Biochem 1 Flashcards

Question

What important thing should you remember about **ZWITTERIONS?** *HINT: WHAT IS THE CONNECTION B/T **ZWITTERIONS**, **AA'S** AND **pH**?*

Answer 1

***ALL** of the amino acids exist as* * Zwitterions **at a pH of 7.4*** * With the **EXCEPTION** of amino acids that have charged –R groups **(Asp, Glu, Lys, Arg, His)** This can be very **confusing** because textbooks **NEVER** draw them this way! * Most texts draw them in their “non-ionized” form * with –COO**H** and –NH**2** groups _That combination **DOES NOT EXIST!**_ at **physiological** pH ...or at **ANY** pH! _**Below** a pH of about **9** the **amine** group will get protonated:_ * **-NH₃⁺** _**Above** a pH of **9** the amine group will be **–NH₂**_ * ****(as is shown in most texts) * ...But at that **very high pH** **(\>9)** the carboxyl group will have **LONG AGO** been **deprotonated!*** * would be ***-COO^-*** at a **pH ~ 2**

Answer 2

equilib b/t a keto form (a ketone or an aldehyde) and an enol (alcohol). Enol and Keto are tautomers of e/o.

Answer 3

a **DIPOLAR** ***VERSION*** of an AA * wherein positively and negatively charged R groups **CANCEL EACH OTHER OUT!** * Results in a **NEUTRAL** ion _Example_: * Isoleucine

Answer 4

* D – and L- amino acids are **MIRROR IMAGES** of one another* * but they are **NOT IDENTICAL** compounds* Think of your left and right hands * They are mirror images * but you **cannot** superimpose one upon the other * because they are **arranged** in a fundamentally different way ***L – amino acids*** ***are predominant** in nature* *Although a few D – amino acids are used by some bacteria*

Answer 5

* Depends on: * the complementary charges on R groups ***and/or*** * hydro**phil**/**phob**icity of the R groups

Answer 6

1) Monosaccharides (CH2)n.2) Disaccharides Cn(H2O)x.

Answer 7

monosaccharides + disaccharides=polysaccharides

Answer 8

1) H-bonding. 2) DSB's. 3) Hydrophobic/philic interxns. 4) Ionic interxns. 5) VDWs. 6) Proline turns.

Answer 9

H-bonding b/t ALL carbonyl O's and the amide H's in the adjacent row. R groups are perpendicular to the plane of the beta sheet, on both sides.Beta sheets have PLEATED conformation. THis lines carboxyl & amide regions up so that each residue is participating in 2 H bonds.

Answer 10

enzyme to substrate is an EXACT FIT (not favored by scientists)

Answer 11

Inhibitor binds COVALENTLY to enzyme and/or the active site, disabling the enzyme for either a long time or permanently

Answer 12

measure of an enzyme affinity for its substrate. Km=[S] at 1/2 Vmax

Answer 13

v=Vmax[S]/(Km+[S]). Shows relationship b/t rxn velocity, Km, and [S].

Answer 14

it means the molecule has a (+) pI value

Answer 15

=a protein that is associated with its cofactors, either covalently or via IMFs. Ex: Hb (which has its NP Heme group). If its a conjugated protein thats an enzyme, its called a "holoenzyme"

Answer 16

***branched**, **α-linked** ("alpha-site" side)* * glucose polymer* * used for **energy storage** in **PLANTS**

Answer 17

* Transition from solvation of **NONPOLAR** regions to* * solvation of **POLAR** or **CHARGED** globular protein* * surfaces results in **INCREASED** entropy* * Even when water interacts with a dissolved **polar** solute, this interaction is **less** entropically favorable that those same water molecules interacting with only other water molecules * However, the driving thermodynamic force that favors protein folding results from the fact that **non-polar** regions require a much **GREATER** ordering of water molecules to accomplish solvation * Therefore, transitioning from solvation of **non-polar** regions to solvation of a **mostly polar** or **charged** globular protein surface represents a net **increase** in entropy* * In fact, it is enough to **overcome** the decreased **entropy** associated with the protein being in a folded rather than an unfolded state This **favorable** **increase** in entropy is a major contributor to the **overall conformational stability** of the folded protein

Answer 18

**2 acidic protons** **-COOH and -NH₃⁺** * 7 AA's have **acidic R groups** * So they have **3** acidic protons in **total**

Answer 19

***Ph group** added to a molecule* * by a **KINASE** (Which is a type of *TRANSFERASE)*

Answer 20

are interactions **between CHARGED R GROUPS** _Functions_: 1. Encourage the **ACT** of folding 2. **STABILIZE** the protein once it **IS** folded

Answer 21

**INTRA**molecular Nucleophilic substitution ## Footnote (*aka is all happening within the same ring-containing molecule)* Here, the **-OH** group * (of the chiral C that is **FURTHEST** from the **carbonyl** C) * acts as a **NUCLEOPHILE--** * Attacking the (*ELECTROPHILIC)* **carbonyl C** * Carbonyl Oxygen is then **protonated** to form a ^-**OH** group

Answer 22

1) Heat. 2) Acid. 3) Urea. 4) Mercaptoethanol.

Answer 23

***branched, α-linked** (α 1,4/1,6)* ***glucose polymer*** used for **energy storage** in **ANIMALS** **_vs. Starch:_** * Both used for energy storage * Starch is found in **PLANTS**, though * Both have **same (α 1,4/1,6)** linkages * Starch is 80% amylopectin (branched) and 20% amylose (**UN**branched) *Glycogen is **100%** amylopectin, thus is **MORE BRANCHED THAN STARCH!***

Answer 24

Hemiketal (R,R,OH,OR). Hemiacetal (R,H,OR,OH)

Answer 25

1) Actin [thin filaments, microfilaments]. 2) Tubulin [MT's]. 3) Keratin [IMFs]. 4) Elastin [collective tissue, ECM].

Answer 26

* all ***native*** AAs are ***L*** * L,D NOT directly correlated with R,S * Should be considered **separate** * Most L AAs are S * but some are R * e.g. cysteine

Answer 27

Inhibitor binds AWAY from active site and ∆es shape of the enzyme. Inhibitor has equal affinity for both the ES complex and the enzyme. Vmax=DECREASES. Km=NO ∆.

Answer 28

x-intercept= - 1/Km

Answer 29

An ***alpha-C stereocenter:*** * all AAs (except for **GLYCINE** ) are **CHIRAL** at the α-carbon _4 ***DIFFERENT*** substituents:_ 1. R group 2. an H 3. a COOH 4. an NH₂

Answer 30

is a layer of H2O that surrounds a dissolved protein. H2O's in the layer interact with w/o and with protein's surface.

Answer 31

covalent bond b/t the Sulfurs (or Seleniums) of 2 Cysteine residues.

Answer 32

L sugars do NOT occur naturally in humans

Answer 33

ß-linked glucose polymer, used for energy storage in plants (like starch), is INDIGESTIBLE to animals w/o some form of symbiotic bacteria

Answer 34

*A Fischer projection is a representation of a **3D** molecule drawn in **2D**s* * A **tetrahedral** carbon is represented as **two** crossed lines * and the groups attached to **that** carbon are displayed * _The **HORIZONTAL** line_ * is extending “**OUT**” of the paper * **Toward** you * _The **VERTICAL** line_ * is **BEHIND** the plane of the paper * **Away** from you Because of this, Fischer projections ***CAN*** be rotated ***180*°** *but **not** 90° or 270°* _180° rotation just **flips** the molecule over:_ * the **same** **R groups** are extending forward or backward _But if you rotate the molecule just **90°** in_ _**either** **direction:**_ * you have **CHANGED which R groups** are *above or below the plane of the paper* .*..which **changes** the **stereochemistry** of the molecule*

Answer 35

**Either L or D** * depending *on which side the **NH₂ group** is located in a Fischer Projection* * L=on the **left** * D=on the **right**

Answer 36

to the equivalence point. Both are in the middle of their respective titration curves.

Answer 37

They're ENANTIOMERS (same molecule, different stereochemistry at last chiral C). In Fischer projections, the furthest -OH group from the carbonyl is to the LEFT for L, to the RIGHT for D

Answer 38

are an inactive enzyme precursor. Useful b/c they can get activated quickly if needed, but are deadly if left on 24/7. Ex: Prothrombin (in blood coagulation).

Answer 39

an AA that your body cannot synthesize. Must be ingested.

Answer 40

BOTH increase rate by lowering Ea. Enzymes are ORGANIC molecules, but catalysts CAN be inorganic. Neither are consumed during a rxn; both can be used & recycled again and again. Enzymes are HIGHLY specific, while catalysts CAN be universal"All enzymes are catalysts, but not all catalysts are enzymes"

Answer 41

Folding of alpha helices, Beta sheets, & other things to form a "functional" globular or structural protein.

Answer 42

aka "salt bridges." Charge to charge interactions b/t a positive (+) AA and a negative (-) AA

Answer 43

**CHYMOTRYPSIN** Cleaves proteins on the **CARBOXYL** side of: * Phenylalanine * Tryptophan * Tyrosine

Answer 44

association of multiple folded proteins into a multi-subunit complex. classic example: Hb has 4 subunits, exhibits (+) cooperativity

Answer 45

class of simple sugars whose molecules contain 6 C atoms. Ex: glucose and fructose

Answer 46

used to calculate Vmax and Km experimentally, and used to identify enzyme inhibition

Answer 47

* Oligopeptide= **VERY SMALL** chain of AAs * Polypeptide= **LONGER** chain of AAs

Answer 48

1) What AAs are present? 2) what is the chemistry of their R groups?

Answer 49

***when a molecule has 0 net charge*** At its isoelectric point, a molecule is in its **ZWITTERIONIC FORM** *(Charges are all canceling each other out)*

Answer 50

1. Oxireductases 2. Transferases 3. Hydrolases 4. Isomerases 5. Lyases 6. Ligases

Answer 51

**_Myosins_** * Found in muscle cells *(Thick portion of sarcolemma)* * Power stroke, cellular transport **_Kinesins_** * **Move along MICROTUBULES** * ****from **+** end to the **-** end * or from **center** of cell to **periphery** **_Dyneins_** * **Move along MICROTUBULES** * From the - end to **+** end * or from **periphery** to **center** of the cell

Answer 52

all human body sugars D-sugars

Answer 53

They're **EPIMERS** **(more broadly, Diastereomers)** * Only differ at 1 chiral center (and it **isnt** the anomeric carbon-- in that case, they'd be **anomers**)* * Are **different** molecules, so they have **different** names!

Answer 54

**"-ose"** ending given to **ALL** **SUGARS** **"deoxy-"** prefix is used if normal location of an -OH group is **REPLACED BY A H**

Answer 55

**pI_acidic=** **AVERAGE** of pK_a of **ACIDIC** R group + pK_a of **CARBOXYL** group

Answer 56

are REDOX rxns (O and H are gained or lost)

Answer 57

a translated protein assumes 2º structure almost instantly, then folds into its globular or structural 3º state

Answer 58

Mono. & Disac. are linked through Oxygen on the same side as (ie, is cis to) the CH2OH group

Answer 59

***GLYCINE & CYSTEINE*** ## Footnote To answer this question, first we need to **define** what L, D, R, and S are **_L and D_** * For amino acids, L and D refer to the **glyceraldehyde** molecule that the amino acid could **theoretically** be **synthesized from** * *****D-glyceraldehyde or L-glyceraldehyde* **_R and S_** * R and S refer to the **absolute stereochemistry** of the molecule * To designate a molecule as R or S, you must rank each R group of a chiral carbon for priority * For almost all the amino acids, the **L** designation and the **S** designation occur **together** * This makes sense, because if they all could theoretically derive from the **same** glyceraldehyde molecule * they would all end up with the **same** stereochemical orientation * Two amino acids, however, differ from this rule **_Glycine_** The tetrahedral carbon of glycine is **not** a chiral center * because it has **TWO** hydrogens attached * ∴ does **NOT** have four **DIFFERENT** R groups Because it does **NOT** have a chiral center, glycine **CANNOT** be designated as **EITHER R or S** **_Cysteine_** Since cysteine has a **SULFUR** at the **second** position in its side chain, * the **side chain** has a **HIGHER** **RANKING** than the **other** side chains (when considering whether to designate it as R or S) * due to cysteine’s **HIGHER** atomic **mass*** * This means that **L –** cysteine will be **R –** cysteine * ...Because the **SULFUR** has **changed** **the direction** the priorities of the R groups turn*

Answer 60

molecule that is acted upon by an enzyme (or, is converted to product BY the enzyme)

Answer 61

dehydration synthesis and acyl substitution. amine group N (Nu:) from the NEW AA attacks the carboxyl C (E:) on the C-terminus of the growing peptide chain (aided by enzymatic function of the ribosome).

Answer 62

Non-protein species that ARE (!!) permanently attached to the enzyme and are req'd for the protein to function.

Answer 63

**It determines an AA's...** 1. Chemistry & 2. Folding pattern

Answer 64

enzymes whose activity is influences by the reversible, NON-covalent binding of ANOTHER molecule

Answer 65

disrupt 2º or contribute to 3º structure

Answer 66

AB A+B. (Cleavage/synthesis, NO H2O, NOT hydrolysis).

Answer 67

Hydrophobic R groups fold into the interior of a globular protein in order to escape H2O. Often bring other smaller POLAR groups with them, which interact in a complementary way to further stabilize protein folding.

Answer 68

graph of velocity vs [S]. Reveals connection b/t 1/2 Vmax and Km

Answer 69

part of an enzyme where substrate is converted to product

Answer 70

Pyranose is a 6-membered ring, Furanose is 5-membered

Answer 71

maltose=glucose+glucose

Answer 72

includes alpha helices, Beta sheets.

Answer 73

Hydrophobic R groups fold INTO the protein core.Hydrophilic R groups are more common on surface of the protein.

Answer 74

1) Fatty Acids. 2) Triaglyerols (aka triaglycerides). 3) Phospholipids. 4) Steroids. 5) Terpenes (Terpenoids). 6) Sphingolipids. 7) Waxes. 8) Prostaglandins.

Answer 75

1) in soluble proteins, hydrophobic AAs collapse into protein core. 2) In membrane proteins, hydrophilic membranes will either be outside the membrane in the cytoplasm or inside the core of the protein, away from the membrane bilayer, with hydrophobic AAs located w/in the membrane bilayer

Answer 76

Fat soluble=A,D,E,K. Water soluble=all the rest.

Answer 77

COOH with a long hydrocarbon chain

Answer 78

stabilize transition state and lower Ea

Answer 79

=average of pKa amine group + pKa carboxyl group

Answer 80

Positive feedback is where the product of a rxn acts as an AGONIST for one of the enzymes earlier in the chain

Answer 81

Volume is inversely related to the radius^3

Answer 82

1) alpha COOH group, pKa~2. 2) -R group, ACIDIC. pKa~4. 3) -R group, His. pKa~6. 4) alpha NH3+ group. pKa~9.5) -R group, BASIC. pKa~11-12.

Answer 83

sucrose=glucose+fructose

Answer 84

**AA sequence**

Answer 85

Non-protein species that are NOT permanently attached to the enzyme, but ARE req'd for the protein to function. ex: NAD+

Answer 86

_Is usually the **FIRST** residue at the **VERY** **END** of an α-helix_ * ...but is rarely found **inside** the helix* * (because it induces a **KINK/TURN**)* _Found at the **END** of **β sheets**_ * where **"TURNING"** happens *because of it*

Answer 87

as substrate binds, affinity for substrate increases. This is an example of Positive (+) Cooperativity.

Answer 88

globule=fully folded. Premolten=just starting to unfold. Molten (aka denatured)=fully UNfolded

Answer 89

=Biological catalysts

Answer 90

addition or synthesis of LARGE molecules. Usually ATP-dependent. Ex: DNA ligase

Answer 91

**REARRANGEMENTS** _Examples:_ * Phosphoglucose isomerase * Epimerases

Answer 92

oxidized cysteine residues form a DSB. This is the STRONGEST TYPE OF FOLDING INTERACTION!

Answer 93

are small, organic molecules that are essential nutrients req'd in SMALL amts for proper metabolism

Answer 94

are a double-inverse graph of the rxn rate (v inverted to 1/v) and substrate concentration ([S] inverted to 1/[S])

Answer 95

trypsin & chymotrypsin cleave proteins on the CARBOXYL side.

Answer 96

b/t of proline's bulky, cyclical shape, putting a Pro in an alpha helix or Beta sheet causes KINKS. Proline can aid in Beta turns

Answer 97

1) Hemoglobin (Hb). 2) Calmodulin. 3) Troponin. 4) Tropomyosin. 5) Histones. 6) Transcription factors (TFs). 7) Cell Adhesion molecules.

Answer 98

(JUST LIKE ELECTROSTATIC INTERXNS,) H-bonding are b/t charged R groups and both 1) encourage folding and 2) stabilize the protein once folded.

Answer 99

_A **MIXED INHIBITOR** has **UNequal** affinity_ ***Favors** either **ES \> E** (or vice versa)* _Effect on V_max_ * V_max **_DECREASES_** **NO MATTER WHAT** it favors _Effect on K_m_ * If favors _**ES** over E_ K_m **DECREASES** * If favors _**E** over ES_ K_m **INCREASES**

Answer 100

inhibitor binds ONLY with ES complex. Vmax=DECREASES. Km=DECREASES.

Answer 101

They're anomers. (Same molecule, different stereochem at anomeric carbon). \*\*Since they're the same molecule, they're still both called glucose\*\*

Answer 102

If phosphorylation (by a kinase) activates it, de-phosphorylation (by a phosphatase) deactivates it, and vice-versa

Answer 103

as substrate begins binding to product, conformational changes occur, so that final shape and characteristics of active site arent "final" until substrate is completely bound

Answer 104

monosaccharides & disaccharides linked through an Oxygen that is on the OPPOSITE side of the plane from the CH2OH group (ie, is trans)

Answer 105

**_Absolute Configuration:_** **All** amino acids are designated as either **L**- or **D**- * depending on the side on which the **AMINE GROUP (!!)** is located in a Fischer Projection * (**L** = Left; **D** = Right) * **ALL** **NATIVE** human amino acids are **L-**amino acids

Answer 106

an AA that your body CAN synthesize on its own.

Answer 107

IMFs that repel atoms away from e/o (due to steric hindrance)

Answer 108

**Hydrolysis**

Answer 109

R/S≠D/L!!

Answer 110

Kinesins move along MTs from the (+) to the (-) end, or from center of cell to periphery or nerve cell body towards the dendrite. Dyneins are the exact opposite.

Answer 111

Inhibitor is not permanently bound & enzyme is not permanently disabled

Answer 112

Resonance b/t π bonds of C=O bond and N's lone pair. The C-N bond yields 2 reso scrutcs for any peptide bond. BOTH the C=O bond and the C-N bond in a peptide have double bond character.

Answer 113

Have a glycerol backbone with 3 FA's attached via ESTER linkages. 2 types are saturated and unsaturated

Answer 114

A type of **TRANSFERASE** that **transfers an R group** (In this case, a phosphate)

Answer 115

the **ISOELECTRIC POINT, pI** ## Footnote * Think about it!* * Zwitterions are variations that have **NO** formal charge, therefore they are **AT** their isoelectric point*

Answer 116

**D** ## Footnote * The oligopeptide which is **least** likely to require a protein carrier for transport in the blood will be composed of **hydrophilic**, or **polar** amino acids * Thus, we are looking for an answer choice with **two polar amino acids** Answer D is **correct**, both **histidine** and **glutamine** are **polar** charged amino acids * Answer A is incorrect, tryptophan is a large nonpolar amino acid * Answer B is incorrect, tyrosine is a large nonpolar amino acid * Answer C is incorrect, phenylalanine is a large nonpolar amino acid

Answer 117

* The structural difference between aspartic acid and glutamic acid is the fact that glutamic acids sidechain carboxylic acid group is **ONE** carbon **FURTHER AWAY** from the amino acid backbone * The amino acid backbone contains **electronegative** groups * which are capable of **withdrawing** electron density from the sidechain carboxylic acid groups * A greater degree of induction results in a more **stable** conjugate base (better charge distribution, more stable molecule) ## Footnote *Because inductive effects **decrease** with distance from the electronegative element, **glutamic acid experiences less charge induction** than aspartic acid*

Answer 118

Anti-oxidants inhibit the oxidation of other molecules **by being oxidized THEMSELVES** * This means they should have a **lower** reduction potential * *...than a similar molecule that is **not** an antioxidant*

Answer 119

**TRIGLYCER**_OLS_**** aka "**TRIAGLYCER**_IDES_**"** * **Glycerol** backbone (HOCH₂CHOHCH₂OH) with three **fatty acids** attached via **ester** linkages _2 FORMS:_ 1. Saturated FAs 2. Unsaturated FAs

Answer 120

*a **lipid** containing a **phosphate** group in its molecule*

Answer 121

_MOST COMMON TYPE:_ **_PHOSPHA_*TIDS*** _Consists of:_ 1. **2 FATTY ACID** sections 2. A **PHOSPHATE** group * ...which is attached directly to the **glycerol** backbone

Answer 122

* Most phospholipids in biological membranes* * have **_OTHER_ FUNCTIONAL GROUPS** attached* * to the phosphate head* _Example of this: **Phosphatids** (most common type of Phospholipids), which consist of:_ 1. **2 FATTY ACID** sections 2. A **PHOSPHATE** group * *...which is attached directly to the **glycerol (R GROUP!)** backbone*

Answer 123

All steroids have **4** carbon rings!! * three **six**-membered * one **five**-membered ring

Answer 124

All steroids have **4** carbon rings!! * three **six**-membered * one **five**-membered ring

Answer 125

Terpenes are made from: ***ISOPRENE*** units _The only difference between terpenes and terpenoids:_ Terp**enes** are **hydrocarbons** *****THINK: TerpENES are made up of alkENES* Terpen**OIDS** contain **additional R groups**

Answer 126

*are a class of lipids containing a backbone of **SPHINGOSINE bases***

Answer 127

_Waxes are **ESTERS** of:_ 1. **Fatty Acids** 2. *Long-chain monohydric* **ALCOHOLS** ("**Mono**hydric" =****have one **hydroxyl** group)

Answer 128

are **LIPIDS** with a **CARBOHYDRATE** attached

Answer 129

* Are lipid **MEDIATORS** that:* * have **AUTO**crine and **PARA**crine functions* * throughout the body* Prostaglandins are like **LOCAL** Hormones! _**UNLIKE** hormones:_ **1) PRODUCED** and **RELEASED** (by tissues) **THROUGHOUT** the body! *....not **_JUST_** in specialized glands (like hormones)* **_2) ACT_:** **LOCALLY!** * ...rather than traveling* *via the bloodstream* * to a **distant** target*

Answer 130

**pI_basic** = _**AVERAGE** of_ pK_a**-****AMINE** group **+** pK_a**-BASIC** R group

Biochem 1 Flashcards

(163 cards)