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mcat orgo textbook > Ch. 7 > Flashcards

Ch. 7 Flashcards

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1
Q

All amino acids have a chiral carbon except

A

glycine

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2
Q

all animals AA’s are in what configuration? why?

A

L-configuration because it is derived from smallest carb called L-glyceraldehyde

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3
Q

all naturally occurring sugars are in what configuration? why?

A

D-configuration because it is derived from smallest carb called D-glyceraldehyde

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4
Q

L and D configurations are what type of isomers

A

enantiomeric stereoisomers

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5
Q

what are the three classifications for organic molecules?

A

1) (+)/d and (-)/l for optical activity
2) R and S based on absolute configuration
3) D and L tells us precursor of molecule

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6
Q

what are the acidic aa’s? include three letter abbreviation, deprotonated name and one letter code, and PKA

A

Glutamic Acid- Glu-E and Glutamate
Aspartic Acid-Asp-D and Aspartate
Pka for both is around 4

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7
Q

what are the basic aa’s? include three letter abbreviation, deprotonated name and one letter code and PKA

A

Arginine-Arg-R Pka:12
Lysine-Lys-K Pka:10
Histidine-His-H Pka:6.5

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8
Q

at 7.4 ph, describe the form in which the basic aa’s are in

A

both arg and lys are protonated but histidine can be both deprotonated or protonated due to its pka close proximity to blood ph

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9
Q

at 7.4 ph, describe the form in which the acidic aa’s are in

A

all acidic aa’s are deprotonated

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10
Q

non polar aa’s have what kind of r group? where are these usually found?

A

they have aliphatic (alkyl) groups and aromatic groups, the more alkyl the more hydrophobic. these are mostly found in globular proteins

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11
Q

what are the two abbreviations for glycine, alanine, valine

A

glycine: gly- G
alanine: ala- A
valine: val- V

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12
Q

what are the two abbreviations for leucine, isoleucine, phenylalanine, and tryptophan?

A

leucine: leu- L
Isoleucine: Ile- I
Phenylalanine: Phe- F
Tryptophan: Trp- W

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13
Q

what are the aromatic aa’s? separate them by polarity

A

polar: histidine, and tyrosine
nonpolar: phenylalanine, and tryptophan

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14
Q

what are polar aa’s

A

they have a side chain that is able to h bond but not act as an acid or base, they are hydrophilic

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15
Q

what is special about AA’s that have -OH groups

A

they work with kinases

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16
Q

what are the two polar AA that are amide derivatives?

A

asparagine and glutamine

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17
Q

what are the polar AA’s? include abbreviations

A

Serine- Ser-S
Tyrosine- Tyr-Y
Threonine- Thr-T
Asparagine-Asn-N
Glutamine-Gln-Q

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18
Q

what are the two sulfur containing aa’s? what is their respected polarity? incude abbreviations

A

cysteine: polar Cys- C
methionine: non polar Met-M

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19
Q

what is special about proline? include its abbreviations

A

it is the only aa that its carbon is covalently attacked to its amino group. it is also very small and causes kinks and turns. Proline-Pro-P

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20
Q

what is an essential aa? name the mnemonic for it

A

nine essential AA are ones our bodies cannot make so we need to eat them.
Kinky Men Want Vaginal FILTH

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21
Q

what are the two ways to synthesizes AA’s in the lab

A

strecker synthesis and gabriel-malonic ester synthesis

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22
Q

what is the strecker synthesis?

A

uses ammonium and cyanide salts to make aldehydes into AA racemic mix

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23
Q

what is the gabriel malonic ester synthesis

A

uses phthlimide with two esters and a strong based that is then protonated with an acid to create a AA racemic mix

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24
Q

what does Ka and Pka show

A

the affinity of a functional group for H+

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25
what does HH equation show? what is the HH equation?
relationship between pH and PKa. Ph=PKa+log [base]/[acid]
26
when pH and PKa are equal what does that mean?
the ratio of base to acid is one to one
27
what aa group is more likely to give up their protons
carb acids are while ammonum group is not. At low pH, carb acid will donate H+
28
the protonated form of an amino group is called? when it is protonated how does it act?
ammonium group. it acts like an acid
29
pH>pKa means
deprotonated
30
pH
protonated
31
what is an isoelectric point (pI)
its the pH in which the AA has no overall charge and it is called a zwitterion
32
what is gel electrophoresis? how?
a separation technique to separate aa's based on charge. the AA are in a gel with two electrode on either side, the AA will migrate to a certain electrode based on the charge
33
when pH > pI, aa is what charge? where will it migrate?
it will be negative and move towards + electrode
34
when pH < pI,what is aa charge? where will it migrate?
its postive and it moves toward - electrode
34
when pH = pI, in what direction will a zwitterion go?
no migration
34
where do polar and nonpolar aas go to in a globular protein
polar on outside and nonpolar on inside
34
what is a primary structure of an AA
AA sequence
34
what are the two common bonds in AA's?
peptide bonds and disulfide bonds
34
what is a secondary structure of an AA
hydrogen bonding between backbone amino and carboxylic groups. it creates alpha helices and beta pleated sheets
35
what is the favorability of peptide formation?
non favorable, needs energy
35
what is important to note about the peptide bond
it is fixed and rigid and will not rotate but this is only for the peptide bond
35
where does a peptide bond form? what rxn is this?
it occurs between a carb acid of one AA with the amino group of the other AA. this occurs through addition elimination rxn
35
what are the two ways to hydrolyze a peptide bond? what is the favorability of this?
1. strong acids and heat 2. proteolytic cleavage. the favorability is very high
35
chemotrypsin cleaves what?
aromatic AA's next to hydrophobic residues
35
trypsin cleaves what?
Lys and Arg at the carb acid
35
what one is more oxidized cysteine or cystine
cystine because we removed a proton
35
what is a disulfide bond? which AA does this? what is the name change?
a disulfide bond is a bond between two cysteine AA's. once the cysteine binds to the residue is now called cystine
35
what are denatured proteins? what causes this? what is important to note
non functional AA's that have misfolded. it disrupts the shape NOT the AA sequence. this is caused by extreme temp, extreme pH, increased salt, and reducing agents like urea
36
what are alpha helices
right handed structures that have proline which causes the kinks/turns. hydrophobic outside and hydrophilic inside. great for membranes
37
what are beta pleated sheets?
most common antiparallel structures but parallel can exist.
38
what is a tertiary structure of an AA
interactions between r-side chains that are far from each other. polar fold outside and nonpolar fold inside. DISULFIDE BRIDGES ARE FORMED HERE
39
what is a quaternary structure of an AA
interactions between polypeptide subunits made up of single polypeptide chains
40
what is the formula for carbs
CnH2nOn
41
what do carbs usually begin with? what is the rxn of breaking these down?
carbs begin with an aldehyde or ketone. they can be broken down into CO2 through oxidation called combustion
42
what is one sugar? examples?
monosacc also called a simple sugar. examples are glucose, fructose , ribose, and glyceraldehyde
43
what are two sugars? examples with their compositions
disaccharides are made up of 2 monosacc. lactose (galactose and glucose), sucrose (glu-fruc), maltose (glu-glu)
44
if poly sacc are subjected to strong acids, what occurs?
it turns into a monosacc but nothing else reduced
45
what does it mean for a sugar to be named aldo? keto?
aldo means it starts with aldehyde, keto it starts with a ketone
46
how do you find carbon #1 of a sugar?
its the sugar of the most oxidized end of the chain
47
how do you know if a sugar is a L sugar for D sugar?
you look at second to last carbon. if OH is on left side, its an L sugar, if its on the right side, its a D sugar
48
What kind of sugars and amino acids do we find in our bodys? (D or L)
D sugars and L aa's
49
what is pyranose?
six membered ring where carbon 5 attacks carbonyl
50
what is furanose?
five membered ring where carbon 4 attacks carbonyl
51
what is an anomeric carbon?
the carbon that is apart of the carbonyl (aldo or keto)
52
if OH is upwards or in cyclic form, straight across with another sugar, its a what sugar
beta sugar
53
if OH is downwards or in cyclic form, pointed down with another sugar , its a what sugar
alpha sugar
54
in cyclic form, how can you find anomeric carbon
carbon connected to two oxygens
55
what kind of absolute configuration do D sugars have?
R
56
how are sugars linked? what do they form on both sugars?
glycosidic linkages: they form acetals
57
what is a reducing sugar?
a sugar that can reduce a compound and oxidize itself. it has to have a free aldo or keto
58
glycogen has what bonds?
alpha bonds
58
starch has what bonds?
beta bonds
59
what do monosacc have in common when it comes to reducing sugars
they are all reducing sugars
60
what are the three main functions of lipids?
make up membranes; stores energy; building blocks for sex hormones
61
what does lipophobic mean? lipophilic?
lipophobic: hydrophilic lipophilic: hydrophobic
62
a lipid that has no double bonds is said to be? with double bonds?
no db: saturated db: unsaturated
63
what kind of lipids are made in the body?
even numbered ones
64
what is the polarity of a micelle?
outisde hydrophilic inside hydrophobic
65
what is a triglyceride? what is it made up of?
storage form of fat , it is made up of three fatty acids and one glycerol backbone
66
why are triglyceride better for energy compared to carbs?
1) packaging: you are able to make fat more compact and densely packed together 2) energy content: carbs are already slightly oxidized while triglycerides are very reduced so youre able to oxidized them alot more than carbs
67
what are the three things that increase fluidity in membranes
more double bonds, cholesterol present, short tails
68
at high temps, what is the effect of cholesterols on fluidity?
less fluid
69
at low temps, what is the effect of cholesterols on fluidity?
more fluid
70
what are terpenes?
compounds made up of isoprene units (C5H8)
71
what is a monoterpene?
2 units
72
what is a sesquiterpene?
3 units
73
what is a diterpene
4 units
74
what is squalene?
6 units and helps make steroids
75
what are steroids made of? whats important to note about its polarity
tetracyclic rings (four rings) and is amphiphatic
76
phosphoric acid is good for what? delta g?
good for energy! very favorable
77
why are phosphoric acids good?
1. (-) charges repel each other 2. has many resonance structures 3. interacts well with water
78
what are nucelotides? what are they made up of
building blocks for nucleic acids, they are made up of 1. ribose or deoxyribose sugar 2. purine or pyrimidine base 3. 1-3 phosphate groups
79
what is ATP
nucleotide, short term energy storage FOR ALL LIVING THINGS

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