Biochem Flashcards
(80 cards)
1
Q
Branched Chain A.A.
A
Valine(V), Leucine(L), Isoleucine(I)
2
Q
non-superimposable
A
something cannot be put on top of another, even if it is rotated
3
Q
Isomers
A
4
Q
Enantiomers
A
5
Q
Henderson Hasselbalch Equation
A
- to determine the pH of a buffer solution
6
Q
Calculate Pka from Ka
A
lower Pka, the stronger the acid
same with Pkb
7
Q
Derive Pka from PH
A
8
Q
Determine Pka from a titration curve
A
9
Q
Action Potential
A
10
Q
Ascorbic Acid/Vitamin C
A
11
Q
Vitamin Bs
A
12
Q
Fat soluble Vitamins
A
“A DEK”
13
Q
Kinase related questions-Super High Yield
A
- What does a kinase do (transfer P from ATP to another molecule)
- Why does a kinase do this (activation of TF, inactivation, etc), where does the kinase get the P (ATP)
- Where does the kinase put the P (on a hydroxyl),
- What gets substituted out (H), what molecule does in the P binds to the target O (the P)
- Which of the following molecules or amino acids can even receive a P (must have a hydroxyl).
14
Q
“spontaneous” rxn
A
not equal to “fast”
15
Q
transferases
A
16
Q
radiolabeling of transferase
A
17
Q
Michaelis-Menten equation
A
- Triple the amount of enzyme-Vmax increases
18
Q
missense mutation
A
a different amino acid at the site
19
Q
equilibrium constant
A
20
Q
proteases
A
- enzymes that break down proteins into smaller polypeptides or amino acids.
- Hydrolysis
- Can’t break di-sulfide bonds
21
Q
Acylation
A
22
Q
Agonists and antagnoists
A
23
Q
Ternary Complexes
A
24
Q
- positive and negative feedback
- Product inhibition
A
25
Enzyme inhibition
**competitive inhibition** : **active site** occupied; less ability of substrate to bind; **thus less affinity thus higher Km**. Once it binds all is good, so **Vmax is unaffected**.
**uncompetitive inhibition.** Think of this as the inhibitor that doesn't compete. So, uncompetitive binds to the **E/S complex** instead of taking up the active site bc it’s a **slut** and only does threesomes where it takes it in the back. The inhibitor binding the E/S complex locks things in place; so, the substrate is **locked in tighter**; **more affinity; less Km**. **The substrate can't leave though bc its locked so lower Vmax**
**Noncompetitive inhibitors** are just a mix of those two types of inhibitors:
Km goes up for competitive and down for Uncompetitive? So that cancels out and **noncompetitive inhibitors do not affect Km** **(Non-Km-petitive inhibitor)**
Vmax is unaffected in competitive inhibitors, and goes down in Uncompetitive? The net direction is down so** Vmax goes down in Noncompetitive**
This should also help you remember that:
(Comp binds E;
Uncomp. binds E/S;
and NonComp can bind both, that is why you can add the effects of the previous two to understand Noncomp)
26
Mnemonics for memorizing LB plots
* Competitive looks like 2 lightsabers crossing in a fight, that’s a competition!
* Uncompetitive - It looks like the whole line got **(u-slut) shifted Up**
* Noncompetitive Inhibitors - Non-Competitive Inhibitors (Non- Km-pitive inhibitor): **Km does NOT move so X-intercept stays the same**
27
*** Turn over number kcat**
* **how fast one enzyme works at using the substrate to make the product when there is no substrate deficiency.** This is **Vmax/[E]**. This is also why the only way to increase Vmax is to increase the concentration of the enzyme.
* Michaelis-Menten equation, and assume that we're at saturating conditions (ie, [S] >> Km). In this scenario, Vmax[S]/(Km+[S]) essentially becomes Vmax[S]/[S] because Km makes a negligible contribution. The [S] terms cancel, which is why at saturating conditions, Vo = Vmax. Since *kcat is a decent surrogate for Vmax* here, what this means is that kcat tells us roughly *how well the enzyme does when there's a lot of substrate around*. In other words, the higher the kcat, the faster the reaction at high substrate concentrations.
28
**Catalytic Efficiency**
* how good the enzyme is at using a specific amount of substrate to reach the desired affects. So if you only have a specific amount of substrate, how efficiently can the enzyme use that substrate to make product.
* This is Kcat/Km, and then when enzyme concentration is constant, this is just Vmax/Km, which again shows that its trying to reach its maximum velocity with the smallest amount of substrate concentration, so the smaller Km is, the higher your catalytic efficiency will be.
29
**size exclusion chromatography**
* **larger molecule elute first** because they don't get trapped as easily as smaller molecules over pores.
30
**Circular Dichroism (CD)**
* a spectroscopic technique that measures the difference in how much **left- and right-handed circularly polarized light is absorbed by a molecule**
* Give infor about the chirality or handedness of molecular systems
31
**Hill Coefficient**
* **Hill coefficients** represent the **level of cooperativity for an enzyme.** Greater than 1 is cooperativity, less than 1 is negative cooperativity and exactly 1 is no cooperativity.
* The Hill Coefficient of 4 looks like a sigmoidal "S" shaped curve demonstrating cooperativity, which means that as more substrate binds, the affinity increases.
* Take hemoglobin for example, which can hold up to 4 O molecules. As more O binds to it, it becomes easier for more oxygen to bind.
* On the other hand, the graph for .2 looks like myoglobin, which has negative cooperativity and is stingy with its oxygen release until the muscles really need it, which is why the slope is so steep. Everything in between are just varying degrees of cooperativity.
32
**Lineweaver-Burk Plot**
* makes a heart
* For -1/km: the bigger the whole part is, the bigger km gets
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Proline
* famous for breaking alpha helices
* successful in makng a beta turn
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Glycine
* the only achiral a.a.
* disrupt alpha helices
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**phosphrylation**
Serine, Threonine, and Tyrosine.
-OH groups
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**Phosphomimetic Effect**
* Modifying a protein to mimic phosphorylation without actually adding a phosphate group.
* D & E can also be phosphorylated if there is no better target.
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**transferases**
move a chemical group from one molecule to another
38
V max proportional to [E]
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enzyme dissociation constant
Higher K_d → Lower affinity (enzyme binds substrate weakly, dissociates easily).
40
protease
an enzyme which breaks down proteins and peptides.
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Alter the shape of active site
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two competing theories regarding enzyme-substrate interaction
43
calculation isoeletric point that occur between
44
proline
* introduce kink in alpha sheets
* the same kink desirable at the end of beta sheets
45
Protein (differences between secondary and tertiary)
* secondrary-backbone of amino acids
* tertiary-interactions between atoms in the side chains
46
Hydrogen bonding
* Hold together DNA bases in a DNA double helix
* adenine (A) pairs with thymine (T) using two hydrogen bonds, while guanine (G) pairs with cytosine (C) using three hydrogen bonds.
47
**kinectic vs thermodynamics**
* kinetics deals with speed of reaction
* Thermodynamics deals with equilibrium
* **very high temperatures decrease enzymatic function as it denatures the protein.**
48
transferase
* Transferases move **functional groups from one molecule to another** (such as **kinases** that move phosphate groups onto their substrates)
* kinases and phosphorylases
49
lyase
* **break molecules into two smaller molecules** without using water or redox reactions
* ex: Pyruvate Decarboxylase
50
Isomerase
* convert a molecule from **one isomer to another** (including stereoisomers and constitutional isomers).
* changes the structure but keeps the same molecular formula
51
Oxidoreductases
***** catalyze oxidation-reduction reactions where electrons are transferred
* ex: reductases, oxidases, and dehydrogenases
52
Hydrolases
* cleavage of a molecule using **water (hydrolysis).**
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Ligases
* Ligases are used in catalysis where **two substrates are stitched together**
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IR spectra high yield functional groups
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Quaternary structure
* MCAT hints at the quaternary structure of a protein is to show that **disulfide bond cleavage splits the protein into two or more pieces on a gel.**
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Tyrosine
57
Stable backbone of proteins
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Polymerization
* the process by which nucleotides are strung together to form a single-stranded RNA strand, not the joining of two complementary strands
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Cytokine
60
**Erythrocytes** (RBC)
* Red Blood Cells-don't contain **DNA or membrane-bound nucleus**
* Major differences between WBC and RBC
61
Anomeric carbon
62
Glycolysis
*** Focus on ireversible steps**
* important things to memorize-
names of each product, when the products split from one molecule to two, when ATP is required or produced, the enzymes that catalyze irreversible steps, where glycolysis occurs (cytoplasm), when NADH is produced.
* **Goal of glycolysis: 2 ATP+2 NADH**
63
Lineweaver-Burk
* y-intercept=1/Vmax
* x intercept=-1/km
64
**Uncompetive inhibition**
* **the slope stays the same**
* K=Km/Vmax
65
Reducing SDS-PAGE
* Used to distinguish multi-subunit proteins with disulfide bonds
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Dependent Variable
* Data=what the experiment gives you as output
67
lipid fluidity
* Higher temps = more kinetic energy → more membrane fluidity/disorder
* Lower temps = tighter packing → less disorder
68
specific activity
* The enzyme units per milligram of total protein in a solution
* Used during **enzyme purification**
69
Amino Acid Hydrophobicity
* Hydrophobic = high ΔG° when moved to surface
* Charged/Polar = low or negative ΔG° on surface
70
ATP
* a nucleoside triphosphate=a nitrogenous base (adenine), a ribose sugar, and three serially bonded phosphate groups
71
Histone acetylation
* Turns genes ON
* By opening chromatin for transcription
72
PCR primer
* high GC content on both ends, ideally
73
Glycogensis
* glycogen synthase-rate limiting enzyme
* Muscle stores glycogen but the liver is the main organ which is capable of increasing circulating glucose
74
Glycogenolysis
* glycogen phosphorylase rate limiting enzyme
75
Ribose-5-phosphate (R5P)
* a sugar phosphate that plays a crucial role in nucleotide and nucleic acid synthesis.
76
pyruvate-->acetyl Co-A
* When acetyl-CoA levels are high, it signals that the body has enough fuel from fats (via β-oxidation) and doesn’t need to burn glucose
77
isocitrate dehydrogenase
* rate limiting enzyme
78
affinity for electrons
* electrons flow from low to high electron affinity
79
Ionization energy
* the energy required to remove an electron from a molecule or atom. In the electron transport chain (ETC)
* components at the beginning of the chain (like Complex I) have the lowest electron affinity, so they give up electrons easily.
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