2) thiol + thiol = covalent sulfur-sulfur bond = disulfide bond
3) important role in stabalizing tertiary protein structure
4) cysteine w/ disulfide bond = *cystine*
94
denaturation
refers to the disruption of a protein's shape without breaking peptide bonds
proteins are denatured by urea (which disrupts h-bonding interactions), by extremes of pH, extremes of temp, and by changes in salt concentration (tonicity)
95
protein structures (1, 2, 3, 4)
**primary:** sequence of amino acids bonded
**Secondary:** hydrogen bonding between backbone groups; initial folding; alpha-helix and B-pleated sheet
**tertiary:** hydrophobic/hydrophilic interactions; interactions of distant R-groups with each other and with the solvent (H20); **hydrophobic effect**: hydrophobic R-groups fold inside and hydrophilic R-groups fold outside
**quaternary:** interactions bw polypeptide subunits; a **subunit** is a sinlge polypeptide chain that is part of a large complex containing many subunits (a **multisubunit complex**); peptide bond = not usually involved bc defines sequence (primary structure)
96
the side chain of proline causes two probelms in polypeptide chains:
1) formatino of peptide bond w/ proline eliminated the only H atom on the nitrogen of proline. no N-H disrupts backbone and no H atom avaible for backbone hydrogen bonding
2) forces kink in polypeptide chain
97
Enzyme Class and reaction (10 types)
98
Thermodynamically unfavorable reactions in the cell can be driven forward by _____ \_\_\_\_\_\_.
**reaction coupling**
one very favorable reaction is used to drive an unfavorable one; this is possible bc free energy changes are additive
99
An enzyme may consist of a single polypeptide chain or several polypeptide subunits held together in a ______ structure.
quaternary
100
The reason for the importance of folding in enzyme function is the proper formation of the ___ \_\_
active site
101
1) the reactants in an enzyme-catalyed rxn are called \_\_\_\_\_
2) the ___ \_\_\_ _____ states that the substrate and active site are perfeclty complementary
3) the ____ \_\_ ____ states that the substrate and active site differ slightly in strcuture and that the bidnig of the sub induces a confirmational change
substrates
active site model
induced fit model
102
proteases
(protein-cleaving enzymes) have an active site with serine residue whose OH group can act as a nucleophile, attacking the carbonyl carbon of an amino acid residue in a polypeptide chain
these enzymes usually have a **recognition pocket** near the active site; this pocket attracts certain residues on a substrate polypeptides
103
When a cofactor is an organic molecule, it is referred to as a \_\_\_\_\_\_\_; these often bind to the substrate during the catalyzed reaction
**coenzymne**
104
regulation of enzyme activity - 4 types
**1) covalent modification:** the addition of a phosphoryl group from a molecule of ATP by a protein **kinase** to the hydroxyl of serine or tyrosine residues is the most common example; **phosphorylases** use free-floating P; **phosphatases** reverse phosorylation
**2) proteolytic cleavage:** many proteins/enzymes are synthesized in inactive forms (zymogens) that are activated by cleavage by a protease
**3) association with other polypeptides:** enzymes that have catalytic activity in one polypeptide subunit regulated by association w/ a sep reg unit; **constitutive activity**
**4) allosteric regulation:** modification of active-site activity through interactions of molecules w/ allosteric sites
105
constitutive activity
some proteins that demonstrate continuous rapid catalysis if their regulatory subunit is removed have this activity
106
allosteric regulation
one mechanism of regulation is the binding of small molecules to particular sites on an enzyme that are distinct from the active site
107
feedback inhibition or negative feedback
feedforward stimulation
when an end product shuts off an enzyme early in apathway of creating a product
involves the stimulation of an enzyme by its substrate or by a molecule used in the synthesis of the substrate
108
**enzyme kinetics**
**reaction rate (V = velocity)**
**saturated**
**enzyme kinetics graphs and Km**
the study of the rate of formation of products from substrates in the presence of an enzyme
is the amount of product formed per unit time, in moles per second (mol/sec); depends on [] of substrate and enzyme
there is so much substrate that every active site is continuously occupied, and adding more substrate doesn't increase the rxn rate at all = enzyme is ______ = Vmax
Michaelis constant = the substrate [] at which the rxn velocity is 1/2 its max
109
cooperativity
sigmoidal curve
the binding of substrate to one subunit modulates the affinity of other subunits for substrate; such enzymes are said to bind substrate **cooperativley**
**positive** (binding of sub to subunit increases affinity of other subunits for sub) and **neg** (opp)
\_\_\_\_ results from positive cooperative binding
ex) Hemoglobin = pos cooperative O2 binding
110
111
What is the relationship between the two notions of allosteric and cooperative?
BCR p. 87
Cooperativity is a sperical kind od allosteric interaction: one active site acts like an allosteric regulatory site for the other active sites. Cooperative enzyme complexes are often allosterically regulated also.
ex) Hb
112
inhibition of enzyme activity
**competitive inhibition -** compete with sub for binding to active site; inhibition can be overcome by adding more sub; Vmax not affected; Km increases
**noncompetitive inhibition -** bind to allosteric site, not the active site; inhibition can't be overcome by more sub; lowers Vmax, but doesn't change Km bc sub can still bind to active site, but inhibitor preventgs the catalytic activity of the enzyme
**uncompetitive inhibition -** only able to bind to the enzyme-sub complex (it can't bind before the sub has bound); bind to allosteric sites; decreases Vmax, decreases Km
**mixed-type inhibition -** occurs when an inhibitor can bind to either the unoccupied enzyme of the enzyme-sub complex (usually noncomp inhib)
113
Changes in the Apparent Vmax and Km in response to various types of inhibition
114
Graph of competative inhibitor
115
Noncompetitive inhibitor
Bind at allosteric site, not active site
Decreases Vmax (adding more enzyme will increase the measured Vmax)
Km is not affected (substrate can still bind to AS)
--\> overall: (decrease Vmax, while having no effect on Km for the inhibited enzyme)
116
Uncompetitive inhibition
decrease Vmax, while decreasing Km for the inhibited enzyme
## Footnote
Only binds to enzyme-substrate complex
Bind to allosteric sites
Decreases Vmax (limiting amt of available enzyme-substrate complex which can be made to product)
Km decreases
Enzyme-complex has greater affinity for the inhibitor → enzyme will have greater affinity for substrate --\> km decreases
117
Lineweaver-burk plot
graphical representation of enzyme kinetics
double reciprocal plot bc the y-axis is the inverse of the rxn rate (1/V) and the x-axis is the inverse of the substrate concentration (1/[S])
Need to know:
1) the slope = Km/Vmax
2) y-interept = 1/Vmax
3) x-intercept = -1/Km
\*\* increaseing the sub concentration increases the rxn rate V _up to a point_\*\*
118
How would the Lineweaver-Burk plot change when a noncompetitive inhibitor is added?
A noncomp inhib does not affect Km (so the x-intercept is unchanged) but does decrease the Vmax (so the y-intercept increases and the slope increases)
119
triglycerides
3 FA and glycerol; amphipathic
(fats) - stored in fat cells as energy source
hydrophobicity: pack closely together
store much more energy than carbohydrates
120
cholesterol
lipid that serves as building block for hydrophobic steroid hormones
3 6 carbon rings, 1 5 carbon ring
functions: bile salts
Steroid cholesterol: component of lipid bilayer (CHOLESTEROL keeps fluidity at optimal level (low temp - increases fluidity - decreases freezing point; high temp - reduces fluidity - increases melting point)
Obtained from diet; synthesized in liver
Carried in blood packaged with fats and proteins into lipoproteins (build up of cholesterol plaques on inside of blood vessels = atherosclerosis: this is high levels of BLOOD cholesterol not membrane cholesterol)
**Hormones are made from cholesterol**
- Testosterone
- Estradiol
psa: if a protein/other molecule is found in cholesterol-rich domains --\> lipid rafts!
121
lipid
hydrophobic
monomer = hydrocarbon; carboxylic acid on one side
122
fatty acid
typically 14-18 C long
Saturated = no double bonds (max # H) ; membrane is more solid (less fluid)
Unsaturated = one or more DB (almost always cis / z) - bent or kinked at DB (bent shape → doesnt fit in as well, less contact with neighboring groups to form van der waals interactions)
Fatty acids in h20: hydrophobic chains will interact with each other to minimize h2o contact and expose charged carboxyl group to aqueous env
- in aqueous soln, they form a micelle - force that drives the tails to the center = hydrophobic interaction
123
lipase
enzyme that hydrolyzes fat
124
phospholipid
membrane lipids; minimize interactions with water by forming lipid bilayer
125
terpene
built from isoprene units (C5H8)
Can be linear or cyclic; classified by # isoprenes they contain (precursors to ring lipids)
Monoterpene: 2 isoprene units
Sesquiterpenes: 3
Diterpenes: 4
compose part of vitamin A (part of its structure has terpene character: terpenoid)
precursor to cholesterol
Squalene: triterpene (6 units)
- Manufacture of steroids
- Component of earwax
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steroid
Hydrophobic (diffuse through the lipid bilayer into cytoplasm); receptors located within cell
Basic tetracyclic ring system
defined by fused 4-ring structure
Two general classes of hormones are those that are small hydrophobic molecules like steroid hormones and those that are peptides...
steroid hormones: include aldosterone and testosterone, diffuse through the plasma membrane to bind to a receptor which enters the nucleus to regulate transcription of a specific set of genes
Peptide hormones: such as glucagon, insulin, and ACTH, cannot diffuse into the cell since they are large and hydrophilic, so they bind to cell-surface receptors to transduce a signal into cells
127
128
prostaglandin
regulate smooth muscle contraction in the intestines; regulate blood vessel diameter; maintain gastric integrity (increase mucus secretion, decrease acid secretion)
129
fatty acid oxidation
chylomicrons (fat and lipoprotein) are transported via lympathic system and BS to liver, heart, etc
this TG is then hydrolyzed to liberate free FA (which can undergo beta oxidation)
process begins at outer mito membrane with activation of fatty acid
rxn catalyzed by acyl-coA synthetase (requires 2 ATP to generate fatty acyl-CoA - transported into mitochondrion)
\*\* fatty acyl-coa is activated fatty acid
in matrix, fatty acyl-coA goes through beta oxidation (each round cleaves 2 carbon acetyl coA from the molecule; final round: cleaves 4 carbon acyl-coA to make 2 acetyl-coA) --\> feeds into krebs cycle
each turn of beta cycle produces 1 FADH2 and 1 NADH; each turn of krebs makes 1 FADH2 and 3 NADH
Break down fatty acid: calculate how many times we need fatty acid oxidation
(#C in fatty acids / 2) - 1
130
unsaturated vs saturated fatty acid oxidation
Unsaturated FA: already have DB, so you isomerize it (only need 1 oxidation vs 2 for saturated)
Difference: less energy (1 oxidation instead of 2 oxidations)
Oxidizing unsaturated requires less energy!!
131
synthesis of malonyl coA (--\> fatty acid synthesis)
takes place in cytoplasm
acetyl-coA is first activated with co2 and atp; acetyl-coA carboxylase --\> malonyl-coA
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fatty acid synthesis (part 2)
bcr p. 154
fatty acid synthase (enzyme)
1) acetyl coa binds to ACP - then shifted to another domain with cysteine residue; malonyl-coa binds to ACP), 2) acetyl group condenses with malonyl group as malonyl is decarboxylated, 3) ACP domain now holds 4 Carbon unit, undergoes 2 reductions (requires 2 NADPH - from pentose phosphate pathway, has reducing power), 4) saturated four-carbon acyl unit shifts to the domain with cysteine residue and another malonyl-coA binds to ACP, 5) process repeats: 4 c unit condenses with malonyl as co2 is lost, 2 reductions occur, and the now 6 c chain is shifted to cysteine residue
- goal: make 16 c fatty acid
133
134
fatty acid synthesis (part 3)
image describes elongation process; process was described in part 2 slide
135
fa oxidation vs fa synthesis
FA OXIDATION:
Matrix
Linked to coA
Coenzymes: FAD, NAD+
Energy: need a little ATP, make e- carriers
FA SYNTHESIS:
CYTOSOL
Linked to ACP
Coenzymes: NADPH
Energy: Need ATP to make malonyl
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ketogenesis
bcr p. 151
during long term starvation, blood glucose falls
fats are oxidized to form acetyl-coa
levels of acetyl coa increase
some acetyl coa feeds into krebs
remaining acetyl-coAs react to form **ketone bodies - acetone, acetoacetate, beta-hydroxybutyrate (ketogenesis)**
**ketone bodies: can enter the brain- this is the primary source of energy for brain during starvation (and be reconverted to acetyl-coa (acetyl coa can then enter krebs cycle)**
**type I diabetes: if patient doesnt receive insulin injection for a while, patient relies on fatty acid oxidation for acetyl-coa to feed krebs**
**but bc acetyl-coa levels are so high, many of them become ketone bodies (acidic --\> ketoacidosis)**
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protein catabolism
PROTEASE: break down proteins into individual AA
From individual AA we can form new proteins or break down into amino group
- Amino group can go off and form nitrogenous compounds (nucleotides) and urea for excretion
remaining carbon skeleton (alpha-keto acid) --\> water and co2, or converted to glucose (glucogenic AA - low glucose levels) or acetyl-coA (ketogenic AA)
138
metabolism summary
BCR p. 156
- cells prefer to use carbohydrates as fuel
- when blood sugar is high: cells will take up glucose and make ATP via glycolysis, liver and muscle cells will store glucose as glycogen (glycogenesis), liver can take some of the acetyl-coa generated by PDC to make fatty acids --\> triglycerides and stored in adipose tissue
- when Blood sugar is low: liver will break down stored glycogen (glycogenolysis) and release glucose into bloodstream (also begin gluconeogenesis to be sent into bloodstream - taken up by other cells and used in glycolysis to make ATP)
- if starved state goes past point where all glycogen stores are used (12-24 hours), fatty acid breakdown occurs (triglycerides from adipose tissue are broken down into fatty acids and run beta oxidation; liver uses glycerol to make glucose in gluconeogenesis; some acetyl-coa made in beta oxidation fuels krebs; some is made into ketone bodies)
- proteins and amino acids as fuel: carbon skeleton of amino acids can be used in gluconeogenesis (glucogenic amino acids) or to make acetyl-coa and ketone bodies (ketogenic AA0
139
which property of lipids contributes most to their higher energy density per carbon in comparison to carbohydrates?
carbohydrates exist in a more oxidized state, while lipids are more reduced
(Notice how all the carbon atoms in glucose (a sugar) have oxidation states of -1, 0 or +1, while all but one carbon atom in palmitic acid (a fatty acid) have oxidation states of -2 or -3. This means that the carbon atoms in fatty acids have more electrons around them. As described in the Electrochemistry tutorial, when electrons move from an atom with a low affinity for electrons (low electronegativity), like carbon, to one with a high affinity for electrons, like oxygen, energy is released. Therefore, when the greater number of electrons around the carbon atoms in fatty acids are transferred to oxygen (when the fatty acids are oxidized), more energy is released than when the same process happens to carbohydrates.)
140
stearic acid is 16 carbon saturated fatty acid. including those made in krebs, how many NADH and FADH2 would be produced by oxidation of stearic acid?
15 fadh2 and 31 nadh
(7 turns of beta oxidation to produce 8 acetyl coA --\> krebs)
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During the initiation of muscle contraction...
mysosin binds actin after troponin binds to Ca
- during the initiation of muscle contraction, free Ca2+ in the cytosol binds to troponin, which pulls tropomyosin away from actin’s myosin-binding site. This allows myosin to bind to actin.
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epilepsy
to treat epilepsy: **increasing the neuron-firing threshold** required to generate an action potential would decrease the chance that individual neurons would fire, thus reducing the overall amount of excitation that spreads from the epileptic focus throughout the cortex.
143
kidney - glomerular filtrate
when urine is being produced, medullary portion of collecting duct = where glomerular filtrate will reach highest concentration
initial filtration step in the glomerulus of the kidney occurs primarily by passive flow due to a pressure difference (Initial filtration in the glomerulus occurs as blood pressure forces the fluid from the glomerulus into the lumen of Bowman’s capsule)
144
which approach doesn't measure activity of Na+K+ ATPase?
1) measuring rate of atp hydrolysis, 2) measuring free energy of ion transport, 3) measuring rate of ADP production, 4) measuring change in ion concentration within liposome
Measuring the free energy of the ion transport (free energy is a thermodynamic quantity and is NOT a kinetic property.)
145
Na+K+ ATPase
during neuronal action potential: restoration of resting potential
- Na+K+ ATPase functions to restore the resting membrane potential by moving the ions against their concentration gradients.
Na+K+ ATPase transports Na out of cell and K into the cell upon atp hydrolysis
- Na+K+ ATPase transports 3 sodium ions out of the cell and 2 potassium ions into the cell with each ATP hydrolyzed.
146
transcription factors
**bind DNA** and subsequently recruit RNA polymerase
check out khan academy:
https://www.khanacademy.org/science/biology/gene-regulation/gene-regulation-in-eukaryotes/a/eukaryotic-transcription-factors
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hydrophobicity
pass through membrane by simple diffusion
molecule shown below: hydrophobic
148
kinase
phosphorylation!
149
ABC transporter
class of active transporters that are used by both prokaryotes and eukaryotes.
While prokaryotes use these transporters to import hydrophilic molecules, both prokaryotes and eukaryotes use them to export molecules such as lipids, steroids, and toxins.
could be used to actively transport antitumor drugs out of cell using ATP (so its like a pump)
150
ATP hydrolysis (ATPase)
ATPase: group of enzymes that catalyze the hydrolysis of a phosphate bond in ATP to form ADP
ATP hydrolysis: produces ADP and inorganic phosphate
151
cyclic oligosaccharide
composed of carbohydrates
152
if a drug prevents the formation of microtubules...
Movement of the chromosomes toward opposite poles of the cell during anaphase would NOT occur (microtubules function in chromosomal movements in cell division)
153
half-life
From the graph, it takes 0.5 h for the plasma concentration of urea to fall by one-half (100 ng/mL to 50 ng/mL). If it took five half-lives for urea to be considered eliminated from the body, 0.5 h should be multiplied by five = 2.5 hours
154
mixed-type inhibition
decrease Vmax, while either increasing or decreasing Km for the inhibited enzyme
## Footnote
Inhibitor can bind to either the unoccupied enzyme or the enzyme-substrate complex
Inhibitor binds to allosteric site and additional substrate cannot overcome inhibition (v max decreases)
155
competitive inhibitor
Compete with substrate for binding at active site
Can be overcome by adding more substrate
Vmax isn't affected; Km increases
Enzyme has greater affinity for inhibitor in free form → enzyme has lower affinity for the substrate → km increases
156
hepatocytes
liver cells
157
single stranded RNA molecules don't have a ratio of \_\_\_\_:\_\_\_\_ (cytosine:guanine), but DNA does
the ratio of cytosine to guanine only has to be 1:1 if the nucleic acid is double stranded
158
What best describes the role of **fructose-2,6-bisphosphate**?
**It exerts reciprocal control on glycolysis and gluconeogenesis by stimulating phosphofructokinase and inhibiting fructose-1,6-bisphosphatase.**
It has no impact on hexokinase activity. Fructose-2,6-bisphosphate stimulates phosphofructokinase, which is used in glycolysis, and inhibits fructose-1,6-bisphosphatase, which is used in gluconeogenesis.
159
Arachidonic acid is a fatty acid contained in cell membranes. The structure of arachidonic acid is:
In which component of the cell membrane would arachidonic acid most likely be found?
\*\*cholesterol vs. triglycerides vs. phospholipids vs. Peptidoglycan layer\*\*
**Phospholipids**
**Cholesterol** is an abundant component of animal cell membranes, but it is a steroid, not derived from fatty acids such as arachidonate. **Triglycerides** could contain a fatty acid like arachidonate, but they are not membrane components. **Peptidoglycans** are not found in eukaryotes, only bacteria, and do not consist of fatty acids.**Phospholipids** are abundant components of the plasma membrane and contain esters of many different fatty acids.
160
The diaphragm plays an important role in respiration. During inspiration, the diaphragm:
**contracts, causing alveolar pressure to drop below atmospheric pressure**
Inspiration is the drawing of air into the lungs. The diaphragm contracts and flattens during inspiration, expanding the chest cavity; the lungs (which are stuck to the inside wall of the chest cavity) expand as well. The expansion of the lungs decreases the pressure in the alveoli, causing air to move into the lungs from the exterior
161
Tryptophan can induce sleep in some people. _Warm_ milk causes greater sleepiness than cold milk because heating the milk:
**releases free tryptophan from proteins, causing more rapid intestinal absorption**
If heating the milk reduced tryptophan solubility, this would decrease, not increase the sleep-inducing properties of milk. Lactose is a disaccharide, not a protein, and its hydrolysis cannot release an amino acid (eliminate choice B - causes hydrolysis of lactose, releasing tryptophan). Amino acids, like most nutrients, are absorbed in the small intestine mostly, not the stomach. Although heating the milk does not create more tryptophan, it might help to hydrolyze some of the milk proteins and release tryptophan so it can be absorbed more rapidly after ingestion and cause greater sleepiness.
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\_\_\_\_\_\_\_ receptor will localize within the **nucleus**, where it regulates genes by binding to ______ and \_\_\_\_\_\_
**estrogen**
**enhancers**
**promoters**
There is no estrogen receptors in the plasma membrane or mitochondria
Some estrogen receptor may be located in the cytoplasm, particularly in the absence of ligand, but it will localize mostly in the nucleus when it has ligand bound.
163
In a population of 18,000 Caucasians, how many are expected to be carriers of cystic fibrosis (It is an autosomal recessive disorder, occurring with a frequency of 1 in 3600)?
**590**
The passage states that the frequency of the autosomal recessive condition cystic fibrosis, q2, is 1 in 3600. The frequency of the recessive allele, q, then is 1 in 60. The frequency of the dominant non-disease producing allele, p, is 59 in 60. The carriers of a population are determined by the expression 2pq. In the given population, the number of carriers would be (2)(1/60)(59/60)(18000) or 590.
164
Southern and Northern blots
**Northern blotting**, used for RNA detection, involves a complex isolation and hybridization procedure which results in labelled probe bound to the RNA sequence of interest. **Southern blotting** is used for the detection of a specific DNA sequence in large, complex samples of DNA.
165
Based on information in the passage, alleles of OCA2 are one of the major determinants of eye color. The OCA2 gene overlaps with another gene called HERC2, which has two alleles: the wild type allele, and a recessive allele A1 which has been linked to a genetic predisposition to Crohn’s disease. A woman with an OCA2305R : HERC2wt chromosome and an OCA2305W : HERC2A1 chromosome mates with a homozygous OCA2305R / 305R : HERC2A1 / A1 man. Their children will most likely be:
**\*\*Genetics: Mendelian Genetics/Probability\*\***
course practice test 1, #50
**50% normal with blue eyes and 50% brown eyed with a risk of Crohn’s disease**
The woman in the question stem will have brown eyes because she is heterozygous for OCA2 and has an allele that is associated with blue eyes (305R) and an allele associated with brown eyes (305W). Since the question stem says that the OCA2 gene and the HERC2 gene overlap, **they must be linked** (they are 0 map units apart). This means that **crossing over will not occur** between these two genes and they will be inherited as a unit. The father in this question is acting like a **testcross**; that is, he is homozygous recessive for both genes. Therefore, the offspring produced will either get the OCA2305R : HERC2wt chromosome or the OCA2305W : HERC2A1 chromosome from the mother and an OCA2305R : HERC2A1 chromosome from the father. The children will be 50% OCA2305R / 305R : HERC2wt / A1 (blue eyed with no increased risk of Crohn’s disease; note that the A1 allele of HERC2 is recessive to the wild type allele) and 50% OCA2305W / 305R : HERC2A1 / A1 (brown eyes with an increased risk of Crohn’s disease).
166
\_\_\_\_\_\_\_\_\_ proteins or genes are those that have evolved from a common ancestor.
\*\*know how to read a phylogenetic tree\*\*
homologous
167
Which of the following intermolecular attractions will exhibit the greatest strength?
London dispersion forces vs. Induced dipole interactions vs. Instantaneous dipole interactions vs. Hydrogen bonds
London dispersion forces, Induced dipole interactions, and Instantaneous dipole interactions are the same.
The various intermolecular forces, in order of decreasing strength, are the following: **Hydrogen bonding \> Dipole–Dipole interactions \> Dipole– Induced dipole interactions \> Induced dipole–Induced dipole interactions** (London forces)
168
Which of the following are products of the pentose phosphate pathway?
1. NADH
2. NADPH
3. Ribose-5-phosphate
\*\*biochemical pathways\*\*
II and III only
Item I is false: NADH is an electron-carrier produced in catabolic reactions, like cellular respiration. Note that since both remaining choices include Item III it must be true and we can focus on Item II, which is true: NADPH is produced by the pentose phosphate pathway. Item III is in fact true: ribose-5-phosphate is a primary product of the pentose phosphate pathway.
169
Some vitamins are essential to humans because they act as precursors of:
**coenzymes**
options provided: auxins, glucose, and enzymes
**Auxins** are plant hormones not found in humans. **Glucose** is not made from vitamins. **Enzymes** are proteins made from amino acids. Many **coenzymes** (which are not themselves amino acids and so cannot be made into enzymes) are required for enzyme activity and are derived from water-soluble vitamins, such as thiamine, biotin, folate, and niacin).
170
Which of the following is NOT a valid **resonance** contributor of the **cationic intermediate** of the reaction shown?
D
Choice D has a hydrogen atom attached to the same carbon as the chlorine, but is missing the hydrogen bonded to the bottom carbon of the ring that choices A, B, C, and the original cation all have. Since atoms and not only electrons have been moved, choice D cannot be considered a resonance structure of the original cation.
171
172
Hardy-Weinberg equation
only be used to describe the frequencies of autosomal recessive or dominant traits or conditions, not changes in chromosome number!
173
trisomies
one cannot predict the occurrence of the carriers in a population since trisomies are not based on dominant or recessive expressions
174
common arterial trunk coming off the right and left ventricles
mixing of blood from the left and right circulations
Since the right circulation is relatively high in carbon dioxide and the left circulation is relatively low in carbon dioxide, the resultant mix will be somewhere between
the right circulation that is typically low in oxygen will mix with the left circulation that is typically higher in oxygen, so the overall aortic arterial oxygen saturation will be less than normal and the pulmonary arterial oxygen concentration will be higher than it is normally
Since a common arterial trunk is receiving blood from both the right and left ventricles, the pulmonary artery will be receiving more blood than usual and therefore will have a higher than normal blood pressure
175
a blind-ending jejunum
prematurely ending small intestine
176
hypotonia
a decrease in muscle tone
177
trisomy
47 chromosomes
178
aldosterone
steroid that increases sodium uptake from and potassium secretion into the filtrate in distal tubule (stimulated by low na, low bp, low blood volume - all problems that will be rectified with this steroid)
released from adrenal cortex
also stimulates ADH secretion so more h2o can be taken up from filtrate
- if you didn't have aldosterone: water and sodium loss, decreased blood volume and decreased blood pressure; In response to decreased blood pressure, renin secretion would increase, not decrease
check out aphys notes!
179
hormones secreted by adrenal glands
epinephrine from the medulla
cortisol, aldosterone, and low levels of sex steroids from the adrenal cortex
180
An activated aldosterone receptor most directly regulates activity of which of the following enzymes?
aldosterone binds to aldosterone receptors to regulate transcription of a specific set of genes. The enzyme that synthesizes mRNA is RNA polymerase II, so this enzyme would be most directly affected by the activated aldosterone receptor
181
RNA polymerase II
enzyme that synthesizes mRNA
182
DNA polymerase
used in replication, not transcription
183
A drug is discovered that reduces smooth muscle contraction by inhibiting the muscle’s response to **acetylcholine**. This is likely to:
reduce the hypertensive effect of angiotensin II
- In the absence of acetylcholine signaling, the overall tone of smooth muscle in artery walls will be reduced, reducing blood pressure
- note: If the smooth muscle in blood vessels fails to contract, then blood vessels would dilate. This would increase, not decrease, renal blood flow
- note: Transcription is not related to smooth muscle contraction!
184
substrate
that on which the enzyme acts
note: enzyme is not changed during the course of the reaction it catalyzes, and can catalyze its reaction over and over again
- Enzyme activity normally **increases** with **increased** temperature (up to a point) and **decreases** with **decreased** temperature
185
cerebellum
confers balance by coordinating the activity of various motor units
Coordination of motor skills
186
Cerebrum
triggers skeletal muscle contraction, but the cerebellum coordinates it
187
medulla
regulates many homeostatic functions
188
hippocampus
component of the limbic system
189
atmospheric pressure
air pressure on mountains is usually lower than air pressure at sea level.
(measuring barometer with mercury in a tube on mountain: Since the mercury in the dish feels less pressure from the atmosphere, it would not be pushed up as high in the tube compared to a barometer at sea level)
190
Which form of the amino acid GABA does not predominate at any pH?
uncharged form B does not predominate at any pH since the pKa of the carboxyl group is lower than the pKa of the protonated amino group, making the former group the stronger acid. The titration of GABA from acidic to basic pH would therefore result in the following changes in its protonation state:
LOOK AT IMAGE BELOW
As a result, form A predominates at pH \< 2.3, form C at 2.3 \< pH \< 9.7, and form D at pH \> 9.7.
191
protein structure
primary: the linear amino acid sequence
secondary: hydrogen bonds b/w backbone groups
tertiary: hydrophobic/hydrophilic interactions
quarternary: various bonds bw separate chains
192
gastrin
stimulates acid production, and its release is inhibited by stomach acid
- negative-feedback loop designed to maintain acid within a certain pH range
- not excreted into the stomach lumen (won't be degraded by stomach acid)
- note: hormone can't be secreted in exocrine manner
193
HCO3–/Cl– exchange
faciliated diffusion (involves movement of molecules down a gradient with the involvement of a protein)
both bicarbonate and chloride ions are moving down a gradient, making this a case of facilitated transport
194
exocytosis
does not generally involve ion transport and does not utilize membrane channels
195
Active transport
involves moving ions or other molecules against a gradient
196
simple diffusion
movement of molecules down a gradient without a protein involved
197
DNA: prokaryotes vs eukaryotes
Both eukaryotes and prokaryotes utilize DNA polymerase and helicase
- only prokaryotes use DNA gyrase to supercoil their DNA; eukaryotes wind DNA around histones through the action of other topoisomerases
198
cross between two double heterozygotes
9:3:3:1, with 9/16 of the offspring double-dominant, 3/16 dominant/recessive, 3/16 recessive/dominant, and 1/16 double-recessive (if actual ratio is close to this, then genes are not linked)
199
recombination frequency
RF = the number of recombinants divided by the total number of offspring; does not have to be 50% for the genes to be unlinked
recombination: can occur between linked genes; it just happens less frequently
200
spermatid
the sperm precursors that have completed meiosis but have not yet fully matured. A mature sperm has fully completed meiosis, and this is true of spermatids as well; it is the ova that are frozen in meiosis II until after fertilization
recombination: occurs in both oogenesis and spermatogenesis during meiotic prophase I, which the spermatid already completed
spermatid has passed through two reductive divisions in meiosis to end up with only one copy of the genome
The cell does have a nucleus. In fact, the sperm has virtually no cytoplasm, but the genome is still packaged into a nucleus
201
cap-independent translation
uses internal ribosomal entry sites (IRESs) and allows a cell to translate proteins during sub-optimal growth conditions (because less regulation is necessary).
- Since tumors typically grow quickly, they are often short of oxygen and nutrients and must deal with acidic and CO2-rich growth conditions. Activating cap-independent translation would allow the tumor cells to continue proliferating even under these less-than-optimal conditions
202
telomerase
Normal somatic cells do not express telomerase; this enzyme is only expressed in the germ line, by some white blood cells, and in some tumor cells
203
isoform
different forms of the same protein and can be due to gene duplication or alternative splicing; the ribosome has no function in splicing
204
pyruvate kinase
catalyzes the last step of glycolysis
phosphoenolpyruvate is converted to pyruvate. Because it is a kinase, pyruvate kinase transfers an inorganic phosphate from phosphoenolpyruvate to ADP to form a molecule of ATP
205
tumor
tumors can grow quite quickly and often the inside of tumors don’t have sufficient blood supply --\> lead to hypoxic conditions inside the tumor. Since glycolysis and fermentation don’t require oxygen, they could facilitate cell growth in anaerobic conditions
if a tumor cell is relying on glycolysis and fermentation instead of mitochondrial cell respiration, it will have less use for the mitochondria in general. Since the mitochondria can initiate apoptosis, less reliance on this organelle could lead to apoptosis resistance, conferring a survival advantage to the cancerous cell
206
pentose phosphate pathway
Glucose-6-phosphate (not fructose-6-phosphate) is shuttled from glycolysis to the pentose phosphate pathway
generates ribose-5-phosphate (not ribose-2-phosphate) and this allows nucleotide anabolism
207
nucleic acids
dna and rna; found in nucleus
monomer = nucleic acids
208
nucleoside vs nucleotide
side: ribose/deoxy w/ purine/pyrimidine linked to 1' carbon
tide: **phosphate** esters of nucleosides, with phosphate groups joined to ribose ring by 5' hydroxy group
209
pyrimidine vs purine
pyrimidine: 1 ring
purine: 2 rings
CUT THE PY
210
dna gyrase
prokaryotic enzyme; uses ATP to create supercoils (breaks dna and twists the two sides of the circle around each other --\> twisted circle composed of ds-dna)
how prokaryotes make single chrom more compact and sturdy!
