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Flashcards in Biochem 1 Deck (163):
1

Estimating pI:

  • pIbasic=? 

pIbasic =

AVERAGE of pK-AMINE group

+

pK-BASIC R group

1

Major (non-enzymatic) protein functions

  • Recognizing proteins:

ANY PROTEIN in a cell must have been ___ for by ___

Ultimately, all proteins are ___ products

  • Must have been coded for by DNA

 

Ultimately, ALL PROTEINS ARE 
GENE PRODUCTS

2

Carbohydrates

  • Common disaccharides
    • Lactose= ___+___?

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LACTOSE=

galactose + glucose (ß-linked)

3

Protein Folding

  • Hydrophobic surface:

The majority of the R groups on the surface of a globular protein are either ___ or ___ed

either POLAR or CHARGED

3

Vitamins & Minerals

  • Define "MINERALS"
    • What are 3 things theyre used for?
    • How do you GAIN them?
    • Are needed in Big/Small quantities?

​MINERALS

Are inorganic elements or compounds

  • Are necessary for:
    • Bone formation
    • ion gradients
    • O2 transport, etc.

They are gained through:  DIET

  • Are needed in very small quantities

which makes them "macronutrients"

5

Substrate-Enzyme specificity

  • The Enzyme-substrate (ES) complex is formed when?
    • Show what the rxn looks like

is formed when substrate is bound to active site

E+S ⇔ES ⇔ EP ⇔ E+P

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6

Protein Folding

  • How do Salt Bridges form?

Formed when acidic & basic R groups undergo a NEUTRALIZATION rxn

  • resulting in a salt

7

AA Rxns

  • Protein hydrolysis
    • TRYPSIN cleaves on the ____ side of WHAT AA's?

Cleaves proteins on the CARBOXYL side of:

  • Arginine  and Lysine

8

What effect do ENZYMES ("Catalysts") have on:

  • Keq
  • Yield
  • % yield

NONE!!

9

Enzyme classification by reaction type

  • Hydrolases do what kind of rxn?

Hydrolysis

9

Enzyme Inhibition

  • Reversible Inhibition
    • MIXED INHIBITORS do what?
      • Effect on Vmax or Km

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A MIXED INHIBITOR has UNequal affinity

Favors either ES > E (or vice versa)

Effect on Vmax

  • Vmax DECREASES NO MATTER WHAT it favors

Effect on Km

  • If favors ES over E

Km DECREASES

  • If favors E over ES

Km INCREASES

9

LIPIDS are:

"Hydro_____ __________s"

"Hydrophobic Biomolecules"

10

Carbohydrates

  • List the "8 Common Monosaccharides" 

  1. glyceraldehyde
  2. dihydroxyacetone
  3. ribose
  4. deoxyribose
  5. glucose
  6. fructose
  7. galactose
  8. mannose

11

Enzyme classification by rxn type

  • What kind of reactions do ISOMERASES participate in?
    • Describe & give examples

REARRANGEMENTS

Examples:

  • Phosphoglucose isomerase
  • Epimerases

11

Enzyme Inhibition

  • Feedback Inhibition

NEGATIVE FEEDBACK

  • is what kind of inhibition?
  • What does it do?
  • What 3 things will you see it in?

​NEGATIVE FEEDBACK

A specific type of non-competitive or

allosteric inhibition 

  • In it, one of the PRODUCTS of the reaction LATER in the chain
    • ...acts as an INHIBITOR for one of the enzymes EARLIER in the chain

Seen in:

  1. Multi-step reactions
  2. Synthetic pathways
    • e.g., GLYCOLYSIS
  3. Cascades

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12

Major (non-enzymatic) protein functions

Immune system

  • Name the 2 (GENERAL) types of proteins

AntiGENS & AntiBODIES

13

3º Protein structure 

6 INTERACTIONS B/T AA's that contribute to 3º structure

  • H-bonding
    • Are ___-_____ bonds between WHAT 2 THINGS?
       

​NON-COVALENT bond between either:

  1. Backbone atoms
    • N-H or
    • C=O
  2. Side chains
    • Amine groups
    • Carboxyl groups
    • Alcohol groups, etc.

14

Protein structure

  • Where will you usually find PROLINE in α-helices and β-sheets?
    • WHY?

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

14

Enzyme Inhibition/Reversible Inhibition/Competitive inhibition does what? Effect on Vmax and Km

inhibitor binds AT the active site, and inhibitor resembles substrate in shape. Can be overcome by [S]. Vmax=NO ∆. Km=INCREASES.

15

PEPTIDES are

WRITTEN, READ, & SYNTHESIZED

from the ___ to ___ terminus

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N to C

16

Protein structure:

  • 1º Structure consists of solely...?

AA sequence

16

Enzyme Inhibition/Feedback Inhibition/ Positive feedback=?

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

16

Lipids/Triaglycerols/ Saturated vs Unsaturated. Compare. Which is healthier? Why?

Saturated=no DBs, solid @ RT, Higher MPs. Unsaturated=at least 1 DB, liquid @ RT, Lower MPs). Unsaturated is healthier b/c they generate fewer calories when metabolized.

17

Mechanisms of Catalysis

  • What are COFACTORS?
    • What 2 things qualify as Cofactors?

General term for any species that is:

  • required by an enzyme to function

Coenzymes and Prosthetic groups are both cofactors

18

Draw a mechanism for:

SULFUR LINKAGE OF TWO CYSTEINES

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19

Enzyme classification by rxn type

  • What kind of reactions do TRANSFERASES participate in?
    • Describe and give an example

transfer of an R group

Example: Kinases, aminotransferases

20

Protein Separation Techniques/Electrophoresis: describe the experiment.

Used to separate by size. Proteins denatured by SDS, are given a uniform (-) charge. Gives protein uniform q/m ratio. Bigger proteins are found at the top of the gel, and smaller proteins move further towards the bottom.

20

Carbohydrates/Carbohydrate Rxns/ Hydrolysis of Glycoside linkage

Polymer (n) + H2O-->Polymer (n-1)+monomer

22

When pH is near the pKa of one of the acidic protons, the AA acts as what?

a buffer

22

Michaelis-Menten Kinetics/Lineweaver-Burke Plots/y-intercept=?

y-intercept= 1/Vmax

23

Protein structure/2º/alpha sheets: H-bonding b/t ___ and ___ that are exactly ___ residues apart. What else is involved in H bonding? Where are R groups directed?

b/t carbonyl O's and amide H's that are exactly 4 residues apart. ONLY every 4th residue is involved in H bonding.R groups directed towards outside of cynlinder.

24

Mechanisms of Catalysis/Simple proteins. If an enzyme is a simple protein, what can it also be called?

are proteins that contains only AAs and NO non-protein cofactors or prosthetic groups. If a simple protein is an enzyme, it's called an "apoenzyme"

25

What important thing should you remember about ZWITTERIONS?

 

HINT: WHAT IS THE CONNECTION B/T ZWITTERIONS, AA'S AND pH?

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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 –COOH and –NH2 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

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26

Protein structure/3º/6 binding forces/Hydrophobic or hydrophilic interxns: Where will hydrophobic/philic AAs be in soluble proteins and membrane proteins?

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

26

Protein Folding/Proline Turns: either considered to ___ _º or ___ to _º structure.

disrupt 2º or contribute to 3º structure

26

Substrate-Enzyme specificity/substrate=?

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

26

Michaelis-Menten Kinetics/Lineweaver-Burke Plots/Applications (2)

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

26

Carbohydrates/Carbohydrate Rxns/ Keto-enol tautomerization is an equilibrium b/t what two things? What are tautomers of e/o?

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

27

What is a ZWITTERION?

  • Give an example

a DIPOLAR VERSION of an AA

  • wherein positively and negatively charged R groups CANCEL EACH OTHER OUT!
  • Results in a NEUTRAL ion

Example:

  •  Isoleucine

28

Draw a Fischer projection of the amino acid alanine in both its L- and D- forms

Which of the two forms is predominant in nature?

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

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29

Draw a mechanism for:

HYDROLYSIS OF A PEPTIDE BOND BETWEEN GLYCINE AND ALANINE

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30

How can you tell if a substrate will bind in an active site?

  • Depends on:
    • the complementary charges on R groups and/or
    • hydrophil/phobicity of the R groups

31

Carbohydrates/what are the 2 types? What MFs to they have?

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

32

Carbohydrates/Carbohydrate Rxns/ Polymerization: ___+___=?

monosaccharides + disaccharides=polysaccharides

33

Protein structure/3º: List the 6 molecular interactions that contribute to 3º structure?

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

34

Protein structure/2º/Beta sheets: H-bonding b/t what? Where are the R groups located? What shape do beta sheets have? What does this serve?

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.

35

Two theories of enzyme specificity/Lock & Key model

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

36

Enzyme Inhibition/Irreversible Inhibition: how does the inhibitor bind? What effect does this have?

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

37

Michaelis-Menten Kinetics/MM constant (Km)= relative measure of what? What is Km equal to?

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

38

Michaelis-Menten Kinetics/MM equation=? Shows relationship b/t?

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

39

What does it mean when pH is lower than pI?

it means the molecule has a (+) pI value

40

Mechanisms of Catalysis/Conjugated proteins. Define & give an example. If an enzyme is a conjugated protein, what is it called?

=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"

41

Carbohydrates

Glucose Polysaccharides

  • What is STARCH?
    • ​What is it found in, and what is it used for?

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branchedα-linked ("alpha-site" side)

glucose polymer

 

  • used for energy storage in PLANTS

42

Protein Folding

  • Entropy & Protein Folding:

Transition from solvation of ___-_____regions to solvation of ___ or ___ed globular protein surface results _______ed ENTROPY

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

43

  • Each AA has a minimum of __ acidic protons, which are?
    • Do ALL AAs have this many?

2 acidic protons

-COOH and -NH3+

  • 7 AA's have acidic R groups
    • So they have 3 acidic protons in total

44

Feedback Inhibition

  • Phosphorylation:
    • ....Is the addition of what?
    • What puts it there?

Ph group added to a molecule

  • by a KINASE (Which is a type of TRANSFERASE)

45

Draw a mechanism for:

STRECKER SYNTHESIS OF ALANINE

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46

Protein Folding

  • Electrostatic Interxns:
    • Are interactions between WHAT?
    • What 2 things do these interactions do?

are interactions between CHARGED R GROUPS

Functions

  1. Encourage the ACT of folding
  2. STABILIZE the protein once it IS folded

47

Carbohydrate Rxns

  • What happens during "RING CLOSING?"

INTRAmolecular Nucleophilic substitution

(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

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48

Protein Folding/ Protein denaturing: name the 4 protein denaturing agents.

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

49

Carbohydrates

Glucose Polysaccharides

  • Describe GLYCOGEN
    • What organisms use it, and what for?
    • How does it compare to STARCH?

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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 (UNbranched)

Glycogen is 100% amylopectin, thus is MORE BRANCHED THAN STARCH!

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50

Amino Acid Reactions

  • Protein Hydrolysis
    • CHYMOTRYPSIN
      • cleaves WHAT side
      • ...of WHAT AA's?

CHYMOTRYPSIN

Cleaves proteins on the CARBOXYL side of:

  • Phenylalanine
  • Tryptophan
  • Tyrosine

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50

Protein structure/3º:

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

50

Carbohydrates/Cyclic Structure & Conformation of hexoses/Hemiacetals vs Hemiketals

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

51

Major (non-enzymatic) protein functions/Structural Proteins: Name the 4 kinds, and what they are found.

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

52

  • All native AAs are L or D?
  • Are L,D and R,S the same?

  • 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

53

Enzyme Inhibition/Reversible Inhibition/Non-competitive inhibition does what? Effect on Vmax and Km

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 ∆.

54

Michaelis-Menten Kinetics/Lineweaver-Burke Plots/x-intercept=?

x-intercept= - 1/Km

55

WRT STEREOCHEMISTRY, what do all AAs (except for ____) have in common?

  • What 4 different substituents does each AA have?

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

56

Protein Folding/ Solvation Layer: what is it and what interacts with what?

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

57

Protein structure/3º/6 binding forces/DSB's

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

58

Carbohydrates/Stereochemistry/L-sugars

L sugars do NOT occur naturally in humans

59

Carbohydrates/Carbohydrate Rxns/ Polymerization/Glucose Polysaccharides/Cellulose

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

60

Describe FISCHER PROJECTIONS:

  • What do the horizontal & vertical lines represent?
  • Fischer Projections CAN be rotated ___°, but CAN'T be rotated ___° or ___°

EXPLAIN WHY YOU CAN'T ROTATE THE MOLECULE IN CERTAIN WAYS 

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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

61

Absolute configuration

  • All AAs are what?
    • What determines this?

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

62

Isoelectric point is similar to the ___ ___ in acid-base titration. Why?

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

63

Carbohydrates/Stereochemistry/How are D-galactose and L-galactose related? What do the D and L represent?

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

64

Enzyme Inhibition/Feedback Inhibition/ Zymogens are what? Why are they useful? What is an example?

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).

65

What is an essential AA?

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

66

What's the difference b/t an enzyme and a catalyst?

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"

68

Protein structure/3º/6 binding forces/Ionic interxns

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

70

Protein structure/4º definition & example

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

71

Carbohydrates/Cyclic Structure & Conformation of hexoses/ what are hexoses? GGive 2 examples

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

73

  • Oligopeptide=?
  • Polypeptide=?

How do they relate to each other when it comes to LENGTH?

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

74

When you see "protein" or "enzyme," think: (2)

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

75

What is the isoelectric point? (pI)

  • If a molecule is AT its isoelectric point, it must be in its ________ic form

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)

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76

Enzyme classification by REACTION TYPE

  • List the 6 types of enzymes

MNEMONIC: "OVER THE HILL"

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

77

  • Major (non-enzymatic) protein functions

MOTOR PROTEINS

  • Name the 3 kinds
    • Where are they found?
    • What do they do?

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

78

Carbohydrates/Stereochemistry/D-sugars

all human body sugars D-sugars

79

Carbohydrates

  • Stereochemistry
    • How are glucose and galactose related?
      • Why are their names different?

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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!

80

Carbohydrates

Nomenclature & classification

  • What suffix is given to all SUGARS?
  • What prefix is used if the normal location of an OH group is replaced by a H?

"-ose" ending given to ALL SUGARS

"deoxy-" prefix is used if normal location of an -OH group is REPLACED BY A H

81

Estimating pI

  • pIacidic=?

pIacidic=

AVERAGE of pKa of ACIDIC R group

+

pKa of CARBOXYL group

82

Enzyme classification by rxn type/Oxireductases

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

83

Protein Folding: a _____ed protein assumes ___ structure almost instantly, and then folds into its ___ or ___ _º state

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

84

Carbohydrates/Carbohydrate Rxns/ Polymerization/Beta Linkage

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

85

Proteins

Absolute Configuration

  • While it is TRUE that L- and D- do NOT correlate DIRECTLY with R and S, among all 20 of the common amino acids...

there are ONLY TWO CASES in which an amino acid CANNOT be said to be BOTH L- and S

  • Name the two exceptions and explain why, specifically, they are exceptions

GLYCINE & CYSTEINE

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

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87

What type of rxn is a peptide bond formation? Describe it.

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).

88

Mechanisms of Catalysis/Prosthetic Groups are what?

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

89

What 2 things do R groups DETERMINE in an AA? 

It determines an AA's...

  1. Chemistry & 
  2. Folding pattern

90

Enzyme Inhibition/Feedback Inhibition/ Allosteric enzymes

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

92

Enzyme classification by rxn type/Lyases

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

93

Protein Folding/Hydrophobic Core: What folds into the interion of a globular protein? Why? What do they often bring with them? What happens as a result of this?

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.

94

Michaelis-Menten Kinetics/MM saturation curve is a graph of ___ vs ___. Reveals connection b/t what?

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

95

Substrate-Enzyme specificity/what is the active site?

part of an enzyme where substrate is converted to product

96

Carbohydrates/Cyclic Structure & Conformation of hexoses/Pyranose vs Furanose

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

97

Carbohydrates/Common Disaccharides/maltose

maltose=glucose+glucose

98

Protein structure: 2º

includes alpha helices, Beta sheets.

99

In what fashion do proteins fold?

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

100

Lipids/What are the 9 types to know for the MCAT?

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

102

Vitamins & Minerals/Vitamins: which are fat soluble & water soluble?

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

104

Lipids/Fatty acids are what?

COOH with a long hydrocarbon chain

105

Protein Folding/Neither alpha helices nor Beta sheets can contain WHAT internally w/o its 2º structure being disrupted?

Proline!

106

Two theories of enzyme specificity/Induced fit/ resulting conformational changes do what?

stabilize transition state and lower Ea

107

Estimating pI: pI neutral

=average of pKa amine group + pKa carboxyl group

109

Protein Folding/Entropy: how does volume relate to radius of globular protein during unfolding? (Equation)

Volume is inversely related to the radius^3

110

AAs: Order of Deprotonation (1-5)

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.

111

Carbohydrates/Common Disaccharides/sucrose

sucrose=glucose+fructose

113

Mechanisms of Catalysis/Coenzymes are what? Give an example

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

115

Two theories of enzyme specificity/induced fit/as ___ binds, ____ for it __es. This is an example of what?

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

116

Protein Folding/Define globule, premolten globule, molten globule

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

117

Enzymes=____ _____s

=Biological catalysts

118

Enzyme classification by rxn type/ Ligases

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

120

Protein Folding/Di-sulfide bonds: ____ed ___ residues form a disulfide (R-S-S-R) bond. What other important thing should you remember?

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

121

Vitamins & Minerals/Vitamins: define them

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

122

Michaelis-Menten Kinetics/Lineweaver-Burke Plots are a ___ ___ graph of?

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

123

AA rxns: protein hydrolysis. What 2 things cleave proteins on the carboxyl side of certain AA residues?

trypsin & chymotrypsin cleave proteins on the CARBOXYL side.

124

Protein structure/3º/6 binding forces/Proline turns

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

125

Major (non-enzymatic) protein functions/Binding proteins: name the 7 we're supposed to know

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

126

Protein Folding/H-bonds: b/t what, and what 2 things does it do?

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

128

Enzyme Inhibition/Reversible Inhibition/Uncompetitive Inhibition does what? Effect on Vmax and Km

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

129

Carbohydrates/Stereochemistry/how are alpha and beta glucose related to e/o?

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

130

Enzyme Inhibition/Feedback Inhibition/ Phosphorylation: If phosphorylation (by what?) activates a protein, what deactivates it? & VICE VERSA

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

131

Two theories of enzyme specificity/induced fit

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

132

Carbohydrates/Carbohydrate Rxns/ Polymerization/alpha linkage

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

133

Proteins

Absolute Configuration

  • ALL amino acids are designated as either__ or __
    • ...depending on the side on which the _____ _____ is located in a Fischer Projection (__= Left; __= Right)
  • ALL NATIVE  human AA's are __-amino acids

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

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134

What is a non-essential AA?

an AA that your body CAN synthesize on its own.

135

Draw a mechanism for:

FORMATION OF A PEPTIDE BOND BETWEEN GLYCINE AND ALANINE

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136

Protein structure/3º/6 binding forces/VDWs

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

138

Carbohydrates/Stereochemistry/ R&S vs D&L

R/S≠D/L!!

139

AA's are ___ acids

weak

140

Major (non-enzymatic) protein functions/Motors/Kinesins & Dyneins: Differentiate

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.

141

Enzyme Inhibition/Reversible Inhibition=?

Inhibitor is not permanently bound & enzyme is not permanently disabled

142

Resonance during AA rxns: what 2 things resonate? What does this mean?

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.

143

Lipids/ Triaglycerols (aka triaglycerides) look like what? What are the 2 types of triaglycerols?

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

144

KINASES are a type of _______ase that does WHAT?

A type of TRANSFERASE 

that transfers an R group

(In this case, a phosphate)

145

On a pH scale, if you ONLY are seeing ZWITTERIONS, that means you MUST have reached....?

Why is this?

the ISOELECTRIC POINT, pI

Think about it!

 Zwitterions are variations that have NO formal charge, therefore they are AT their isoelectric point

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146

147

Small oligopeptides are often dominated by one or two amino acid residues

An oligopeptide made up primarily of which pair of amino acids would be LEAST likely to require a protein carrier for transport in the blood?

  • A. glycine and tryptophan
  • B. tyrosine and lysine
  • C. arginine and phenylalanine
  • D. histidine and glutamine

D

  • 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

148

Aspartate has a pKa of 3.7, while the structurally similar glutamate has a pKa of 4.5

Which phenomenon best explains this difference?

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  • 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)

Because inductive effects decrease with distance from the electronegative element, glutamic acid experiences less charge induction than aspartic acid

149

How do "ANTIOXIDANTS" prevent OTHER things from getting oxidized?

What does this mean with regards to their REDUCTION potential when comparing it to a similar, non-antioxidant molecule?

 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

150

Classes of Lipids

Draw the general structure of  TRIAGLYCEROLS, aka "________s"

  • _____backbone with three _____ _____s attached via _____ linkages
  • What are the 2 forms TAGs can come in? 

HINT: think H-bonds

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TRIGLYCEROLS

aka "TRIAGLYCERIDES"

  • Glycerol backbone (HOCH2CHOHCH2OH) with three fatty acids attached via ester linkages

2 FORMS:

  1. Saturated FAs
  2. Unsaturated FAs

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151

Classes of Lipids

Draw the general structure of  STEROIDS

  • Have a characteristic molecular structure containing __#__ rings of carbon atoms, consisting of:
    • ​3 ___-membered rings
    •  
  • All steroids are four-membered ring structures. In the figure below, the rings are labeled, and carbons are numbered.

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152

Classes of Lipids

Draw the general structure of  PHOSPHOLIPIDS

  • is a ____ containing a _______ group 

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a lipid containing a phosphate group in its molecule

 

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153

Classes of Lipids

 PHOSPHOLIPIDS

  • What is the most common type of phospholipid?
    • What are the only 2 things that make it up?

What is the phosphate head directly attached to?

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MOST COMMON TYPE: PHOSPHATIDS

Consists of:

  1. 2 FATTY ACID sections
  2. PHOSPHATE group
    • ...which is attached directly to the glycerol backbone

 

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154

Classes of Lipids

 PHOSPHOLIPIDS

  • Most phospholipids in biological membranes have other________ _____s attached to the ______head

  •  

    Give an example of this, using PhosphaTIDS ( the most common type of phospholipid) as an example

     

     

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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. PHOSPHATE group
    • ...which is attached directly to the glycerol (R GROUP!) backbone

 

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155

Classes of Lipids

Draw the general structure of  STEROIDS

  • Each contain HOW MANY carbon rings?
    • ​What 2 types of cycloalkanes are found in steroids?

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All steroids have 4 carbon rings!!

  • three six-membered
  • one five-membered ring

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156

Classes of Lipids

  • Draw the general structure of  TERPENES, a class of lipid

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157

Classes of Lipids

Draw the general structure of  STEROIDS

  • Each contain HOW MANY carbon rings?
    • ​What 2 types of cycloalkanes are found in steroids?

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All steroids have 4 carbon rings!!

  • three six-membered
  • one five-membered ring

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158

Classes of Lipids

TERPENES

  • What are the building blocks of terpenes?

What is the only difference between:

a TerpENE and a TerpeNOID? 

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Terpenes are made from:

 ISOPRENE units

 

 The only difference between terpenes and terpenoids:

Terpenes are hydrocarbons 

THINK: TerpENES are made up of alkENES

TerpenOIDS contain additional R groups

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159

Classes of Lipids

Draw the general structure of  SPHINGOLIPIDS

  • Are a class of lipids that contain a backbone of _____ bases

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are a class of lipids containing a backbone of SPHINGOSINE bases

 

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160

Classes of Lipids

Draw the general structure of  WAXES

  • Waxes are ESTERS (ROOR) made up of WHAT R-GROUPS?

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 Waxes are ESTERS of:

  1. Fatty Acids
  2. Long-chain monohydric ALCOHOLS

 

("Monohydric" =​​have one hydroxyl group)

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161

Classes of Lipids

Draw the general structure of  GLYCOLIPIDS

  • Are _____s with a _______ attached

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are LIPIDS with 

CARBOHYDRATE attached

 

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162

Classes of Lipids

PROSTAGLANDINS

  • Are lipid _______ors that have ________ and ______ functions throughout the body
  • Another way to think of Prostaglandins is as "_____ Hormones"

What 2 things make Prostaglandins different from Hormones?

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Are lipid MEDIATORS that:

have AUTOcrine and PARAcrine 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