Mcat Biology 12

Front 1

classifications of biological molecules

Back 1

lipids
proteins
carbohydrates
nucleotide derivatives
(all have carbon skeletons)

Front 2

water

Back 2

- solvent in which chemical reactions of living cells occur
- 70-80% of cell's mass
- small, polar molecule that can hydrogen bond (which allows it to remain liquid & squeezes hydrophobic molecules away, and helps solvate hydrophilic molecules)

Front 3

How are most macromolecules in living cells formed and broken apart?

Back 3

- formed by dehydration synthesis
- broken apart by hydrolysis
- water acts as reactant or product in these rxns

Front 4

lipid

Back 4

- any biological molecule with low solubility in water & high solubility in nonpolar organic solvents
- hydrophobic (thus good barriers in aq environments)

Front 5

What are the 6 major groups of lipids?

Back 5

(1) fatty acids
(2) triacylglycerols
(3) phospholipids
(4) glycolipids
(5) steroids
(6) terpenes

Front 6

fatty acids

Back 6

- building blocks for most compelx lipids
- long carbon chains w/ carboxylic acid at one end
- usually an even # carbons (max 24 C's)
- saturated only have single C-C bonds
- unsaturated have one or more C=C double bonds
- oxidation yields a lot of chemical energy for cell
- most fats reach cell in this form

Front 7

triacylglycerols

Back 7

- also called "triglycerides" or "fats & "oils"
- made from glycerol (3-C backbone) attached to 3 fatty acids
- stores energy in cell & may provide thermal insulation/padding
- adipocytes' cytoplasm contains mainly triglycerides

Front 8

phospholipids

Back 8

- glycerol backbone w/ polar phosphate group replacing one fatty acid (on the opposite side from the fatty acid)
- amphipathic (polar & nonpolar), so good membrane component

Front 9

glycolipids

Back 9

- similar to phospholipids, but have 1+ carbohydrates attached to glycerol backbone instead of phosphate group
- amphipathic
- found in membranes of myelinated cells in nervous system

Front 10

steroids

Back 10

- four ringed structures
- some hormones, vitamin D & cholesterol are steroids

Front 11

terpenes

Back 11

- include vitamin A (important for vision)

Front 12

eicosanoids

Back 12

- a class of lipids (often listed as a fatty acid) w/ 20 carbons
- include prostaglandins, thromboxanes & leukotrienes
- released from cell membranes as local hormones that regulate blood pressure, body temperature & smooth muscle contraction

Front 13

aspirin

Back 13

inhibits prostaglandin synthesis

Front 14

lipoproteins

Back 14

- transport lipids through blood (since they're insoluble)
- lipid core surrounded by phospholipids & apoproteins
- can dissolve lipids in hydrophobic core then move through aqueous solution b/c it has a hydrophilic shell
- classified by density (greater lipid:protein ratio = lower density)
- includes chylomicrons (VLDL), low density (LDL) & high density (HDL)

Front 15

proteins

Back 15

- built from chain of amino acids linked together by peptide bonds ("polypeptides")
- mainly built from same 20 alpha-amino acids, 10 of which are essential (must ingest)
- "peptides" = very small polypeptides

Front 16

alpha-amino acids

Back 16

- amine is attached to carbon in alpha position to carbonyl
- each amino acid in polypeptide chain called "residue"
- only differ in side chain (R group), which is also attached to alpha carbon
- in solution, amino acids always have 1+ charges (which depend on pH of solution)

Front 17

Which amino acids have nonpolar R groups?

Back 17

glycine
alanine
valine
leucine
isoleucine
phenylalanine
tryptophan
methionine
proline

Front 18

Which amino acids have polar R groups?

Back 18

serine
threonine
cysteine
tyrosine
asparagine
glutamine

Front 19

Which amino acids have acidic R groups?

Back 19

aspartic acid
glutamic acid

Front 20

Which amino acids have basic R groups?

Back 20

lysine
arginine
histidine

Front 21

glycine structure

Back 21

side chain = H

Front 22

alanine structure

Back 22

side chain = CH3

Front 23

valine structure

Back 23

side chain = CH(CH3)2

Front 24

leucine structure

Back 24

side chain = CH2-CH(CH3)2

Front 25

isoleucine structure

Back 25

side chain = CHCH3-CH2-CH3

Front 26

phenylalanine structure

Back 26

side chain = CH2-phenyl

Front 27

tryptophan structure

Back 27

side chain = CH2-CCHNH(ring)-phenyl

Front 28

methionine structure

Back 28

side chain = CH2-CH2-S-CH3

Front 29

proline structure

Back 29

side chain = C-NH-C-C-C(ring)

Front 30

serine structure

Back 30

side chain = HCOH-CH3

Front 31

cysteine structure

Back 31

side chain = CH2-SH

Front 32

tyrosine structure

Back 32

side chain = CH2-phenyl-OH

Front 33

asparagine structure

Back 33

side chain = CH2-C(=O)NH2

Front 34

glutamine structure

Back 34

side chain = CH2-CH2-C(=O)NH2

Front 35

aspartic acid structure

Back 35

side chain = CH2-COOH

Front 36

glutamic acid structure

Back 36

side chain = CH2-CH2-COOH

Front 37

lysine structure

Back 37

side chain = CH2-CH2-CH2-CH2-NH2

Front 38

arginine structure

Back 38

side chain = CH2-CH2-CH2-NH-C(=NH)NH2

Front 39

histidine structure

Back 39

side chain = CH2-CNHNC(ring)

Front 40

primary structure

Back 40

- number & sequence of amino acids in a polypeptide
- all proteins have a primary structure

Front 41

alpha-helix

Back 41

- single chain of the primary structure of a polypeptide can twist into this
- reinforced by hydrogen bonds b/t carbonyl oxygen & hydrogen on amino group

Front 42

beta-pleated sheet

Back 42

- single chain of primary structure of a polypeptide can lie along itself to form this
- connecting segments of 2 strands can lie in same direction (parallel) or opposite directions (anti-parallel)
- reinforced by hydrogen bonds b/t carbonyl oxygen & hydrogen on amino group

Front 43

secondary structure

Back 43

- alpha helices & beta-pleated sheets
- contribute to conformation of protein
- most proteins have a secondary structure

Front 44

tertiary structure

Back 44

- 3D shape formed from peptide chain curling & folding
- created by:
(1) covalent disulfide bonds b/t 2 cystein AA's on
diff. parts of chain
(2) electrostatic (ionic) interactions (usually b/t
acidic & basic side chains)
(3) hydrogen bonds
(4) van der Waals forces
(5) hydrophobic side chains pushed away from
water toward center of protein
[proline also induces turns that disrupt alpha-helix & beta-pleated sheet formation]

Front 45

quarternary structure

Back 45

- 2+ polypeptides bind together
- due to same 5 forces that form tertiary structure

Front 46

denatured protein

Back 46

- conformation is disrupted
- lost most of secondary, tertiary & quarternary structure
- often spontaneously refolds when denaturing agent is removed (thus AA sequence prob. plays key role in conformation)

Front 47

What are the 2 types of structural proteins?

Back 47

(1) GLOBULAR

(2) STRUCTURAL

Front 48

globular proteins

Back 48

- more types of these than structural
- enzymes (pepsin)
- hormones (insulin)
- membrane pumps & channels (Na+/K+ pump, voltage-gated Na+ channels)
- membrane receptors (nicotininc receports on post-synaptic neuron)
- inter/intracellular transport & storage (hemoglobin, myoglobin)
- osmotic regulators (albumin)
- immune response (antibodies)

Front 49

structural proteins

Back 49

- made from long polymers
- maintain & add strength to cellular & matrix structure
- e.g. collagen, microtubules (made from globular tubulin that polymerizes to become structural protein)

Front 50

collagen

Back 50

- structural protein made from helix
- most abundant protein in body
- add strength to skin, tendons, ligaments, bones

Front 51

glycoproteins

Back 51

- proteins w/ carbohydrate groups attached
- component of cellular plasma membranes

Front 52

proteoglycans

Back 52

- mixtures of proteins & (usually more than 50%) carbs
- major component of EC matrix

Front 53

cytochromes

Back 53

- proteins that require prosthetic (nonproteinaceous) heme group to function
- get name from color
- hemoglobin, cytochromes of ETC

Front 54

conjugated proteins

Back 54

proteins containing nonproteinaceous components

Front 55

carboyhdrates

Back 55

- "sugars"/"saccharides"
- made from carbon and water
- empirical formula C(H2O)
- 5-C (pentoses) and 6-C (glucoses) most common in nature

Front 56

glucose

Back 56

- most commonly occurring 6-C carbohydrate
- usually accounts for 80% of carbohydrates absorbed by humans (all digested carbs converted to this by liver/enterocytes)
- exists in aq. solution in unequal equilibrium favoring ring over chain form

Front 57

anomers of glucose

Back 57

- in alpha glucose, hydroxyl group on anomeric carbon (C1) & methoxy group (C6) are on opposite sides of the ring
- in beta glucose, hydroxyl & methoxy groups are on same side of carbon ring

Front 58

glucose for energy use/storage

Back 58

- can be oxidized to ATP for readily usable energy
- can be polymerized to polysaccharide glycogen or stored as fat if cell has enough ATP

Front 59

glycogen

Back 59

- branched glucose polymer with alpha linkages
- found in all animal cells, but especially in muscle/liver
- alpha linkages can be digested by animals

Front 60

glucose absorption

Back 60

- only some epithelial cells in digestive tract & proximal tubule can absorb glucose against concentration gradient with secondary activty transport mechanism down Na+ concentration gradiant)
- other cells absob glucose via facilitated diffusion (insulin increase rate of faciliated diffuson for glucose/monoscaccharides)
- neural & heaptic cells are the only cells that can absorb enough glucose via faciliated transport in the absence of insulin

Front 61

starch

Back 61

- formed from glucose in plants
- alpha-linkages can be digested by animals
- AMYLOSE: isomer of cellulose that can be branched or unbranched & has same alpha linkages as glycogen
- AMYLOPECTIN: resembles glycogen but with different branching structrue

Front 62

cellulose

Back 62

- formed from glucose in plants
- has beta linkages that cannot be digested by any enzymes in animals (though some have bacteria in digestive system that can)

Front 63

nucleotides

Back 63

- made of (1) 5-C sugar, (2) nitrogenous base, (3) phosphate group
- nitrogenous base usually adenine, guanine, cytosine, thymine & uracil
- form polymers to create nucleic acids (DNA & RNA)
- other nucleotides: ATP (adenosine triphosphate), cyclic AMP (impt. in 2nd messengery systems), NADH & FADH2 (coenzymes in Krebs)

Front 64

nucleic acids

Back 64

- DNA, RNA
- nucleotides joined to gether by phosphodiester bonds b/t phostphate group of one nucleotide & 3rd carbon of pentose of other nucleotide
- strands written as list of bases from 5'-->3' end
- in DNA, 2 strands are joined by hydrogen bonds to form double helix; top strand runs 5'-->3' and bottom runs 3'-->5'
- no double helix formed in RNA (only 1 strand) & uracil replaces thymine

Front 65

How many hydrogen bonds to adenine and thymine form?

Back 65

2

Front 66

How many hydrogen bonds do cytosine guanine form?

Back 66

3

Front 67

minerals

Back 67

- dissolved inorganic ions inside & outside cell
- create electrochemical graidents across membranes to assist in transport
- can combine/solidify to add strength to matrix (ie: hydroxyapatite in bone)
- act as cofactors to assist enzyme/protein function (e.g. iron is mineral in heme, the prosthetic group of cytochromes)

Front 68

enzymes

Back 68

- usually globular proteins
- act as catalysts to lower energy of activation for biological reaction & increase reaction rate
- are not consumed/permanently altered in rxns
- do not alter the equilibrium of a reaction

Front 69

substrates

Back 69

- generally smaller than enzyme
- binds to active site on enzyme
- when enzyme is bound, it is enzyme-substrate complex

Front 70

lock & key theory

Back 70

active site of enzyme has specific shape that fits only specific substrate

Front 71

induced fit model

Back 71

shape of both enzyme & substrate are altered upon binding, which increases specificity & helps reaction proceed (enzymes can also orient multiple substrates in optimal ways for rxns to occur)

Front 72

Vmax

Back 72

- rxn rate increases with relative concentration of substrate up to this point, since all active sites are occupied
- proportional to enzyme concentration

Front 73

Km

Back 73

- Michaelis constant
- substrate concentration at which rxn rate = 1/2 Vmax
- does not vary when enzyme concentration changes
- good indicator of enzyme's affinity for a substrate

Front 74

How does temperature affect enzymatic reactions?

Back 74

- rxn rate increases with temperature up to a point, then enzyme denatures and rate plummets
- optimum temp around 37 degrees C in humans

Front 75

How does pH affect enzymatic reactions?

Back 75

- varies depending on enzyme
- pepsin (stomach) works below pH of 2
- trypsin (small intestine) works b/t pH of 6-7

Front 76

cofactors

Back 76

- a non-protein component that helps enzymes reach optimal activity
- COENZYMES or METAL IONS

Front 77

coenzymes

Back 77

- organic molecules
- COSUBSTRATES: reversibly bind to specific enzyme & transfer some chemical group to another substrate, then reverted back to original form (which distinguishes it fro ma normal substrate); e.g. ATP
- PROSTHETIC GROUPS: remain covalently bound to enzyme through reactions & emerge from rxn unchanged; often vitamins/vitamin derivatives; e.g. heme

Front 78

metal ions

Back 78

- can act alone or w/ prosthetic group
- ion, copper, manganese, magnesium, calcium & zinc

Front 79

apoenyzme

Back 79

- enzyme w/out its cofactor
- completely nonfuctional

Front 80

holoenzyme

Back 80

enzyme w/ its cofactor (*think "holo" = "whole")

Front 81

What are the 3 types of enzyme inhibitors?

Back 81

(1) irreversible inhibitors
(2) competitive inhibitors
(3) non-competitive inhibitors

Front 82

irreversible inhibitors

Back 82

- typically bind covalently to enzymes
- penicillin binds to bacterial enzyme that assists in making peptidoglycan cell walls

Front 83

competitive inhibitors

Back 83

- compete w/ substrate by binding reversibly to active site
- raise apparent Km, but do not change Vmax
- can overcome by increasing substrate concentration
- often resemble substrate

Front 84

noncompetitive inhibitors

Back 84

- bind noncovalently to enzyme spot other than active site & change enzyme conformation
- don't prevent substrate from binding & can bind to enzymes that have OR don't have substrate
- do not resemble substrate, so can act on more than one enzyme
- lower Vmax, but do not change Km
- cannot be overcome by excess substrate

Front 85

What are the 4 primary means of enzyme regulation?

Back 85

(1) proteolytic cleavage (irreversible covalent modification)
(2) reversible covalent modification
(3) control proteins

Front 86

proteolytic cleavage

Back 86

- irreversible covalent modification
- enzymes released into environment in inactive form (zymogen/proenzyme)
- irreversibly activated when specific bonds cleaved
- activation can be from other enzymes or chain in environment (e.g. pepsin from low pH)

Front 87

reversible covalent modification

Back 87

- enzymes activated/deactivated by phosphorylation or other modifier like AMP
- modifier removed by hydrolysis
- phosphorylation usually occurs in presence of protein kinase

Front 88

control proteins

Back 88

- protein subunits that associate w/ certain enzymes to activate or inhibit actitivity
- e.g. calmodulin, G-proteins

Front 89

allosteric interactions

Back 89

- modification of enzyme configuration from binding of activator or inhibitor at specific binding site on enzyme
- can inhibit or activate
- not necessarily noncompetitive b/c they may alter Km w/out affecting Vmax
- allosteric enzymes don't follow typical kinetics d/t multiple binding sites

Front 90

negative feedback/feedback inhibition

Back 90

shutdown mechanism for series of enzymatic reactions when there is enough product

Front 91

positive feedback

Back 91

product returns to activate the enzyme (less common than negative feedback)

Front 92

positive cooperativity

Back 92

- in allosteric enzymes, at low substrate concentrations, small increases in substrate can ave large effect
- after first substrate changes enzyme shape, it allows other substrates to bind more easily
- e.g. sigmoidal oxygen dissociation curve for Hgb

Front 93

negative cooperativity

Back 93

substrate binding to allosteric enzyme makes it harder for other substrates to bind

Front 94

6 categories of enzymes

Back 94

1. oxidoreductases
2. transferases
3. hydrolases
4. lyases (synthase catalyzes addition of one substrate to a double bond of a second substrate; e.g. ATP synthase)
5. isomerases
6. ligases (governs addition reaction but requires energy from ATP or another nucleotide; sometimes called synthetases)

Front 95

kinase

Back 95

enzyme that phosphorylates something (often in order to activate or deactive it); e.g. hexokinase phosphorylates glucose when it enters a cell

Front 96

phosphatase

Back 96

enzyme that dephosphorylates something

Front 97

hexokinase

Back 97

enzyme that phosphorylates glucose when it enters a cell

Front 98

metabolism

Back 98

- all cellular chemical reactions
- anabolism
- catabolism
- molecular degradation

Front 99

What are the 3 stages of metabolism?

Back 99

(1) macromolecules (polysaccharides, proteins, lipids) broken down into constituent parts (monosaccharides, amino acids, fatty acids/glycerol) w/ little/no energy release
(2) constituent parts oxidized to acetyl CoA, pyruvate or other metabolites forming ATP & reduced coenzymes (NADH, FADH2) in process not directly using oxygen
(3) if oxygen available, metabolites go into citric acid cycle & oxidative phosphorylation to form a lot of energy (NADH, FADH2, ATP) or recycle/expel NAD+/byproducts

Front 100

respiration

Back 100

2nd and 3rd stages of metabolism, which require energy; "aerobic" if oxygen used, "anaerobic" if not

Front 101

anaerobic respiration

Back 101

- glycolysis is first stage
- fermentation includes glycolysis & reduction of pyruvate to ethanol or lactic acid, and oxidation of NADH to NAD+

Front 102

glycolysis

Back 102

- first stage of aerobic & anaerobic respiration
- series of reactions that breaks a 6-C glucose molecule into two 3-C molecules of pyruvate
- also produces 2 ATP (from 2 ADP), inorganic phosphate & water, 2 molecules of NADH (from reduction of NAD+)
- occurs in cytosol

Front 103

pyruvate

Back 103

conjugate base of pyruvic acid

Front 104

steps of glycolysis

Back 104

(1) Glucose enters cell & is phosphoylated by hexokinase to glucose 6-phosphate (w/ phosphate from ATP) - irreversible
(2) glucose 6-phosphate goes to fructose 6-phosphate
(3) second phosphate group added from ATP - irreversible & committed to glycolytic pathway
(4) 6-carbon fructose 1,6-bisphosphate broken into Glyceraldehyde-3-phosphate (PGAL) & dihydroxyacetone phosphate [--> 2 ATP's spent at this point]
(5) each 3-C molecule phosphorylated, reducing one NAD+ to NADH
(6) 3-C molecules each transfer 1 phosphate to ADP to form 1 ATP each in substrate level phosphorylation
(7) 3-C mol. then go through 3 more steps before donating phosphate group to ADP to yield ATP & pyruvate

Front 105

Can phosphorylated molecules diffuse through a cell membrane?

Back 105

No.

Front 106

substrate level phosphorylation

Back 106

formation of ATP from ADP & inorganic phosphate using the energy released from the decay of high energy phosphorylated compounds as opposed to using energy from diffusion

Front 107

What are the inputs & outputs of glycolysis?

Back 107

2 ATPs spent
4 ATPs produced
2 pyruvate produced
2 NADH produced

Front 108

products of carbohydrate digestion

Back 108

~80% glucose
~20% fructose & galactose

Front 109

How can fructose enter glycolysis?

Back 109

as fructose 6-phosphate or glyceraldehyde 3- phosphate

Front 110

How can galactose enter glycolysis?

Back 110

can be converted to glucose 6-phosphate

Front 111

How is lactose broken down?

Back 111

- disaccharide
- broken into glucose & galactose in small intestine

Front 112

fermentation

Back 112

- anaerobic respiration
- includes glycolysis and reduction of pyruvate to ethanol/lactic acid + oxidation of NADH to NAD+
- yeasts/some microorganisms produce ethanol
- humans/some microorganisms produce lactic acid
- occurs when cell can't assimilate energy from NADH & pyruvate, or has no oxygen available to do so
- NADH recycled back into NAD+ to be coenzyme in glycolysis, and lactic acid/ethanol is expelled along w/ CO2

Front 113

aerobic respiration

Back 113

- requires oxygen
- glycolysis products move to mitochondrial matrix
- outer mitochondrial membrane permeable to small molcules & pyruvate/NADH pass thru porin via facilitated diffusion
- inner mitochondrial membrane less permeable; pyruvate enters via facilitated diffusion, but NADH entry might require ATP hydrolysis
- pyruvate converted to acetyl CoA in matrix, producing NADH & CO2

Front 114

Kreb's (citric acid) cycle

Back 114

- acetyl CoA (coenzyme) transfers 2 carbons to 4-carbon oxacloacetic acid
- each turn of cycle produces:
1 ATP
3 NADH
1 FADH2
- ATP produced via substrate-level phosphorylation
- 2 C's lost as CO2
- oxaloacetic acid reproduced to begin cycle over agian

Front 115

triglyceride catabolism for energy production

Back 115

- fatty acids converted to acyl CoA along outer mitochondrial membrane & ER (uses 1 ATP)
- acyl CoA brought into matrix, where 2 C's at a time are cleaved to make acetyl CoA (this produces FADH2 & NADH for every 2 carbons taken from original fatty acid)
- acetyl CoA enters Krebs cycle
- glycerol backbone converted to PGAL

Front 116

amino acids used for energy

Back 116

deaminated in liver then chemically converted to pyruvic acid or acetyl CoA, or may enter Krebs cycle at various stages

Front 117

electron transport chain

Back 117

- series of proteins (including cytochromes w/ heme) in inner mitochondrial membrane
- first protein complex accepts NADH's high energy electrons and oxidizes it to NAD+
- electrons passed down protein series & finally accepted by oxygen to form water (why aerobic needs oxygen)
- during this process, protons are pumped into IM space (lower pH than matrix) for each NADH, establishing proton-motive force (gradient) that propels protons through ATP synthase to make ATP ["oxidative phosphorylation"]
- 2-3 ATPs made for each NADH
- FADH2 reduces a protein further along in ETC than NADH does, so only produces 2 ATPs

Front 118

net equation for cellular respiration

Back 118

C6H12O6 + 6O2 --> 6 CO2 + 6 H2O
[combustion reaction]