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MCAT > BIOCHEMISTRY FINAL REVIEW > Flashcards

BIOCHEMISTRY FINAL REVIEW Flashcards

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1
Q

Only amino acid with an R absolute configuration

A

Cysteine, still qualifies as an L-amino acid though

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2
Q

pKa for carboxyl group of amino acid

A

usually around 2

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3
Q

pKa for amino group of amino acid

A

between 9 and 10

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4
Q

amino acid charge under acidic conditions and basic conditions

A

AAs are positively charged under acidic conditions, negatively charged under basic conditions -acidic AAs are negatively charged, basic AAs are positively charged

(under physiological pH the acidic group is removed on acidic amino acids)

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5
Q

Calculating pI

A

pI of an acidic amino acid = average two most acidic groups pI of a basic amino acid = average two most basic groups

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6
Q

Peptide bond formation, rotation, and hydrolysis

A

peptide bond formation is a condensation or dehydration reaction between an amino terminus and a carboxy terminus

no rotation because of partial double bond character

in living organisms hydrolysis is catalyzed by trypsin and chymotrypsin

in organic chemistry hydrolysis can be catalyzed by acids or bases

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7
Q

Proline effects on DNA

A

Because of its rigid cyclic structure, proline will introduce a kink in the peptide chain when it is found in the middle of an alpha helix however, in beta-pleated sheets it is found in the turns

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8
Q

Tertiary structure interactions

A

Tertiary structure is determined by hydrophilic and hydrophobic interactions between R groups, as well as hydrogen bonding and acid-base interactions between amino acids with charged R groups, and disulfide bonds

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9
Q

Disulfide bonds

A

Disulfide bonds form from two cysteines oxidized to cystine create loops in the protein chain, determine how wavy hair is forming requires the loss of two protons and two electrons (oxidation)

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10
Q

Quarternary structures special characteristics

A

Quaternary structures can induce cooperativity or allosteric effects

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11
Q

Conjugated proteins

A

Conjugated proteins derived part of their function from covalently attached prosthetic groups Lipoproteins, glycoproteins, and nucleoproteins are named differently due to the type of prosthetic group

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12
Q

Oxidoreductases

A

oxidation-reduction reactions, the transfer of electrons Includes dehydrogenases, reducatases, and oxidases

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13
Q

Transferases

A

catalyze the movement of a functional group includes kinases, which transfer a phosphate group

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14
Q

Hydrolases

A

catalyze hydrolysis (cleavage of a compound using water)

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15
Q

Lyases

A

catalyze the cleavage of a single molecule into two products without water

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16
Q

Isomerases

A

Rearrange the bonds within a molecule Some can also be classified as oxidoreductases, transferases, or lyases

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17
Q

Ligases

A

catalyze addition or synthesis reactions encountered in nucleic acid synthesis and repair

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18
Q

Cofactors and Coenzymes

A

Cofactors are generally inorganic molecules or metal ions, coenzymes are small organic groups derived from vitamins

Participate in the catalysis of the reaction, usually by carrying charge through ionization, protonation, or deprotonation

Enzymes without their cofactors are called apoenzymes, whereas those containing them are holoenzymes

Tightly bounds ones are known as prosthetic groups

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19
Q

Michaelis-Menton plot and equation

A

A Michaelis-Menton plot relates velocity to concentration

v = (vmax*[S]) / (Km + [S]) velocity of reaction =

(maximum velocity * concentration) / (concentration at half vmax + concentration)

Km is known as the Michaelis constant, lower Km = higher affinity

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20
Q

Lineweaver-Burk

A

A Lineweaver-Burk plot is a double reciprocal of the Michaelis-Menton equation

The y-intercept is the reciprocal of Vmax, the x-intercept is the reciprocal of Km

Both Vmax and Km increase in value as they go towards the origin

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21
Q

Cooperativity enzyme kinetics; Hill’s coefficient

A

show a sigmoidal relationship on a Michaelis-Menton plot

Binding of a substrate encourages the transition of other subunits from the T(tense) state to the R(relaxed) state

Hill’s coefficient quantifies cooperativity; >1 = positively cooperative, <1 = negatively cooperative

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22
Q

Effect of Temperature on enzyme kinetics

A

enzyme-catalyzed reactions tend to double in velocity for every 10C until optimal temperature is reached, for the human body, this is 37C

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23
Q

Effect of pH on enzyme kinetics

A

optimal pH is 7.4 for most enzyme catalyzed reactions

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24
Q

effect of Salinity on enzyme kinetics

A

Increasing levels of salt can disrupt hydrogen and ionic bonds

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25
Q

Feedback regulation enzymes

A

enzymes being subject to the products of their reactions

negative feedback

opposite is forward regulation

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26
Q

Competitive inhibition

A

Occupies the active site

Does not change Vmax but increases Km

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27
Q

Noncompetitive inhibition

A

Occupies the allosteric site

Decreases Vmax but does not change Km

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28
Q

Mixed inhibition

A

Inhibitor can bind to either enzyme or the ES complex, but has different affinity for each

Bind to allosteric site

Alters the Km depending on the preference of the inhibitor for the enzyme vs the enzyme-substrate complex

  • if it binds to the enzyme, it increases the Km
  • if it binds to the complex, it lowers Km
  • always decreases the Vmax
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29
Q

Uncompetitive inhibition

A

binds to the ES complex and locks the substrate in the enzyme

-can be interpreted as increasing affinity

Lowers Km and Vmax

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30
Q

Irreversible inhibition

A

the active site is made unavailable or the enzyme is permanently altered

-a prime drug mechanism

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31
Q

allosteric enzymes

A

Alternative between an active or inactive form

Molecules that bind may either be activators or inhibitors

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32
Q

covalently modified enzymes

A

Enzymes can be activated or deactivated by phosphorylation or dephosphorylation

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33
Q

collagen

A

has a characteristic trihelical fiber and makes up most of the extracellular matrix of connective tissue

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34
Q

elastin

A

another important component of the extracellular matrix primary role is to stretch and recoil

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35
Q

keratin

A

intermediate filament proteins found in epithelial cells contribute to the mechanical integrity of the cell makes up hair and nails

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36
Q

actin

A

makes up microfilaments and the thin filament in myofibrils most abundant protein in eukaryotes have a positive side and a negative side allows motor proteins to travel unidirectionally along

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37
Q

tubulin

A

makes up microtubules

important for structure, chromosome separation, intracellular transport using kinesins and dyneins

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38
Q

myosin

A

primary motor protein that interacts with actin

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39
Q

kinesins and dyneins

A

motor proteins associated with microtubules have two heads, one of which remains attached to tubulin at all times

align chromosomes, bring vesicles toward one end

positive-kinesins, negative-dyneins

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40
Q

examples of binding proteins

A

hemoglobin, calcium-binding proteins, DNA-binding proteins, etc

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41
Q

Cell adhesion molecules

A

CAMs proteins found on the surface of most cells and aid in binding the cell to the extracellular matrix of other cells (Ex: cadherins, interns, selections)

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42
Q

cadherins

A

group of glycoproteins that mediate calcium-dependent cell adhesion

usually hold similar cells together, such as epithelial cells

bind to each other

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43
Q

integrins

A

have two membrane-spanning chains called alpha and beta

binding and communicating with the extracellular matrix

cellular signalling can promote cell division, apoptosis, or other processes

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44
Q

selectins

A

bind to carbohydrate molecules that project from other cell surfaces

weakest bonds formed by the CAMs

expressed on white blood cells and the endothelial cells that line blood vessels

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45
Q

Antibody three functions

A

Neutralize - unable to exert its effect

Opsonize - mark for destruct

Agglutinate - clump together

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46
Q

Ion channels - ungated channels

A

no gates and therefore unregulated

ex: ungated potassium channels to keep potassium at equilibrium

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47
Q

ion channels- voltage-gated channels

A

regulated by the membrane potential change near the channel

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48
Q

ion channels- ligand-gated channels

A

regulated by the binding of a specific substance or ligand to the channel

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49
Q

enzyme-linked receptors

A

Membrane receptors that display catalytic activity in response to ligand binding

Have three primary protein domains

Often results in the initiation of a second messenger cascade

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50
Q

three domains of enzyme linked receptors

A

Membrane spanning domain- anchors the receptor in the cell membrane

Ligand-binding domain- stimulated by the appropriate ligand

Induces a conformational change that activates the catalytic domain

Catalytic domain exhibits the function, often second messenger

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51
Q

G protein-coupled receptors

A

Large family of integral membrane proteins involved in signal transduction

Has 7 membrane spanning alpha-helices

In order to transmit signals, they use a heterotrimeric G protein

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52
Q

heterotrimic G protein of G protein-coupled receptors

A

alpha, beta, and gamma subunits interaction

alpha subunit binds GDP and is in a complex with the beta and gamma subunits

Once GDP is replaced with GTP, the alpha subunit is able to dissociate from the beta and gamma subunits

the activated alpha subunit alters the activity of adenylate cyclase, either activating or inhibiting it

Once the GTP is dephosphorylated to GDP, the alpha subunit will rebind to the beta and gamma subunits

The binding of the G protein represents a switch to the active state and affects the intracellular signalling pathway

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53
Q

Three main types of G proteins

A

Gs stimulates adenylate cyclase - increases levels of cAMP

Gi inhibits adenylate cyclase - decreases levels of cAMP

Gq activates phospholipase C - forms PIP - increases levels of IP3

-IP3 opens calcium channels in the endoplasmic reticulum, increasing calcium levels

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54
Q

Homogenization of protein

A

crushing, grinding, or blending the tissue into an evenly mixed solution

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55
Q

migration velocity equation

A

V = Ez/f

migration velocity is proportional to to electric field strength and the net charge on the molecule, inversely proportional to the frictional coefficient f

f is dependent on the mass and shape of the molecule

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56
Q

native PAGE and limitations/benefits

A

Polyacrylamide gel electrophoresis

Analyzes proteins in their native states

Limited by varying size combined with varying mass-to-size ratios of cellular proteins

multiple proteins may experience the same level of migration functional

native protein can be recovered if no stain has been use

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57
Q

SDS Page and limitations/benefits

A

separates proteins based on mass alone

The addition of sodium dodecyl sulfate neutralizes the proteins original charge with large chain negative charges and denatures the proteins

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58
Q

Isoelectric focusing; anode/cathode

A

Separated on the basis of isoelectric point

mixture of proteins is placed in a gel with a pH gradient

acidic at positive anode, basic at negative cathode

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59
Q

Chromatography general principles

A

the more similar the compound is to its surroundings the more slowly it will move through its surroundings

Stationary phase/adsorbent + mobile phase

varying retention times of each compound in the solution results in separation of the components within the stationary phase, or partitioning

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60
Q

column chromatography

A

a column is filled with polar beads and a nonpolar solvent is poured through

the solvents qualities can be changed to help elute the protein of interest

the less polar the compound the faster it can elute through

can be used to separate and collect other macromolecules besides protein, such as nucleic acids

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61
Q

ion-exchange chromatography

A

a column is filled with charged beads to attract compounds with an opposite charge

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62
Q

size-exclusion chromatography

A

a column is filled with beads containing tiny pores, small compounds get caught in the pores and take longer to travel through

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63
Q

affinity chromatography

A

customized column to bind any protein of interest once the protein is retained in the column, it can be eluted by washing the column with a free receptor (or target or antibody), which will compete with the bead-bound receptor and free the protein from the column

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64
Q

typical methods of determining protein structure

A

X-ray crystallography and nuclear magnetic resonance can determine protein structure

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65
Q

determining composition of small proteins

A

Small proteins are best analyzed with the Edman degradation, which uses cleavage to sequence proteins of up to 50 to 70 amino acids selectively and sequentially removes the N-terminal amino acid of the protein, which can be analyzed via mass spectroscopy

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66
Q

determining composition of larger proteins

A

Larger proteins can use chymotrypsin, trypsin, and cyanogen bromide

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67
Q

activity analysis typical procedure

A

protein activity is generally determined by monitoring a known reaction with a given concentration of substrate and comparing it to a standard

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68
Q

Concentration determination- spectroscopy

A

Concentration is determined almost exclusively through spectroscopy

UV spectroscopy can detect aromatic side chains

This is sensitive to sample contaminates

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69
Q

Concentration determination- Bradford protein assay

A

one of several reactions that causes colorimetric changes in response varying levels of concentration -most popular because reliable and simple

mixes a protein with Coomassie Brilliant Blue

-The dye gives up protons in response to amino links

increased concentration causes larger concentrations of blue dye

-less accurate for multiple proteins, limited by presence of detergent or excessive buffer

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70
Q

Carbohydrate nomenclature

A

Aldoses are carbohydrates that contain an aldehyde group

Ketose are carbohydrates that contain a ketone group (completely oxidized)

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71
Q

Glyceraldehyde structure

A

simplest aldose (CH2-OH)-(CHOH)-(CHO)

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72
Q

Dihydroxyacetone

A

simplest ketose (CH2-OH)-(CO)-(CH2-OH)

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73
Q

Stereoisomers, enantiomers, epimers

A

In terms of difference in chirality:

Stereoisomers differ at more than one

enantiomers differ at all

epimers differ at only one

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74
Q

number of stereoisomers with common backbone equation

A

2^number of chiral centers

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75
Q

D or L assignment

A

All monosaccharides are assigned D or L based on whether the furthest hydroxide from the carbonyl points towards the right(D) or the left(L)

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76
Q

Fischer projection conversion

A

Sides of a skeleton model = Wedge = coming towards you

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77
Q

Cyclic sugar formation

A

Monosaccharides contain both a nucleophilic hydroxyl group and an electrophilic carbonyl group, which can allow them to form cyclic hemiacetals and hemiketals

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78
Q

nomenclature cyclic monosaccharides

A

hemiacetals are from aldoses

hemiketals are from ketones

pyranoses are six carbon

furanose are five carbon

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79
Q

anomer definition

A

anomers are epimers that differ at their anomeric carbon

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80
Q

alpha vs beta anomer

A

alpha anomer has the -OH group trans and down to the CH2OH substituent

beta anomer has the -OH group cis and up to the CH2OH substituent

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81
Q

Haworth and Fischer conversion

A

When we convert from straight chain to haworth (cyclic) projection, any group on the right in the fischer projection will point down in the Haworth projection

in determining L or D assignment, remember that D can equal down and l can equal left

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82
Q

Mutarotation

A

exposing hemiacetal rings to water will cause them to spontaneously cycle between the open and closed form

Because the substituents on the single bond between C-1 and C-2 can rotate freely, either the alpha or beta anomer can be formed

the alpha is less favored due to the axial hydroxyl group adding steric strain

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83
Q

Oxidized aldoses and reducing sugars

A

Oxidized aldoses are called aldonic acids

any monosaccharide with a hemiacetal ring is considered a reducing sugar

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84
Q

test for reducing sugars (hemiacetal rings)

A

Tollen’s reagent is Ag(NH3)2, tests for reducing sugars -produces a mirror like product

Benedict’s reagent is from copper, tests for reducing sugars -produces a dark red product

ketose sugars are also reducing sugars and give positive results to those tests under basic conditions, where they tautomerize to form aldoses

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85
Q

Esterification of carbohydrates

A

carbohydrates can participate in reactions with carboxylic acids and derivatives to form esters

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86
Q

Glycoside formation from carbohydrates

A

Hemiacetals react with alcohols to form acetals

The resulting carbon-oxygen bond are called glycosidic bonds, the acetals formed are glycosides

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87
Q

Disaccharide formation and three important disaccharides

A

Glycosidic bonds formed between hydroxyl groups of two monosaccharides form a disaccharide

Sucrose(GluFru), lactose(GluGal), and maltose(GluGlu)

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88
Q

Cellulose

A

beta-D-glucose molecules linked via beta-1,4 glycosidic bonds

hydrogen bonds holding the chains together for support

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89
Q

Starches

A

alpha-d-glucose molecules linked via alpha-1,4-glycosidic bonds (amylose) or alpha-1,4 AND alpha-1,6-glycosidic bonds (amylopectin)

Iodine tests for starch

beta-amylase cleaves at nonreducing end, alpha-amylase cleaves randomly

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90
Q

Glycogen and Glycogen phosphorylase

A

similar to starch but with more alpha-1,6-glycosidic bonds

-1/10 as opposed to 1/25

Glycogen phosphorylase cleaves glucose from the nonreducing end and phosphorylates it, producing glucose 1-phosphate -important for metabolism

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91
Q

Lipid saturation

A

saturated only have single bonds, more stable structure, form solids

unsaturated have double bonds, less stable structure, form liquids

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92
Q

phospholipids

A

contain a phosphate and alcohol joined to a fatty acid tail by phosphodiester linkages

can be further classified according to the backbone

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93
Q

glycerophospholipids

A

a type of phospholipid that contains a glycerol backbone bonded by ester linkages to two fatty acids and by a phosphodiester linkage to a highly polar head group membrane lipid

important in cell recognition, signalling, and binding

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94
Q

sphingolipids

A

like glycerophospholipids in that they are sites of recognition and bonded at cell surface

has a sphingosine or sphingoid backbone

many are phospholipids because they contain a phosphodiester linkage four groups

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95
Q

Four groups of sphingolipids

Sphingophospholipids

Sphingomyelins

Glycosphingolipids

Gangliosides

A

Sphingophospholipids contain phosphodiester bond and are therefore a type of phospholipids

Sphingomyelins are the major class of sphingophospholipids and contain a phosphatidylcholine or phosphatidylethanolamine head group

-major component of the myelin sheath

Glycosphingolipids are attached to sugar moieties instead of a phosphate group

  • Cerebrosides have one sugar, globosides have more than one sugar
  • Outer surface of the plasma membrane

Gangliosides contain oligosaccharides with at least one terminal

-NANA, sialic acid -Cell interaction, recognition, and signal transduction

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96
Q

waxes

A

esters of long-chain fatty acids with long-chain alcohols function for protection and to prevent evaporation (plants) or dehydration (animals)

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97
Q

signaling lipids general mechanisms

A

lipids serve as coenzymes in the electron transport chain and in glycosylation reactions

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98
Q

terpenes and terpenoids

A

built from isoprene (C5H8)

metabolic precursors to steroids and other lipid signaling molecules like vitamin A

varied independent functions

Terpenoids are derivatives of terpenes that have undergone oxygenation or rearrangement of the carbon skeleton

Further modified (like terpenes) by the addition of an extensive variety of functional groups

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99
Q

terpene/terpenoid nomenclature

A

Group according to the number of isoprene units

a single terpene unit contains two isoprene units

Monoterpenes (C10H16) are two isoprene units

Sesquiterpenes are three isoprene units

Diterpenes are four isoprene units…

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100
Q

steroids and cholesterol

A

metabolic derivatives of terpenes, nonpolar

steroid hormones are steroids that act as hormones

testosterone, estrogens, cortisol, aldosterone

Cholesterol

  • steroid and steroid precursor
  • major component of the phospholipid bilayer responsible for membrane fluidity
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101
Q

prostaglandins

A

produced by all cells, not just prostate gland cells

unsaturated carboxylic acids derived from arachidonic acid

regulate the synthesis of cAMP, which in turn regulates other hormones

  • downstream effects include effects on smooth muscle, sleep-wake cycle, elevation of body temperature
  • NSAIDs like aspirin inhibit the production COX, part of the prostaglandins pathway
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102
Q

which are the fat-soluble vitamins

A

ADEK

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103
Q

vitamin A

A

vitamin A - carotene unsaturated hydrocarbon important in vision, growth and development, and immune function aldehyde form retinal

  • eyesight carboxylic acid form retinoic acid
  • regulates gene expression during epithelial development
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104
Q

vitamin D

A

vitamin D

  • cholecalciferol can be consumed or formed from UV light in the skin

converted to calcitriol in kidneys (biologically active)

increases calcium and phosphate uptake, which promotes bone growth

Rickets if lack of vitamin D

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105
Q

vitamin E

A

substituted aromatic ring with a long isoprenoid reacts with free radicals (biological antioxidant)

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106
Q

vitamin K

A

a group of compounds including phylloquinone and the menaquinones vital to the production of prothrombin (clotting factor)

also introduces calcium-binding sites on several calcium-dependent proteins

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107
Q

triacylglycerols

A

most efficient way to store energy, twice as good as carbohydrates

three fatty acids bonded by ester linkages to glycerol

adipocytes store large amount of triacylglycerols

physical characteristics primarily determined by the level of saturation primarily observed as oily droplets in cytosol

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108
Q

Free fatty acids and saponification

A

Free fatty acids are unesterified fatty acids with a free carboxylate group

Saponification is the ester hydrolysis of triacylglycerols using a strong base known as lye creates soaps which act as surfactants (lower surface tension)

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109
Q

Nucleosides vs nucleotides

A

Nucleosides are a pentose bonded to a nitrogenous base with a covalent linkage to C-1’ of the sugar

Nucleotides are formed when one or more phosphate groups are attached to the C-5’ of the sugar

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110
Q

sugar-phosphate backbone

A

the backbone of DNA is alternating sugar and phosphate group

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111
Q

purines and pyrimidines, identiy each one

A

Purines are Adenine (-NH2) and Guanine (=O) two rings

Pyrimidines are Cytosine (-NH2), Uracil (=O x2), and Thymine(-CH3) examples of biological aromatic heterocycles

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112
Q

B-DNA and Z-DNA

A

The double helix of most DNA is a right-handed helix (B-DNA) makes a turn every 3.4nm and contains about 10 bases within that span

left-handed Z-DNA has a zigzag appearance has a turn every 4.6nm and contains about 12 bases within each turn high GC content or high salt concentration

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113
Q

Denaturation of protein

A

Heat, alkaline pH, formaldehyde and urea can denature DNA

DNA can be annealed if the denaturing condition is slowly removed important step in PCR

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114
Q

Eukaryotic chromosome organization - Histones

A

DNA that makes up a chromosome is wound around a group of small basic proteins called histones, forming chromatin

There are five histone proteins, two copies each form a histone core

about 200 base pairs of DNA wrap around this complex, forming a nucleosome examples of nucleoproteins (proteins that associate with DNA)

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115
Q

Eukaryotic chromosome organization- Heterochromatin and Euchromatin

A

During interphase chromosomes have a diffuse configuration, chromatin

A small percentage of the chromatin remains compacted during interphase and is referred to as heterochromatin, whereas the rest is called euchromatin

Heterochromatin - appears dark under light, is transcriptionally silent

Euchromatin - appears light under light, is genetically active

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116
Q

Eukaryotic chromosome organization- Telomeres and Centromeres

A

Telomeres are maintained by telomerase, which is more highly expressed in rapidly dividing cells

have a high GC content

Centromeres are regions of DNA found in the center of chromosomes, composed of heterochromatin, and also with high GC content

During cell division, the two sister chromatids can therefore remain connected at the centromere until microtubules separate the chromatids during anaphase

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117
Q

DNA replication- origin

A

The replisome or replication complex is a set of specialized proteins that assist the DNA polymerases

DNA begins replication at the origin of replication

-In bacterial chromosomes there is a single origin of replication on a closed, double-stranded circular DNA molecule

As the replication forks move toward each other and sister chromatids are created, the chromatids will remain connected at the centromere

Helicase is responsible for unwinding the DNA ssDNA-binding proteins bind to the unraveled strand, preventing both the reassociation of the DNA strands and the degradation of DNA by nucleases

DNA topoisomerases reduce the torsion of supercoiling be introducing negative supercoils

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118
Q

DNA replication- Synthesis of daughter strands

A

primase synthesizes a short RNA primer to start replication on each strand

DNA polymerase III (prokaryotes) or DNA polymerases alpha, beta, and epsilon begin synthesizing the daughter strands of DNA in the 5’ to 3’ direction

-DNA polymerases read the template in a 3’ to 5’ direction

DNA polymerase I (prokaryotes) or RNase H (eukaryotes) removes the RNA primer

DNA polymerase I (prokaryotes) or DNA polymerase gamma (eukaryotes) adds DNA nucleotides to where the primer had been

DNA ligase seals the ends of the DNA molecules together

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119
Q

DNA replication- Replicating the ends

A

DNA polymerase cannot complete synthesis of the 5’ end so it keeps getting shorter -telomeres help protect against this

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120
Q

DNA repair- oncogenes and tumor suppressor genes

A

mutated genes that cause cancer are termed oncogenes

-before these genes mutate, they are referred to as proto-oncogenes

tumor suppressor genes, like p53 or Rb (retinoblastoma), encode proteins that inhibit the cell cycle or participate in DNA repair processes

-sometimes called antioncogenes

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121
Q

DNA proofreading and mismatch repair

A

proofreading

  • part of the DNA polymerase enzyme proofreads the enzyme
  • looks at the level of methylation to determine which one needs to be repaired, the template strand will have higher methylation
  • DNA ligase lacks proofreading ability
  • the lagging strand is much more likely to have mutations

mismatch repair

  • G2 phase cells have machinary for mismatch repair
  • detect and remove errors introduce in replication that were missed during S phase encoded by genes MSH2 and MLH1
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122
Q

nucleotide excision repair

A

UV light induces the formation of dimers between adjacent thymine residues in DNA, which distorts the shape of the double helix.

These are eliminated by a nucleotide excision repair (NER)

  • cut and patch process, specific proteins scan the DNA molecule and recognize the lesion as a bulge
  • an excision endonuclease makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligonucleotide
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123
Q

base excision repair

A

the affected base is recognized and removed by a glycosylase enzyme, leaving behind an apurinic/apyrimidinic (AP) site, or abasic site
this site is recognized by an AP endonuclease that removes the damaged sequence from the DNA

DNA polymerase and DNA ligase can then fill in the gap and seal the strand

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124
Q

recombinant DNA biotechnology purpose

A

Recombinant DNA technology allows a DNA fragment from any source to be multiplied by either gene cloning or polymerase chain reaction

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125
Q

DNA cloning steps

A

1 Cloning requires the investigator ligate the DNA of interest into a piece of nucleic acid referred to as a vector, forming a recombinant vector Vectors are usually bacterial or viral plasmids

2 The vector is then transferred to a host bacterium which is grown in colonies, and a colony containing the recombinant vector is isolated (accomplished because the recombinant vector also contains a gene for antibiotic resistance)

3 The bacteria can then be made to express the gene of interest to gather protein, or be lysed to reisolate the replicated recombinant vectors

126
Q

Restriction enzymes

A

Endonucleases that recognize specific palindromic double-stranded DNA sequences

  • Isolated from bacteria
  • some produce offset cuts, yielding sticky ends that are advantageous in facilitating the recombination of a restriction fragment with the vector DNA
127
Q

DNA libraries and cDNA

A

DNA fragments are cloned into vectors and can be utilized for further study

cDNA (complementary DNA) libraries are constructed by reverse-transcribing processed mRNA

-cDNA lacks introns, these libraries are sometimes called expression libraries

128
Q

hybridization definition

A

the joining of complementary base pair sequences

129
Q

polymerase chain reaction (PCR)

A

1 Know the sequences that flank the desired region of DNA

2 Use primers with high GC content that are complementary to the DNA that flanks the desired region

3 DNA polymerase from an extremophile bacteria is used to replicate due to hot temperatures

4 The DNA of interest is denatured, replicated, and then cooled to allow reannealing of the daughter strands with the parent strands. This process is repeated several times, doubling the amount of DNA with each cycle, until enough copies are available

130
Q

Gel electrophoresis

A

all DNA strands will migrate toward the anode of an electrochemical cell

the longer the strand the slower it will migrate

131
Q

Southern blot

A

A southern blot detects the presence and quantity of various DNA strands by using radiolabeled or indicator probes made from complementary DNA

-DNA is cut by restriction enzymes beforehand

132
Q

DNA sequencing

A

uses template DNA, primers, DNA polymerase, all four dNTPs, and ddNTPs as well

  • the ddNTPs contain a hydrogen rather than a hydroxyl group, once they are added the chain cannot extend the fragments are separated by size using gel electrophoresis, and the last base for each fragment can be read
  • because it separates by size, the bases can be read in order
133
Q

Gene therapy

A

transfers a normal copy of the gene efficient gene delivery vectors must be used, most are modified viruses

134
Q

Transgenic and Knockout Mice

A

transgenic mice are altered at their germ line through the introduction of a cloned gene, referred to as a transgene

knockout mice are transgenic mice with a gene removed instead of introduced

serve as models

135
Q

mRNA purpose

A

carries the information specifying the amino acid sequence to the ribosome in eukaryotes

monocistronic (only codes for one protein product), in prokaryotes can be polycistronic

-starting the process of translation at different locations in the mRNA can result in different proteins in prokaryotes

136
Q

tRNA purpose

A

responsible for converting the language of nucleic acids into the language of amino acids/proteins

Each type of amino acid requires two high-energy bonds from ATP, the attachment of the amino acid is an energy-rich bond

The aminoacyl-tRNA synthetase transfers the activated amino acid to the 3’ end of the correct tRNA

Each tRNA has a CCA nucleotide sequence where the amino acid binds

137
Q

rRNA purpose

A

synthesized in the nucleolus for the ribosomal machinery

many rRNA molecules function as ribozymes (enzymes made of RNA molecules)

138
Q

Codons, stop codons

A

three letter gene sequence recognized by anticodons to translate into an amino acid

Stop codons are UGA, UAG, UAA

139
Q

Missense, nonsense, and frameshift mutations

A

Missense one amino acid substitutes for another

Nonsense premature stop codon

Frameshift insertions or deletions shift the reading frame

140
Q

Transcription location and why

A

the machinery to generate a protein is located in the cytoplasm

DNA cannot leave the nucleus, so it must use RNA to transmit genetic information

141
Q

Mechanism of transcription

A

helicase and topoisomerase unwind the double-stranded DNA

RNA polymerase locates genes by searching for specialized DNA regions known as promoter regions

RNA polymerase II binds to the TATA box of the promoter region

  • transcription factors help the RNA polymerase locate and bind
  • TATA box is -25 nucleotides upstream travels in a 3’ -> 5’ direction does not proofread
142
Q

Types of Eukaryotic RNA polymerase

A

RNA Polymerase I - synthesizes rRNA

RNA Polymerase II - synthesizes hnRNA (pre-processed mRNA)

RNA Polymerase III - synthesizes tRNA and some rRNA

143
Q

types of posttranscriptional processing in eukaryotes

A

splicing, 5’ Cap, 3’ Poly-A tail

144
Q

splicing

A

removing introns and ligating exons using the spliceosome, where snRNA/snRNPs complex recognize both the 5’ and 3’ ends of the introns, and they are excised in the form of a lariat

145
Q

5’ cap

A

a 7-methylguanylate triphosphate cap added to the 5’ end protects the mRNA from degradation

146
Q

3’ Poly-A tail

A

a polyadenosyl tail is added to the 3’ end of the mRNA transcript to protect against degradation

the longer the tail the more time the mRNA will be able to survive before being digested in the cytoplasm

147
Q

alternative processing

A

the primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of protein

148
Q

Ribosome relationship to RNA

A

has three binding sites for tRNA: A site, P site, E site

has one binding site for mRNA,

once the mRNA binds the two subunits come together, creating a compact that keeps the mRNA and tRNA in stable and proper orientation for protein synthesis

149
Q

prokaryotic vs eukaryotic ribosomes

A

Eukaryotic has a 40S and a 60S subunit making an 80S ribosome

Prokaryotic has a 30S and a 50S subunit making a 70S ribosome

150
Q

timing of translation prokaryotes vs eukaryotes

A

In prokaryotes, the ribosomes start translating before the mRNA is complete

In eukaryotes, transcription and translation occur at separate times and in separate locations

151
Q

Initiation of translation

A

In prokaryotes, the small subunit binds to the Shine-Dalgarno sequence in the 5’ untranslated region of the mRNA

In eukaryotes, the small subunit binds to the 5’ cap structure

The charged initiator tRNA binds to the AUG start codon

The large subunit then binds to the small subunit

-assisted by initiation factors

152
Q

Elongation of translation

A

The A site receives the incoming amino acid

The P site holds the tRNA that carries the growing chain

  • also where the first amino acid (met) binds
  • A peptide bond is formed between the P and A site AA

–this requires peptidyl transferase, GTP is used

The E site is where the now uncharged tRNA unbinds

Elongation factors assist by locating and recruiting aminoacyl-tRNA along with GTP

Signal sequences in some eukaryotic proteins designate a particular destination for the protein

153
Q

Termination of translation

A

When any of the three stop codons moves into the A site, a release factor binds to the termination codon, causing hydrolysis of the completed polypeptide chain from the final tRNA

154
Q

Posttranslational processing

A

Chaperones assist in the protein-folding process after synthesis

Many proteins are modified by cleavage events

Other biomolecules may be added to the peptide

155
Q

covalent additions to peptide in posttranslation

A

Phosphorylation - addition of phosphate group

Carboxylation - addition of carboxylic acid group

Glycosylation - addition of oligosaccharides

Prenylation - addition of lipid groups

156
Q

Prokaryotic translation- operons definition

A

“On-off switch” in which genes share a promoter and are transcribed as a group

157
Q

Jacob-Monod model

A

Jacob-Monod model describes the structure and function of operons

structural genes - codes for proteins of interest

operator site - capable of binding a repressor protein

promoter site - similar to eukaryotic promoters, RNA polymerase binds

a regulator gene - codes for a protein known as the repressor

158
Q

Inducible systems

A

the repressor is bonded tightly, this system is negative control

to remove the block an inducer must bind the repressor protein

operate similar to competitive inhibition, as the concentration of inducer increases it pulls more of the repressor off of the operator region, freeing up those genes for transcription

159
Q

lac operon

A

inducible system bacteria can digest lactose but prefer glucose

the lac operon only operates in the presence of lactose

assisted by binding of catabolite activator protein (CAP)

example of positive control

160
Q

Repressible Systems

A

allow for constant production, the repressor is inactive until it binds to a corepressor

tends to serve as negative feedback

161
Q

trp operon

A

tryptophan acts as a corepressor, the cell turns off its machinery to synthesize its own tryptophan

162
Q

eukaryotes- transcription factors

A

recognizes specific sequences and recruits transcriptional machinery

DNA binding domain - recognizes certain sites and binds

Activation domain - allows for the binding of several transcription factors and important regulatory proteins

163
Q

Enhancers

A

Response elements can be recognized by specific transcription factors, several response elements may be grouped together to form an enhancer, which allows for the control of one gene’s expression by multiple signals

Signal molecules such as cyclic AMP, cortisol, and estrogen bind to specific receptors

Enhancer regions can be up to 1000 bp away from the gene they regulate, even located within an intron

-in contrast, upstream promoter elements must be within 25 bases

164
Q

Gene duplication

A

genes can be duplicated in series on the same chromosome

genes can also be duplicated in parallel by opening the gene with helicases and permitting DNA replication only of that gene

165
Q

Regulation of Chromatin Structure - Histone Acetylation

A

histone acetylases are recruited by transcription factors

these acetylate lysine residues of histone proteins, decreasing the positive charge on lysine residues and weakening the interaction of the histone with DNA, resulting in an open chromatin conformation

histone deacetylases do the opposite

166
Q

DNA Methylation

A

DNA methylases add methyl groups to cytosine and adenine nucleotides linked to gene silencing

  • important in development, where it silences genes that no longer need to be activated
  • heterochromatin is much more heavily methylated
167
Q

general membrane structure and function

A

fat-soluble compounds cross easily, while larger and water-soluble compounds need alternative entry

Carbohydrates associated with membrane-bound proteins create a glycoprotein coat

Proteins embedded act as cellular receptors during signal transduction

168
Q

Membrane dynamics in the fluid mosaic model, lipid rafts, flippases

A

Phospholipids move rapidly in the plane of the membrane through simple diffusion

lipid rafts are collections of similar lipids (maybe with associated proteins) that serve as attachment points for other biomolecules and play a role in signalling

lipid rafts and proteins travel more slowly through the membrane

flippases assist in the transition or “flip” between layers

Many cells can up- or downregulate the number of specific cellular receptors on their surface in order to meet cellular requirements

169
Q

Membrane components - Fatty Acids and Triacylglycerols

A

when incorporated into phospholipid membranes, saturated fatty acids decrease the overall membrane fluidity

170
Q

Membrane components - Phospholipids

A

substituting one of the fatty acid chains of triacylglycerol with a phosphate group

a polar group joins the nonpolar tails

spontaneously assemble into micelles or liposomes

serve structural roles and can act as second messengers

171
Q

Membrane components - Sphingolipids

A

similar to phospholipids but without a glycerol

have various classes depending on the identity of their hydrophilic regions

172
Q

Membrane components - Cholesterol and Steroids

A

cholesterol regulates membrane fluidity

at lower temperatures, cholesterol occupies the space between adjacent phospholipids prevents crystal structure formation

at higher temperatures it limits movement of phospholipids within the bilayer

by mass, it composes 20%; by mole fraction, 50%

173
Q

Membrane components - Waxes

A

long chain fatty acid and long chain alcohol, rarely present in cell membrane unless in plants

can provide both stability and rigidity within the nonpolar tail region only

174
Q

Membrane components - Proteins

A

together, transmembrane (through) and embedded (interior) proteins are considered integral because they associate with the interior of the membrane

membrane-associated (peripheral) proteins are bound to the lipid bilayer

175
Q

Membrane components - Carbohydrates

A

generally attached to protein molecules on the extracellular surface, act as signaling and recognition molecules

blood antigens are sphingolipids that differ only in carbohydrate sequence

176
Q

Membrane receptors

A

can activate or deactivate transporter for facilitated diffusion

tend to be transmembrane proteins

  • ligand-gated ion channels
  • g-protein coupled receptors
177
Q

Gap Junctions/Connexons

A

allow for direct cell-cell communication

permit movement of water and some solutes (not proteins)

formed by the alignment and interaction of pores composed of six molecules of connexin

178
Q

Tight Junctions

A

prevent solutes from leaking into the space between cells via a paracellular route form a continuous band around the cell

179
Q

Desmosomes

A

bind adjacent cells by anchoring to their cytoskeletons

formed by interactions between transmembrane proteins
associated with intermediate filaments

primarily found at the interface between two layers of epithelial tissue

hemidesmosomes attach epithelial cells to underlying structures

180
Q

Concentration Gradients

A

determine whether active or passive transport

181
Q

Simple diffusion

A

most basic, substrates move down their concentration gradient directly across the membrane

182
Q

Osmosis

A

simple diffusion of water driven by osmotic pressure, a colligative property

-dependent only on concentration

183
Q

Osmotic pressure equation

A

Osmotic Pressure (∏) = iMRT

M is molarity, R is ideal gas constant, T is the absolute temperature, i is the van’t Hoff factor

thought of as a “sucking” pressure

184
Q

Facilitated diffusion

A

simple diffusion for molecules that are impermeable to the membrane using proteins uses carriers and channels

185
Q

Facilitated diffusion - carriers

A

open to only one side, like a revolving door in their function

binding of the substrate molecule induces the occluded state, where neither side is open

186
Q

Facilitated diffusion - channels

A

may be in open or closed conformation, in open conformation both sides are exposed much more rapid transport kinetics

187
Q

Active transport, primary vs secondary

A

primary active transport

-uses ATP or another energy molecule

secondary active transport -“coupled transport”

  • harnesses the energy released by one particle going down its electrochemical gradient to drive a different particle up
  • Symport- both particles same direction
  • Antiport- particles flow in opposite directions
188
Q

Endocytosis

A

pinocytosis- the endocytosis of fluids and dissolved particles

phagocytosis- the ingestion of large solids like bacteria

189
Q

Exocytosis

A

secretory vesicles fuse with the membrane, releasing their contents to the environment

important in the nervous system and intracellular signalling neurotransmitters from synaptic vesicles

190
Q

Nernst equation

A

used to determine the membrane potential from the intra- and extracellular concentrations of the various ions

E = 61.5/(charge of ion) * log([ion]outside/[ion]inside)

191
Q

Sodium potassium pump

A

Cell membranes are more permeable to K+ ions than Na+ ions at rest due to more K+ channels

Na+/K+ channels maintain the gradient

192
Q

outer mitochondrial membrane special characteristic

A

highly permeable

193
Q

inner mitochondrial membrane special characteristics

A

more restricted permeability

contains numerous infoldings known as cristae which increase surface area

encloses the mitochondrial matrix

-citric acid cycle high level of cardiolipin, no cholesterol

194
Q

GLUT 2 (location, Km)

A

hepatocytes and pancreatic cells the Km is quite high, the liver will pick up glucose in proportion to its concentration in the blood (first-order kinetics)

195
Q

GLUT 2 (purpose)

A

captures excess glucose after a meal for storage

When the glucose concentration drops below the Km for the transporter, much of the remainder bypasses the liver and enters the peripheral circulation

the liver will pick up excess glucose and store it preferentially after a meal, when blood glucose levels are high

In the beta-islet cells of the pancreas, GLUT 2 along with glucokinase serves as the glucose sensor

196
Q

GLUT 4 (location, Km)

A

adipose tissue and muscle

the Km is close to normal blood glucose levels, so the transporter is saturated when blood glucose levels are slightly above normal

197
Q

GLUT 4 (purpose)

A

responds to the glucose concentrations in peripheral blood

when a person has high blood sugar the transporter still maintains only a constant rate of glucose influx (first-order kinetics)

Muscle and adipose tissue requires more glucose

Muscle stores excess glucose as glycogen

adipose tissue requires glucose to form dihydroxyacetone phosphate (DHAP), which is converted to glycerol phosphate to store incoming fatty acids as triacylglycerol

198
Q

Glycolysis and order

A

Glucose Glucose-6-P Fructose-6-P Fructose-1,6-bP Glyceraldehyde-3-phosphate 1,3-Biphosphoglycerate 3-Phosphoglycerate 2-Phosphoglycerate Phosphoenolpyruvate Pyruvate

Cytoplasmic pathway that converts glucose into 2 pyruvate molecules, releasing a modest amount of energy captured in two substrate level phosphorylations and one oxidation reaction

All cells undergo glycolysis

Provides intermediates for other pathways

199
Q

Important enzymes of glycolysis, first step

ATP or NADH?

A

Hexokinase and glucokinase

the first steps of glycolysis, phosphorylation of glucose to glucose-6-P to prevent glucose from leaving via the transporter

-glucose enters the cell by facilitated diffusion or active transport

Hexokinase is widely distributed and inhibited by its product, G-6-P

Glucokinase is found only in liver cells and pancreatic beta-islet cells, and is induced by insulin in the liver

200
Q

Important enzymes of glycolysis, fructose 6-phosphate -> ?

ATP or NADH?

A

Phosphofructokinase-1

rate-limiting enzyme of glycolysis

phosphorylates fructose 6-phosphate to fructose 1,6-phosphate

inhibited by ATP and citrate, and activated by AMP

insulin stimulates and glucagon inhibits PFK-1 -through the PFK-2 mechanism, which activates F2,6-bp, which activates PFK-1

201
Q

Important enzymes of glycolysis, glyceraldehyde-3-P -> ?

ATP or NADH?

A

Glyceraldehyde-3-Phosphate dehydrogenase

Glyceraldehyde-3-Phosphate -> 1,3-biphosphoglycerate and reduction of NAD+ to NADH

If glycolysis is aerobic, the NADH can be oxidized by the mitochondrial matrix

202
Q

Important enzymes of glycolysis, 1,3-biphosphoglycerate -> ?

ATP or NADH?

A

3-Phosphoglycerate Kinase transfers the high-energy phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate

203
Q

Important enzymes of glycolysis, Phosphoenolpyruvate -> ?

ATP or NADH?

A

Pyruvate Kinase

Phosphorylation of ADP to ATP and phosphoenolpyruvate to pyruvate

activated by fructose 1,6-bisphosphate feed-forward activation

204
Q

Irreversible enzymes of glycolysis

A

Glucokinase/Hexokinase

PFK-1

Pyruvate Kinase

205
Q

Fermentation; key enzyme and purpose

A

Occurs in the absence of oxygen

key enzyme is lactate dehydrogenase

reduces pyruvate to lactate and oxidizes NADH to NAD+`

206
Q

Dihydroxyacetone phosphate

A

an important intermediate of glycolysis used in hepatic and adipose tissue for triacylglycerol synthesis

formed from fructose 1,6-bisphosphate

207
Q

1,3-biphosphoglycerate and PEP uses

A

important intermediate of glycolysis

1,3-biphosphoglycerate (1,3-BPG) and phosphoenolpyruvate (PEP) are high-energy intermediates used to generate ATP by substrate-level phosphorylation

only ATP in anaerobic respiration

208
Q

Glycolysis in erythrocytes

A

anaerobic glycolysis is the only pathway for ATP production

have bisphosphoglycerate mutase, 2,3-BPG-> 1,3-BPG

209
Q

Galactose metabolism

A

Galactose comes from dietary lactose

Phosphorylated by galactokinase, trapping in the cell

Galactose-1-phosphate uridyltransferase converts galactose 1-P to glucose 1-P

210
Q

Fructose metabolism

A

fructose is absorbed into the hepatic portal vein, the liver phosphorylates fructose using fructokinase to trap in the cell

aldolase B converts fructose 1-phosphate into glyceraldehyde

211
Q

Pyruvate dehydrogenase

A

Pyruvate from aerobic glycolysis enters mitochondria, where pyruvate dehydrogenase converts it into acetyl-CoA

irreversible

activated in the liver by insulin

requires thiamine, NAD+

212
Q

Three possible fates of pyruvate

A

conversion to acetyl-CoA by PDH

conversion to lactate by lactate dehydrogenase

conversion to oxaloacetate by pyruvate carboxylase

213
Q

Glycogen storage location

A

Glycogen is stored in the cytoplasm as granules

Glycogen stored in the liver is a source of glucose between meals

214
Q

Glycogenesis and enzymes

A

synthesis of glycogen granules, begins with a core protein called glycogenin

Glycogen synthase and branching enzyme

215
Q

Glycogen synthase

A

the rate-limiting enzyme of glycogen synthesis

forms an alpha-1,4-glycosidic bond found in the linear glucose chains of the granule

stimulated by insulin

216
Q

Branching enzyme

A

responsible for introducing alpha-1,6-linked branches into the granule as it grows

  • hydrolyzes one of the alpha-1,4 bonds to release a block of oligoglucose which is then moved and added in a slightly different location
  • forms an alpha-1,6 bond to create a branch
217
Q

Glycogenolysis and enzymes

A

reverse of glycogenesis, degradation of glycogen to glucose

glycogen phosphorylase and debranching enzyme

218
Q

Glycogen phosphorylase

A

the rate limiting enzyme of glycogenolysis

breaks an alpha-1,4 glycosidic bond

activated by glucagon in the liver, AMP and epinephrine in skeletal muscle

219
Q

Debranching enzyme

A

deconstructs the branches introduce by branching enzyme

220
Q

Gluconeogenesis, important substrates

A

Glycerol-3-Phosphate

Lactate

Glucogenic amino acids (from muscle proteins)

221
Q

Important enzymes of gluconeogenesis

A

Most steps in gluconeogenesis represent a reversal of glycolysis, the four enzymes to know are those required to circumvent the irreversible steps of glycolysis in the liver

Pyruvate carboxylase (Pyruvate -> OAA)

Phosphoenolpyruvate carboxykinase (PEPCK) (OAA -> PEP)

Fructose-1,6-bisphosphatase (f 1,6 bp -> f-6-P)

Glucose-6-phophatase

222
Q

Pyruvate carboxylase

A

Activated by acetyl-Coa

pyruvate can go through pyruvate dehydrogenase as well, but that is only if the cell needs acetyl-Coa

the source is fatty acids, to produce glucose fatty acids need to be burned

Pyruvate -> OAA

OAA cannot leave the the mitochondrion so it is temporarily reduced to malate to leave

223
Q

phosphoenolpyruvate carboxykinase (PEPCK)

A

induced by glucagon and cortisol converts OAA to phosphoenolpyruvate (PEP) in a reaction that requires GTP

PEP goes on to produce fructose-1,6-bP

combination of pyruvate carboxylase and PEPCK circumvent the action of pyruvate kinase by converting pyruvate back into PEP

224
Q

fructose-1,6-bisphosphatase

A

activated by ATP and inhibited by AMP and fructose 2,6-bisphosphate

removes phosphate from fructose 1,6-bisphosphate to produce fructose 6-phosphate

reverses the action of phosphofructokinase-1, the rate limiting step of glycolysis

225
Q

glucose-6-phosphatase, absence in skeletal muscle

A

found only in the lumen of the endoplasmic reticulum in liver cells

Glucose-6-phosphate is transported into the ER, and free glucose is transported back into the cytoplasm, from where it can diffuse out of the cell using GLUT transporters

The absence of glucose-6-phosphatase in skeletal muscle means that muscle glycogen cannot serve as a source of blood glucose and rather is for use only within the muscle

Glucose -6-phosphatase is used to circumvent glucokinase and hexokinase, which convert glucose to glucose 6-phosphate

226
Q

fructose-2,6-biphosphate

A

thought of as a marker for satisfactory energy levels in liver cells and controls both gluconeogenesis and glycolysis produced by PFK-2

227
Q

Pentose phosphate pathway / Hexose monophosphate shunt and phases

A

occurs in the cytoplasm

Produces NADPH and serves as a source of ribose 5-phosphate for nucleotide synthesis

1st oxidative phase: rate limiting enzyme glucose-6-phosphate dehydrogenase glucose 6-phosphate to ribulose 5-phosphate produces NADPH induced by insulin

2nd nonoxidative phase: ribulose 5-phosphate to ribose-5-phosphate could be used for glycolysis or for nucleotide synthesis

228
Q

Functions of NADPH

A

potent reducing agent (NAD+ is oxidizing agent)

biosynthesis of fatty acids or cholesterol

assisting in cellular bleach production in WBCs

natural antioxidant

-H2O2 is a byproduct in aerobic metabolism that can break apart to form harmful hydroxide radicals

229
Q

Methods of forming Acetyl-CoA

A

Pyruvate dehydrogenase

Dihydrolipoyl transacetylase

Dihydrolipoyl dehydrogenase

Fatty acid oxidation

230
Q

Pyruvate dehydrogenase and requirements

A

pyruvate is oxidized, yielding CO2 while the remaining two-carbon molecule binds covalently to TPP (vitB1).

starts the process towards production of pyruvate

Mg2+ is also required

231
Q

Dihydrolipoyl transacetylase

A

The two-carbon molecule bonded to TPP is oxidized and transferred to lipoic acid, a coenzyme that is covalently bonded to the enzyme

lipoic acid’s disulfide group acts as an oxidizing agent, creating the acetyl group.

The acetyl group is now bonded to lipoic acid via thioester linkage

After this, dihydrolipoyl transacetylase catalyzes the CoA-SH interaction with the newly formed thioester link, causing transfer of an acetyl group to form acetyl-CoA

232
Q

Dihydrolipoyl dehydrogenase

A

Flavin adenine dinucleotide (FAD) is used as a coenzyme in order to reoxidize lipoic acid, allowing lipoic acid to facilitate acetyl-CoA formation in future reactions

As lipoic acid is reoxidized, FAD is reduced to FADH2

In subsequent reactions, this FADH2 is reoxidized to FAD, while NAD+ is reduced to NADH

233
Q

Fatty acid oxidation

A

In the cytosol, a process called activation causes a thioester bond to form between carboxyl groups of fatty acids and CoA-SH

The fatty acyl group is transferred to carnitine, whose function is merely to carry the acyl group from a cytosolic CoA-SH to a mitochondrial CoA-SH

Once acyl-CoA is formed in the matrix, beta-oxidation can occur, which removes two-carbon fragments from the carboxyl end

234
Q

Amino Acid catabolism

A

Certain amino acids can be used to form acetyl-CoA.

These amino acids lose their amino group via transamination; their carbon skeletons can then form ketone bonds

235
Q

Ketones -> acetyl-CoA

A

Although acetyl-CoA is typically used to produce ketones when the pyruvate dehydrogenase complex is inhibited, the reverse reaction can occur as well

236
Q

Alcohol -> acetyl-CoA

A

The enzymes alcohol dehydrogenase and acetaldehyde dehydrogenase convert it to acetyl-CoA

This reaction is accompanied by NADH buildup, which inhibits the Krebs cycle

-the acetyl-CoA formed through this process is used primarily to synthesize fatty acids

237
Q

Citric acid cycle general details

A

takes place in the mitochondrial matrix and begins with the coupling of a molecule of acetyl-Coa the a molecule of oxaloacetate

GTP and energy carriers (NADH and FADH2) are produced will not occur anaerobically

NADH and FADH2 will accumulate if oxygen is not available for the electron transport chain and will inhibit the cycle

238
Q

Citric acid cycle order

A

Can I keep selling sex for money officer

Citrate isocitrate alpha-ketoglutarate succinyl-coa succinate fumarate malate oxaloacetate

239
Q

Citric Acid cycle- Step 1 - CITRATE FORMATION

A

Acetyl-CoA and oxaloacetate undergo a condensation reaction to form citryl-COA, an intermediate

Hydrolysis of citryl-CoA yields citrate and CoA-SH

catalyzed by citrate synthase

240
Q

Citric Acid cycle- Step 2 - CITRATE isomerized to ISOCITRATE

A

Citrate is isomerized to isocitrate

Water is lost from citrate, yielding cis-aconitate.

Water is added back to form isocitrate

uses the enzyme aconitase, requires Fe2+ results in a switching of a hydrogen and a hydroxyl group

241
Q

Citric Acid cycle- Step 3 - alpha-KETOGLUTARATE and CO2 formation

A

Isocitrate is first oxidized to oxalosuccinate by isocitrate dehydrogenase

rate limiting enzyme

Oxalosuccinate is decarboxylate to produce alpha-ketoglutarate and CO2

First NADH produced

242
Q

Citric Acid cycle- Step 4 - SUCCINYL-COA and CO2 formation

A

Carried out by the alpha-ketoglutarate dehydrogenase complex, similar in mechanism to the pyruvate dehydrogenase complex

alpha-ketoglutarate and CoA come together and produce a molecule of carbon dioxide

This carbon dioxide represents the second and last carbon lost from the cycle

Another NADH is produced

243
Q

Citric Acid cycle- Step 5 - SUCCINATE formation

A

Hydrolysis of the thioester bond on succinyl-CoA yields succinate and CoA-SH, and is coupled to the phosphorylation of GDP to GTP

catalyzed by succinyl-CoA synthetase

-synthetases, unlike synthases, create new covalent bonds with energy input

244
Q

Citric Acid cycle- Step 6 - FUMARATE formation

A

Takes place on the inner membrane, not the mitochondrial matrix

Succinate undergoes oxidation to yield fumarate catalyzed by succinate dehydrogenase

  • considered a flavoprotein because it is covalently bonded to FAD
  • integral protein on the inner mitochondrial membrane

As succinate is oxidized to fumarate, FAD is reduced to FADH2

–FAD is the electron acceptor in this reaction because the reducing power of succinate is not great enough to reduce NAD+

245
Q

Citric Acid cycle- Step 7 - MALATE formation

A

The enzyme fumarase catalyzes the hydrolysis of the alkene bond in fumarate, yielding malate

246
Q

Citric Acid cycle- Step 8 - OXALOACETATE formed anew

A

malate dehydrogenase catalyzes the oxidation of malate to oxaloacetate

a third and final molecule of NAD+ is reduced to NADH

247
Q

Net Results and ATP Yield of pyruvate dehydrogenase complex, citric acid cycle, glycolysis

A

Pyruvate dehydrogenase complex

Pyruvate + CoA-SH + NAD+ => acetyl-CoA + NADH + CO2 + H+

Citric Acid Cycle

Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi + 2H2O => 2 CO2 + CoA-SH + 3 NADH + 3H+ + FADH2 + GTP ATP

Production 4 NADH + 1 FADH2 + 1 GTP = 25ATP per glucose + glycolysis = 30-32 ATP

248
Q

Pyruvate dehydrogenase complex modification/regulation

A

can be phosphorylated by pyruvate dehydrogenase kinase

-deactivates in response to high ATP

can be dephosphorylated by pyruvate dehydrogenase phosphatase

-activates in response to high ADP

249
Q

Takeaway major control of citric acid cycle

A

the ATP/ADP ratio and NADH/NAD+ ratio determine inhibition/activation

future products (succinylcholine CoA, citrate for citrate synthase) inhibit enzymes

250
Q

Electron transport chain electron flow and complexes

A

Complex I - NADH dehydrogenase transfers electrons from NADH to coenzyme Q

Complex II - Succinate dehydrogenase transfers electrons from FADH2 to coenzyme Q

Ubiquinone (Coenzyme Q) - transfers electrons from complex I and II to complex III

Complex III - Cytochrome C reductase enzyme, carriers electrons to to cytochrome C

Cytochrome C - transfers electrons from complex 3 to complex 4

Complex IV - Cytochrome C oxidase enzyme, converts oxygen to water, pumps protons into intermembrane space, creating the proton motive force

251
Q

NADH shuttles purpose

A

NADH formed through glycolysis cannot directly cross into the mitochondrial matrix

252
Q

Glycerol 3-Phosphate shuttle

A

one isoform of glycerol-3-phosphate dehydrogenase, which oxidizes cytosolic NADH to NAD+

-FAD is then reduced on the other side to FADH2, which transfers its electrons to the ETC via complex II

253
Q

Malate-aspartate shuttle

A

Cytosolic oxaloacetate is reduced to malate by malate dehydrogenase, accompanied by the oxidation of cytosolic NADH to NAD+

254
Q

Chemiosmotic coupling, ATP synthase structure

A

ATP synthase contains a F0 portion and a F1 portion

The F0 portion functions as an ion channel, allowing protons to travel back along their gradient

The F1 portion utilizes the energy released from this electrochemical gradient to phosphorylate ADP to ATP

-hypothesized to work as a turbine

255
Q

Regulation of oxidative phosphorylation

A

ADP and O2 are the key regulators of oxidative phosphorylation.

If O2 is limited, the rate of oxidative phosphorylation decreases, and the concentrations of NADH and FADH2 increase. The accumulation of NADH inhibits the citric acid cycle.

-respiratory control

ADP accumulation signals the need for ATP synthesis.

ADP allosterically activates isocitrate dehydrogenase, thereby increasing the rate of the citric acid cycle and the production of NADH and FADH2

256
Q

Lipid digestion

A

in the duodenum and rest of small intestine pancreas

secretes pancreatic lipase, colipase, and cholesterol esterase

257
Q

Micelles and Chylomicrons

A

Micelles are clusters of lipids soluble in the intestine, vital to digestion

Micelles diffuse to the brush border of the intestinal mucosal cells to be absorbed

-Chylomicrons leave the intestine via lacteals (lymphatic system) and re-enter via the thoracic duct

258
Q

Lipid mobilization (hormone sensitive lipase and lipoprotein lipase)

A

a fall in insulin levels activates hormone sensitive lipase

hydrolyzes triacylglycerols, yielding fatty acids and glycerol

Epinephrine and cortisol can also activate HSL is effective within adipose cells, but lipoprotein lipase (LPL) is necessary for the metabolism of chylomicrons and very-low-density lipoproteins

can release free fatty acids from triacylglycerols

in these lipoproteins released glycerol from fat may be transported to the liver for glycolysis or gluconeogenesis

259
Q

Lipoproteins, lipoproteins sorting

A

free fatty acids are transported through the blood with albumin, but triacylglycerol and cholesterol are transported in the blood as lipoproteins; aggregates of apolipoproteins and lipids

Sorted by density least to highest

-density increases in direct proportion to the percentage of protein in the particle

260
Q

Lipoproteins- Chylomicrons

A

highly soluble in both lymphatic fluid and blood and function in the transport of dietary triacylglycerols, cholesterol, and cholesteryl esters to other tissues

261
Q

Lipoproteins- VLDL (very-low-density lipoprotein)

A

metabolism similar to chylomicrons; however, VLDL is produced and assembled in liver cells

Main function is the transport of triacylglycerols to other tissues

262
Q

Lipoproteins- IDL (intermediate-density lipoprotein)

A

once a triacylglycerol is removed from VLDL, the resulting particle is referred to as a VLDL remnant or IDL

exists as a transition particle between triacylglycerol transport (chylomicrons and VLDL) and cholesterol transport

263
Q

Lipoproteins- LDL (low-density lipoprotein)

A

the majority of cholesterol in the blood is associated with LDL

264
Q

Lipoproteins- HDL (high-density lipoprotein)

A

dense, protein-rich used to clean up excess cholesterol from blood vessels for excretion

265
Q

Apolipoproteins

A

form the protein component of the lipoproteins, have diverse purposes

266
Q

Sources of cholesterol, de novo synthesis, regulation

A

Most cells derive their cholesterol from LDL or HDL, but de novo synthesis of cholesterol does occur in the liver

driven by acetyl-CoA and ATP

Synthesis of mevalonic acid in the sER is the rate limiting step in cholesterol biosynthesis and is catalyzed by HMG CoA reductase

  • increased levels of cholesterol can inhibit further synthesis
  • insulin promotes cholesterol synthesis
267
Q

LCAT (Lecithin-cholesterol acyltransferase)

A

an enzyme found in the bloodstream that is activated by HDL apoproteins

adds a fatty acid to cholesterol, which produces soluble cholesteryl esters such as those in HDL (these can be distributed to other lipoproteins)

-cholesteryl ester transfer protein (CETP) facilitates this transfer process

268
Q

Essential fatty acids

A

alpha-linolenic acid and linoleic acid maintain cell membrane fluidity

269
Q

fatty acid nomenclature

A

omega (ω) numbering system describes the position of the last double bond relative to the end of the chain and identifies the major precursor fatty acid

270
Q

lipid and carbohydrate synthesis description

A

lipid and carbohydrate synthesis are often called nontemplate synthesis because they do not rely directly on the coding of a nucleic acid

271
Q

Fatty acid biosynthesis

A

occurs in the liver, products are transported to adipose tissue

Enzymes acetyl-CoA carboxylase and fatty acid synthase

stimulated by insulin

palmitic acid (palmitate) is the primary end product of fatty acid synthesis

272
Q

Acetyl-CoA shuttling

A

Citrate, a product of acetyl-CoA through the ETC, can diffuse across the mitochondrial membrane

-in the cytosol, citrate lyase splits citrate back into acetyl-CoA and oxaloacetate

273
Q

Acetyl-CoA carboxylase

A

activates acetyl-CoA in the cytoplasm for incorporation into fatty acids

rate-limiting enzyme of fatty acid biosynthesis

requires biotin and ATP to function, and adds CO2 to acetyl-CoA to form malonyl-CoA

activated by insulin and citrate

274
Q

Fatty acid synthase

A

palmitate synthase, palmitate is the only fatty acid humans can synthesize de novo

large complex found in the cytosol that is rapidly induced in the liver following a meal high in carbohydrates due to elevated insulin levels

requires pantothenic acid (vit B5) and NADPH and eight acetyl-CoA groups

275
Q

Triacylglycerol (triglyceride) synthesis

A

addition of three fatty acids to glycerol primarily in the liver and somewhat in adipose tissue

276
Q

beta oxidation location and regulation

A

B-oxidation occurs in the mitochondria and somewhat in peroxisomes

insulin indirectly inhibits while glucagon stimulates

277
Q

beta oxidation- activation

A

when fatty acids are metabolized, they first become activated by attachment to CoA, which is catalyzed by fatty-acyl-CoA synthetase

278
Q

beta oxidation- fatty acid entry into mitochondria

A

long-chain fatty acids require transport via a carnitine shuttle

Carnitine acyltransferase I is the rate-limiting enzyme of fatty acid oxidation

279
Q

beta oxidation- in mitochondria (four steps)

A

beta-oxidation is the reverse of fatty acid synthesis

1 Oxidation of the fatty acid to form a double bond

2 Hydration of the double bond to form a hydroxyl group

3 Oxidation of the hydroxyl group to form a carbonyl (beta-ketoacid)

4 Splitting of the beta-ketoacid into a shorter acyl-CoA and acetyl-CoA

280
Q

beta oxidation products

A

Each four-step cycle releases one acetyl-CoA and reduces NAD+ and FAD (producing NADH and FADH2) these go to ETC

acetyl-CoA enters the citric acid cycle in muscle and adipose tissue, in the liver it stimulates gluconeogenesis; much is used to synthesize ketone bodies

281
Q

odd-numbered chain fatty acids beta oxidation differences

A

Odd-numbered chain fatty acids undergo the same process but with propionyl-CoA as the five carbon remaining fragment

-converted to glucose, exception to the rule that fatty acid is not converted to glucose

282
Q

Ketone bodies

A

acetoacetate and 3-hydroxybutyrate

283
Q

ketogenesis

A
  • occurs in the mitochondria of livers cells when excess acetyl-CoA accumulates in the fasting state
  • HMG-CoA is formed and broken down into acetoacetate which can then be reduced to 3-hydroxybutyrate with acetone side product
284
Q

ketolysis

A

3-hydroxybutyrate is oxidized to acetoacetate

-the liver lacks this enzyme

Ketolysis in the brain

-During a prolonged fast the brain derives up to two-thirds of its energy from ketone bodies

285
Q

protein catabolism

A

protein is rarely used as an energy source but proteins must be digested and absorbed to provide a reservoir of amino acids

stomach- pepsin, trypsin, chymotrypsin, carboxypeptidases A and B

-zymogens

small intestine- dipeptidase and aminopeptidase

primarily muscle and liver amino acids released from proteins usually lose their amino group with the remaining carbon skeleton used for energy

-urea cycle removes the excess energy

286
Q

relationship between enthalpy and heat exchange

A

At constant pressure and volume, enthalpy (deltaH) and thermodynamic heat exchange (Q) are equal ΔG = ΔH - TΔS

287
Q

physiological conditions modified standard state

A

H+ = 10^-7 and the pH is 7

288
Q

deltaG relation to Q equation

A

ΔG = ΔG* + RTlnQ

289
Q

flavoproteins

A

contain a modified B2 or riboflavin nucleic acid derivatives, present in the mitochondria and chloroplasts as electron carriers

involved in the modification of other B vitamins to active forms

function as coenzymes for enzymes in the oxidation of fatty acids

290
Q

postprandial (absorptive) state

A

anabolic not catabolic

high insulin

glycogen synthesis in liver and muscle

excess glucose to fatty acids and triacylglycerols in liver

triacylglycerol synthesis in adipose tissue

nervous tissue and rbcs are insensitive to insulin, nervous tissue derives energy from oxidizing glucose to CO2

291
Q

postabsorptive (fasting) state

A

glucagon, cortisol, epinephrine, norepinephrine, and growth hormone

opposite of absorptive state

292
Q

prolonged fasting (starvation)

A

glucagon and epinephrine very elevated

gluconeogenic activity continues

gluconeogenesis is the predominant source of glucose

lipolysis is rapid, resulting in excess acetyl-CoA used in the synthesis of ketone bodies

-shift from glucose to ketones

–rbcs and cells w/o mitochondria still dependent on glucose

293
Q

metabolic effects of insulin; tissue not affected

A

peptide hormone secreted by beta-islet cells of pancreas, key player in uptake and storage of glucose

increases rate of glucokinase and glycogen synthase in liver while decreases the activity of glycogen phosphorylase and glucose-6-phosphatase

increases glucose and triacylglycerol uptake by fat cells, lipoprotein lipase activity (clears VLDL and chylomicrons from the blood), triacylglycerol synthesis above 100mg/dL or 5.6

insulin secretion is proportional to plasma glucose

tissue not affected: nervous, kidney tubules, intestinal mucosa, rbcs, beta-cells of pancreas

294
Q

metabolic effects of glucagon

A

peptide hormone secreted by the alpha-cells of the pancreatic islets of langerhans

increased liver glycogenolysis, activates glycogen phosphorylase and inactivates glycogen synthase

promotes the conversion of pyruvate to PEP by pyruvate carboxylase and phosphoenolpyruvate

increased ketogenesis decrease lipogenesis

increased lipolysis in the liver, activates hormone-sensitive lipase basic amino acids promote secretion secreted in response to protein rich meal

295
Q

Glucocorticoids effect on metabolism

A

from the adrenal cortex, responsible for stress response, especially cortisol

promote mobility of energy

-elevates blood glucose and inhibits glucose uptake

296
Q

metabolic effect of catecholamines

A

secreted by the adrenal medulla, includes epinephrine and norepinephrine

increase the activity of liver and muscle glycogen phosphorylase, promoting glycogenolysis and increasing glucose output

act on adipose tissue to increase lipolysis

increase basal metabolic rate

297
Q

metabolic effect of thyroid hormones

A

action is largely permissive, levels are kept more or less constant

increase basal metabolic rate, T4 takes longer but is longer lasting

primarily lipid and carb metabolism

epinephrine requires thyroid hormones to have a significant metabolic effect

298
Q

Tissue-specific metabolism - connective tissue and epithelium

A

little metabolism

299
Q

Tissue-specific metabolism - liver

A

maintain a constant level of blood glucose and synthesize ketones when excess fatty acids are being oxidized

replenishes glycogen with excess glucose, any glucose remaining is converted to acetyl-CoA and used for fatty acid synthesis

300
Q

Tissue-specific metabolism - adipose tissue

A

insulin triggers fatty acid release from VLDL and chylomicrons and can suppress the release of fatty acids

decreased insulin activate hormone-sensitive lipase in fat cells, releasing fatty acids

301
Q

Tissue-specific metabolism - skeletal muscle (resting and activated)

A

resting muscle

  • body’s major consumer of fuel, insulin promotes glucose uptake
  • excess glucose and AAs can be oxidized for energy
  • in fasting state, fatty acids derived from free fatty acids are utilized

activated muscle

  • short lived energy from creatine phosphate, which transfers a phosphate group to ADP to form ATP
  • after 1-3 hours of continuous exercise, muscle glycogen stores become depleted and intensity rate declines
302
Q

Tissue-specific metabolism - cardiac muscle

A

unlike other tissues of the body, cardiac myocytes prefer fatty acids as their major fuel, even in the well-fed state

303
Q

Tissue-specific metabolism - brain

A

consumes much of the glucose fatty acids cannot cross the blood-brain barrier, between meals, the brain relies on blood glucose supplied by either hepatic glycogenolysis or gluconeogenesis

Only during prolonged fasting does the brain gain the capacity to use ketone bodies for energy

304
Q

Respirometry quotient

A

Respirometry quotient (RQ) indicates what fuels the body is using

RQ = CO2 produced/O2 consumed

305
Q

Calorimeters

A

Calorimeters can measured BMR based on heat exchange

-can also be estimated based on age, weight, height, and gender

306
Q

regulation of body mass

A

Lipids stored in adipocytes are the primary factor in the gradual change of body mass over time

Caloric changes has a threshold level that differs between individuals

307
Q

ghrelin, orexin, leptin

A

Ghrelin - in response to signals of meals, increases appetite

orexin - further increases appetite also sleep-wake cycle

leptin - decreases appetite by suppressing orexin production

308
Q

BMI

A

BMI = mass/height^2

309
Q

D-fructose structure

A
310
Q

D-glucose structure

A
311
Q

D-galactose structure

A
312
Q

D-mannose structure

A

MCAT (10 decks)

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