Bioc Chapters 4-7

Front 1

2 ways acids are released from our body

Back 1

respiration & urine

Front 2

T/F: water dissociates readily to form H+ & OH-

Back 2

false; water's ampipathic

Front 3

Acids or Bases release H+; which one is oxidized & which one is reduced?

Back 3

Acids releases H+, gets oxidized
OIL RIG (oxidation is loss; reduction is gain)

Front 4

What's the mixture for buffers

Back 4

undissociated acid & conjugate base

Front 5

what are the buffer effectiveness factors

Back 5

pKa & concentration

Front 6

T/F: buffers resist changes to pH best when pH is near its pKa

Back 6

true

Front 7

What are 2 metabolic and inorganic acids generated by metabolism

Back 7

metabolic: lactic acids & KB
inorganic acids: sulfuric acids

Front 8

Does the kidney eliminate NH4+ or NH3

Back 8

NH4+, pKa is >9

Front 9

What's the breakdown of water in the body
(ECF, ICF, ISF, plasma)

Back 9

overall: 60% of body weight
60% ICF
40% ECF --> 2/3 ISF, 1/3 plasma

Front 10

T/F: H-bonds are strong noncovalent bonds

Back 10

false; weak

Front 11

2 biochemical elements (atoms) that are highly e-

Back 11

O & N

Front 12

T/F: hydration shells can be form w/ cations or anions

Back 12

true

Front 13

Major components of ECF (3)
Major components of ICF (2)

Back 13

ECF: Na, Cl, HCO3
ICF: K, HPO4,

Front 14

what is osmolarity of fluid proportional to

Back 14

concentration of organic metabolites, ions, proteins

Front 15

T/F: water moves from high to low osmolality

Back 15

false; low --> high

Front 16

T/F: water @ pH=7; [OH-] = [H+]

Back 16

True

Front 17

How is the ion product of water calculated (Kw)

Back 17

[OH][H]

Front 18

Strong or weak acids dissociate completely
2 examples of strong acids
1 example of weak acid

Back 18

Strong
2: H2SO4, HCl
1: KB

Front 19

T/F: the pKa of weak acids is 7

Back 19

False; diff for diff acids; must be given by barbosa or determined experimentally

strong/weak acids: <7
strong/weak base: >7

Front 20

T/F: undissociated acid has a "ate" ending & dissociated anion has a "ic acid" ending

Back 20

False; other way around

Front 21

T/F: the higher the Ka, the more OH+ dissociation

Back 21

F; high Ka = low pKa = low pH = the more H+ dissociation = less OH dissociation

Front 22

T/F: when pH = pKa, there are equal dissociation & undissociation for WEAK acids

Back 22

True

Front 23

Henderson-Hasselbalch

pH=pKa + log [A-]/[HA]
pOH=pKb + log [HA]/[A-]

*not a question*

Back 23

just remember it; pKa 2 is always more acidic than pKa of 5

Front 24

T/F: buffers compensate pH changes of +/-1 from pH 7

Back 24

false; changes of +/-1 from its own pKa

Front 25

4 Major buffer systems in body & where they are

KNOW THIS!

Back 25

bicarbonate-carbonic acids (ECF)
hemoglobin (RBC)
Phosphate (intracelullar)
protein (intracellular + plasma)

Front 26

what's the physiological blood pH
what's the intracellular pH

Back 26

7.36 - 7.44
7.1

Front 27

What does CO2 + H2O make via carbonic anhydrase

Back 27

Carbonic acid --><-- bicarbonate

Front 28

T/F: CO2 is readily available for carbonic anhydrase

Back 28

true; concentration is usually 500x of carbonic acid; hence changing pKa of rxn from 3.8 to 6.1 (physiologically sign.)

Front 29

In the RBC, where are H+ uptaken up to (2 places)

Back 29

HPO4 & HbH

Front 30

Hb & proteins can uptake H+ b/c of which amino acid

Back 30

histidine

Front 31

When Hb is unprotonated, there is high affinity for CO2

Back 31

false; protonated in capillary --> loss O2; unprotonated in lungs --> attracts O2

Front 32

where in the brain senses pH; what happens when blood acidity is high

Back 32

Hypothalamus; increase breathing to let out CO2

Front 33

What happens to HCO3 when RBC is basic; What happens to excess H+ when RBC is acidic

Back 33

HCO3 leaves cell in xchange of Cl-
H+ leave cell in xchange for Na+

Front 34

T/F: phosphate buffer is only found in RBC

Back 34

false; phosphate is for all cells (RBC, hepatic etc)

Front 35

Main buffering protein in the blood stream

Back 35

albumin

Front 36

5 inorganic acids produced in body

Back 36

phosphate, NH4+, uric acid, di & tricarboxylic acids

Front 37

where are sulfuric acids generated from

Back 37

sulfate-containing foods & cys/met metabolism

Front 38

what components of urine help excrete H+

Back 38

H2PO4- & NH4+ (major)

Front 39

major source of body acid & major source of nonvolatile body acids

Back 39

CO2; H2SO4

Front 40

How is HCl neutralized in the digestive tract

Back 40

by bicarbonate from pancreas @ the small intestine

Front 41

Function organic groups other than C & H

Back 41

P O N S

Front 42

types of classification of carbohydrates

Back 42

carbonyl group
number of Cs
position of OH on asymmetric C

Front 43

T/F: iso for branched; ene for double; aliphatic for straight; aromatic for benzene

Back 43

true

Front 44

order these from most oxidized to most reduced

acid anhydride
ketone
aldehyde
carboxylic acid
alcohol

Back 44

acid anh > acid > ketone > aldehyde > OH

Front 45

T/F: C=C is more reduced than C-C

Back 45

false; less reduced

Front 46

How are ester generated? amide? anhydride?

Back 46

dehydrations
COOH + OH
OH + NH2
OH + OH

Front 47

what is the name for an acidic group w/ a H that left; what charge is on it

Back 47

_____ate (anionic), - charge

Front 48

Major anionic substituents

Back 48

carboxylate, phosphate, sulfate

Front 49

T/F: N in amines usually have - charge

Back 49

false; + charge

Front 50

define polar bonds & solubility

Back 50

polar: covalent bonds w/ a e- coloud on a atom
solubility: proportion of polar vs nonpolar

Front 51

T/F: In C-number nomenclature system (C1,C2,C3 etc), C1 is the C right next to the most oxidized group

Back 51

False; most oxidized C is C1; the one beside is alpha (C2)

Front 52

T/F: in monosaccharides; there is >1 C=O

Back 52

false; only 1 C=O
CnH2nOn

Front 53

Glucose = ____hexose; Fructose = ___hexose

keto or aldo

Back 53

aldo; keto

Front 54

T/F: chiral molecules are not superimposable

Back 54

true

Front 55

sugar are usually ____ & aa are usually ___

D or L

Back 55

sugar: D; aa: L

Front 56

Definition of epimers

Back 56

stereoisomers w/ only 1OH differing

Front 57

Which C is the anomeric C when monosaccharides go becomes a ring

Back 57

the C that used to be C=O

Front 58

what enzyme mutorotate b/w the alpha & beta

Back 58

none; it's spontaneous

Front 59

common substituted sugars (4) types;

Back 59

phosphate, amino, sulfate, n-acetyl

Front 60

what's the physiological advantage of phosphylating glucose in the cell
(glucose --> G6P)

Back 60

prevents transport out (concentrate glucose in the cell)

Front 61

T/F: monosaccharides can only be reduced

Back 61

false; can oxidize @ aldehyde C to form acid; such as uronic acid

aldehyde/ketone --> COOH

Front 62

what does sugars become when the aldehyde is reduced (all C has an OH)

Back 62

polyol

Front 63

T/F: DEOXYribose (DNA) is an example of a polyol

Back 63

False; DNA has 1 C where the OH is reduced to H

Front 64

2 types of glycosidic bonds

Back 64

N & O

Front 65

where are O glycosidic bonds found & give 1 example of N glycosidic bonds

Back 65

O: monosaccharides (chains of glucose)
N: ATP, nucleotides, nucleosides

Front 66

name for oligosaccharides attaching to protein

Back 66

glycoprotein

Front 67

2 examples of polymers of glycosyl residues
a1-4 and a1-6

Back 67

amylopectin, glycogen

Front 68

alipathic FA chains have what groups on each end

Back 68

CH3 on 1 end; COOH on the other end

Front 69

T/F: omega 3 means 1 unsaturated bond on the 3rd C from the CH3 end

Back 69

false; you don't know if it's mono or polyunsaturated; the 2nd half is right

Front 70

How many Cs does palmitate & oleate have

Back 70

16; Oleate is unsaturated @ C9

Front 71

what's arachidonic acid a precursor to (3)

Back 71

prostaglandins, thromboxanes, leukotrienes

Front 72

T/F: trans FA are produced naturally

Back 72

false; chemical hydrogenation of polyunsaturated FA in vegetable oils

Front 73

monoacylglyercol has ______ FA chain

Back 73

1

Front 74

on which C is the phosphate group found in phophoacylglycerol

Back 74

C3

Front 75

Phosphatidylcholine (lecithin) is found where mostly; are they polar, nonpolar?

Back 75

Membranes; amphipathic

Front 76

what is the carbon backbone for sphingolipids

Back 76

serine

Front 77

T/F: sphingosine is made from serine & acetyl-Coa

Back 77

false; serine + palmitate

Front 78

T/F: ceramide is sphingosine + FA to amino group

Back 78

true

Front 79

Cerebrosides, gangliosides, sphingomyelin --> all examples of sphingolipids

Back 79

true

Front 80

T/F: precusor of all steriods is cholesterol

Back 80

true

Front 81

Cholesterol has ___ carbons & ___ rings

Back 81

27:4

Front 82

What is cholesterol synthesized from

Back 82

5C isoprenyl units which is in turn from acetyl-coa

Front 83

T/F: aa in neurotransmitters are all Lalpha

Back 83

false; GABA is gamma-b; all protein aa are La

Front 84

3 types of n-containing rings

Back 84

purines, pyrimidines pyridines

Front 85

T/F: niacin is pyridines & vit B6 is pyridoxine

Back 85

true

Front 86

T/F: nucleoside is nitrogen base + sugar

Back 86

true

Front 87

which is more reactive --> keto (C=) or enol (=COH)

Back 87

enol; can lose that H in OH easily

Front 88

what physiological disease does urate acid cause

Back 88

gout

Front 89

NO2 are found where (2)

Back 89

smog & cigar smoke

Front 90

T/F: superoxide is produced in our bodies

Back 90

true; fight bacteria infections

Front 91

T/F: DDT & CDD have multiple benzene rings

Back 91

true

Front 92

Essential aa

Back 92

WTF Very Hot Milk
arginine is conditional (pregnancy & newborn)

Front 93

Nonpolar hydrophobic aa (6)

Back 93

alanine, valine, leucine, isoleucine, phenylalanine, methionine

Front 94

unchaged polar aa (5)

Back 94

serine, threonine, asparagine, glutamine, tryosine

Front 95

sulfur group (2)

Back 95

methionine, cysteine

Front 96

acidic - charge (2)

Back 96

aspartate, glutamate

Front 97

acidic + charge

Back 97

lysine, arginine, histidine

Front 98

T/F: all alpha aa are zwitterions @ pH 7.4

Back 98

true; NH3+ & COOH-

Front 99

what bonds do side chains of nonpolar, aliphatic aa form

Back 99

hydrophobic & van der waals forces

Front 100

Where is the N located in tryptophan

Back 100

indole ring

Front 101

T/F: cysteine is polar & methionine is nonpolar

Back 101

true; SH at the end on cysteine

Front 102

where are the N located in histidine & arginine

Back 102

imidazole; guanidinium

Front 103

what types of bonds do acidic & basic amino acids form in their R groups

Back 103

ionic (electrostatic) bonds

Front 104

T/F: as a buffer; histidine picks up an H @ in the imidazole ring on its R group

Back 104

true

Front 105

T/F: when histidine picks up an H, the medium is at the isoelectric point (pI)

Back 105

false; isoelectric = no charge on the aa

Front 106

T/F: if pKa of his is ~6, his is protonated @ pH of 9.3

Back 106

false; depronotated

Front 107

T/F: if pKa of his is ~6, amino group on the alpha C is NH2 @ pH of 2

Back 107

false; NH3+

Front 108

T/F: if the pKa of his is ~6, the imidizole ring is protonated @ pH=3

Back 108

true

Front 109

T/F: aa sequence varies b/w individual, tissues or stages of development

Back 109

true

Front 110

what is polymorphism; how much of our genetic loci is polymorphic

Back 110

variants of an allele that occurs @ sign. freq
1/3

Front 111

Sickle cell allele is stable/unstable

Back 111

stable

Front 112

Example of paralogs talked in class

Back 112

myoglobulin & hemoglobin

Front 113

what is a superfamily

Back 113

very large families of homoglous proteins

Front 114

Myoglobin has how many peptides; hemoglobin has how many peptides

Back 114

1; 4

Front 115

where is myoglobin & where is hemoglobin

Back 115

intracellular; RBC

Front 116

where did the myoglobin peptide evolved from

Back 116

a-chain of hemoglobin

Front 117

Different isozymes of hemoglobin: embryonic, fetal, adult

Back 117

Embryonic: e & z
Fetal: 2a & 2y
Adult: 2a & 2b

Front 118

T/F: embryonic Hb & myoglobulin has higher affinity for O2 than hemoglobulin

Back 118

true

Front 119

Different tissue specific isoforms of creatine kinase

Back 119

MM (muscle)
BB (brain)
MB (heart)

Front 120

What does AC do intracellular

Back 120

synthesis of cAMP from ATP

Front 121

Which peptides are found in mature insulin; how are they connected

Back 121

a & b chain; disulfide bridges

Front 122

3 types of lipid addition on aa

Back 122

palmitoylation; myristoylation; prenylation

Front 123

regulatory modifications of aa (3)

Back 123

phosphorylation, acetylation, ADP-robosylyation

Front 124

what does carboxylation of glutamate C4 do

Back 124

attaching clots to surface in blood clotting proteins

Front 125

where can we find hydroxyproline

Back 125

collage; forms H-H bonding b/w fibrous protein strands

Front 126

difference b/w selenocysteine & cysteine

Back 126

SeH instead of SH

Front 127

4 classification of proteins

Back 127

globular, fibrous, TM proteins, DNA binding proteins

Front 128

primary structure

Back 128

linear sequence

Front 129

secondary structure

Back 129

arrangement of aa near each other stabilized by H bonds

Front 130

teritary structure

Back 130

folding of secondary structure into 3D conformation

Front 131

quaternary structure

Back 131

polypeptide subunits associated together

Front 132

T/F: proteins have some rigidty & flexibility

Back 132

true

Front 133

T/F: aa sequence are linked by ionic peptide bonds

Back 133

false; covalent

Front 134

where are peptide bonds formed, type of rxn & what enzymes

Back 134

ribosomes, dehydration, peptidyl transferase

Front 135

T/F: peptide bonds are rigid & planar

Back 135

true; double bond character

Front 136

T/F: R groups are found on opposite sides of the bond

Back 136

true; limits the secondary & tertiary structures formed

Front 137

T/F: peptide bonds are charged

Back 137

false

Front 138

T/F: CO & OH groups in peptide bonds readily accepts H as a buffer

Back 138

false

Front 139

T/F: sequence is read from the N to the C terminus

Back 139

true

Front 140

correct folding of protein is required for ____ (2)

Back 140

stability & function

Front 141

T/F: folding occurs while peptide is being translated

Back 141

true

Front 142

what types of aa will be buried in the inside of globular proteins; what on the outside

Back 142

usually hydrophobic R groups inside & hydrophilic R groups outside

Front 143

aa w/ polar side chains can form what bonds on the surface

Back 143

H-bonds w/ water

Front 144

aa w/ cysteine r groups for what bonds

Back 144

disulfide bridges

Front 145

T/F; proteins are folded very slowly on a energy biased method

Back 145

false; very fas (ms-s)

Front 146

what is the main function of chaperones

Back 146

mediate folding & assembly
stabilize protein during synthesis

Front 147

T/F: chaperones are part of the final protein structure

Back 147

false

Front 148

T/F: chaperones uses an ATP-dependent mechanism

Back 148

true

Front 149

there are diff types of chaperones, some are escorting, others are machinery for folding

Back 149

true

Front 150

where are co/post-translational modifications found at
2 examples of modifications

Back 150

rER
sugar added; disulfide bonds

Front 151

what happens when nascent polypeptides are not folded properly (2)

Back 151

degradation or aggregation (precipitation --> cell death)

Front 152

T/F: protein folding occurs through unique intemediate structures via the energy biased process

Back 152

true

Front 153

how are nearby aa stabilized by in a linear sequence

Back 153

H-bonds

Front 154

3 structures in secondary protein structure

Back 154

a-helix, b-sheet, random coil

Front 155

T/F: a-helix has more H-bonds than b-sheets

Back 155

false

Front 156

3 main places where a-helix are found

Back 156

globular proteins, membrane spanning domains, DNA -binding proteins

Front 157

T/F: secondary structures determine domains

Back 157

false; MOTIFS

Front 158

T/F: r groups faces outside in the a-helix

Back 158

true

Front 159

H-bonds b/w CO & NH in a-helix are ___aa apart

Back 159

4

Front 160

T/F: a-helix is composed of aa from multiple polypeptides

Back 160

false; only 1 for both ahelix & bsheets

Front 161

T/F: r groups are involved in h-bonds in the a-helix

Back 161

false

Front 162

3 types of aa that disrupt a-helix

Back 162

protein
large charged aa
aa w/ bulky/branched side chains

Front 163

T/F: bsheets involves 2 stands of the same polypeptide

Back 163

true

Front 164

what's the diff parallel & aniparallel sheets

Back 164

parallel: same terminus on the same side
antiparallel: same terminus on diff sides

Front 165

T/F: the R groups are above & below the plane on the b-sheet

Back 165

true

Front 166

T/F: norepeatitive secondary structures are random

Back 166

false; less regular structure but not random

Front 167

T/F: non-repetitive sheets form hinge regions to allow segments of peptide to move & usually found on the surface of protein

Back 167

true

Front 168

B-bends contain 4aa (2 are ____) & what's it's function

Back 168

proline & glycine
reverse direction of chain to form a compact globular shape

Front 169

helical globular domains usually have ___aa & b-sheets are ___aa wide

Back 169

12, 6

Front 170

what are motifs

Back 170

combination of adjacent secondary structures

Front 171

T/F: motifs are defined by functions

Back 171

false; domains are

Front 172

what is the zinc finger motif composed of

Back 172

BBA

Front 173

T/F: motifs are unique to each protein & can be used to predict the biological function

Back 173

false

Front 174

Teritary structure have bonds b/w distant aa via ___

Back 174

R group

Front 175

T/F: tertiary structures produce 3D conformation to create specific binding sites for ligands

Back 175

true

Front 176

T/F; domains are formed from continuous sequence of aa

Back 176

true

Front 177

T/F: domains fold dependently to each other

Back 177

false

Front 178

The core of a domain is a combination of _____

Back 178

motifs

Front 179

T/F: tertiary bonds can be stronger than H-bonds

Back 179

true

Front 180

4 interactions stabilizing tertiary structures

Back 180

H bonds, ionic, hydrophobic effect, disulfide bond

Front 181

T/F: chaperons promote the formation of S bonds when it's folding

Back 181

false; prevents

Front 182

T/F: Aromatic ring stacking is an example of hydrophobic interaction

Back 182

true

Front 183

Ionic interactions are also called ____

Back 183

salt bridges

Front 184

Give an example of hydrophobic aa facing the outside & hydrophilic aa facing inside

Back 184

transmembrane domain

Front 185

T/F: the lower the Kd, the tighter the binding

Back 185

true; low Kd = high Ka = tight binding

Front 186

T/F: association constant is the rate constant of association

Back 186

false; association constant is @ equilibrium

Front 187

3 domains in transmembrane proteins

Back 187

ligand binding domain
transmembrane (channel) domain
effector (eg GPCR) domain

Front 188

most hormone receptors have ______ a-helices domains in the membrane

Back 188

7

Front 189

T/F: all polypeptides form quaternary structures

Back 189

false

Front 190

T/F: peptide subunits are usually held together by covalent bonds

Back 190

false; usually by noncovalent; rarely disulfide

Front 191

what's heterodimeric & what's homodimeric

Back 191

hetero: diff subunits
homo: same subunits