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biochem MCAT section Flashcards

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1
Q

what is catalytic efficiency equation?

A

Kcat/Km

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2
Q

what is RNA replicase used for?

A

single stranded RNA can either be negative or positive sense

+ sense can be directly translated to functional proteins

  • sense must be made into a complimentary strand by RNA REPLICASE first, then can be translated into protein
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3
Q

describe the two methods of transgenic mice production

A
  1. transgene into fertilized ovum - good for dominant gene effects because uncontrolled induction of allele into offpsring
  2. embryonic stem cell transgene - will be a mixture of the host blastocyst cells and transgene stem cells –> chimera mice will be produced (with different patches of colours from the different cell lines) - will produce homozygous and heterozygous transgenic offspring
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4
Q

what is the difference between parynchema and stroma?

A

parynchema - the functional part of the tissue (i.e epithelial)

stroma - the support structure of the tissue (i.e connective tissue)

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5
Q

-CH2CH2CONH2

A

glutamine

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6
Q

what is it called when cells that, when exposed to a self antigen, would produce an immune response are destroyed?

A

negative selection (for example, T cells would react with self-proteins are normally inactivated in the thymus)

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7
Q

if you have DNA that is 5’ TCTTTGAGACATCC 3’, what is the mRNA?

A

5’ GGAUGUCUCAAAGA 3’

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8
Q

what are the aromatic AAs?

A

tryptophan and phenylalanine

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9
Q
A

phenylalanine

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10
Q

what type of enzyme will bind to molecules together via covalent bond while creating water?

A

ligase

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11
Q

-CH2(OH)CH3

A

threonine

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12
Q

what is chargoffs rule for pyrimidine/purine concentrations in the DNA strand?

A

amount of purines will equal amount of pyrimidines because same amount of A as T, and same amount of G as C

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13
Q

michaelis-menten equation

A

Vo = Vmax [S]/Km + [S]

Km = [S] where V = 1/2 Vmax

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14
Q

what is pI

A

isoelectric point -the pH where the charge of the AA is zero (pKa1 + pKa2/2)

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15
Q

what is the transfer of genes from one bacterium to another using a viral vector called?

what is analogous to sexual reproduction in eukaryotes; requiring a sex pilus, a physical bridge?

what involves the uptake of ‘naked’ DNA through the cell membrane. (no virus needed)?

what are ‘jumping genes’ that can insert and remove themselves from the genome (no vector needed)?

A

transduction

conjugation

transformation

transposon

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16
Q

-CH(CH3)CH2CH3

A

isoleucine

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17
Q

name three different prosthetic groups that can be attached to proteins and name their conjugated protein

A

lipids, nucleic acids, carbs

lipoprotein, nucleoprotein, glycoproteins

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18
Q

what are the basic AAs?

A

HAL - all have amino groups

Histidine

arginine

lysine

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19
Q

what is telomere?

A

repeating sequence (TTAGGG) at the end of chromosomes to help reduce losing sequences during replication

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20
Q

which base pairs have a triple H bond and which have a double H bond?

A

GC - triple

AT - double

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21
Q

initiation: difference between prok and euk?

A

prok - small unit binds at shine-dalgaro sequence of 5’ UTR

euk - small unit will bind at mRNA cap

prok - tRNA initiation with N-formylmeth

euk - methionine (AUG)

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22
Q

what does a higher Km value indicate? lower?

A

higher indictes a lower affinity of [S] for enzyme because more substrate required to reach 1/2 saturation

lower indicates a higher affinity of [S]

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23
Q

michaelis menton equation?

A

v = (Vmax [S])/ Km + [S]

or

v = (Kcat [E][S])/ Km + [S]

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24
Q
A

proline

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25
Q

secondary structure of a protein includes what kind of bonds and structure?

A
  • hydrogen bonds
  • alpha helix and B - sheets
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26
Q

what does Hill’s coefficient mean?

>1?

<1?

0?

A

degree of cooperativity of a substrate binding and affecting the affinity of subsequent ligands from binding

positive cooperativity

negative

none

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27
Q

what does every eukaryotic protein start with?

A

methionine - AUG (start codon)

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28
Q

A person with B- blood will produce what type of antigen/antibodies?

A

will produce B antigens (because they present the B antigen in their blood, identify as ‘self’)

will produce anti-Rh antibodies because they are ‘-‘, which means do not present the Rh antigen, and Rh antigen is not considered ‘self’

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29
Q

what are RNA polymerase I and III for?

A

I - transcribes rRNA in nucleolus

III - some rRNA, but mostly tRNA

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30
Q

why is histidine considered a special AA?

A

its pKa is 6.5, which is close to physiological pH - means it will be half protonated and half unprotonated at physiological

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31
Q

what is Kcat?

A

the amount of substrate an enzyme can turn into product in one second at Vmax

Kcat = Vmax/[E]

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32
Q

L- AA means what, D- AA means what?

A

L - amino group is on the left D- amino group is on the right

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33
Q

what is the difference between cysteine and cystine?

A

cystEine is the reduced form (gain electron, reduced) - in the SH form w/o disulfide bond cystine is the oxidized form (lose electron, oxidized) - in the S-S form w/ disulfide bond

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34
Q

what are two unique structures of bacteriophages compared to normal viruses? what do they do?

A

tail sheath - acts as syringe to inject genetic material into bacterium

tail fibers - helps recognize/connect to bacerium

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35
Q

difference between nucleotide/base excision repair?

A

nucleotide - uses excision endonuclease to cut backbone and remove it

base excision - base is removed by glycosolase, leaving abasic site (AP) - AP endonuclease will come in and cut fragment out

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36
Q

what are the DNA polymerases in eukaryotes? in prokaryotes?

A

euk - a, B, y , E

prok - I and III

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37
Q

water soluble vitamins vs fat soluble?

A

water - B and C

fat - A, D, E, K

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38
Q

where does trypsin cleave peptide bonds?

A

at the carboxyl end of R and K

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39
Q

-CH2CONH2

A

asparagine

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40
Q

what do osteoclasts in bones do?

A

dissolve bone to release calcium (related to macrophages)

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41
Q
A

alanine

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42
Q

ideal temperature of enzymes in body

ideal pH for most enzymes

ideal pH for gastric enzymes

ideal pH for pancreatic enzymes

A

37 or 98.6

  1. 4
  2. 4
  3. 5
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43
Q

what structure/bonds are involved in primary, secondary, tertiary and quatenary structures of proteins?

A

1 - linear, peptide bonds

2 - a-helices/B-sheets, H bonds

  1. hydrophilic-/phobic interactions, acid base interactions (salt bridge), disulfide bonds (cysteine –> cystine), H bonds, covalent/ionic bonds, van der waal
  2. interactions between polypeptide subunits - H bonds, covalent/ionic bonds, Van der waal
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44
Q

when transferring AA to peptide chain, what is required? what enzyme is required and what is that enzyme a part of?

A

GTP

  • peptidyl transferase which is part of the large subunit
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45
Q

what is the x-intercept/y-intercept of linebeaver-burk plot?

A

x: -1/Km
y: 1/Vmax

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46
Q
A

tryptophan

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47
Q

if the codon for valine is GUA, what is the appropriate anticodon for tRNA?

A

UAC

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48
Q

what are the purines/ pyrimidines?

A

purines - A and G

pyrimidines - CUT

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49
Q

what type of system is the lac operon, trp operon? (positive, negative inducible, repressible?)

A

lac - negative inducible

trp - negative repressible

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50
Q

where does chymotrypsin cleave peptide bonds?

A

carboxyl end of aromatic amino acids (F, Y, W)

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51
Q

what is mismatch repair for DNA replication?

what genes encode for these enzymes?

A

during G2 phase (after S phase) to correct errors during replication

MSH1 and MLH

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52
Q

if a strand of RNA contained 15% C, 15% A, 35% G and 35% U, does this violate chargaffs rule?

A

no, because RNA is single stranded!!

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53
Q

CH2CH2(COOH)

A

glutamic acid

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54
Q
A

valine

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55
Q

quatinary structure of a protien forms what

A

multiple polypeptide formations that make the proper conformational protein

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56
Q

what would an increase in blood CO2 levels do to the saturation of hemoglobin at a fixed concentration of oxygen?

A

it would increase the amount of carbonic acid in the blood, which would decrease the pH. A decrease in pH would result in less affinity of hemoglobin for oxygen. (decrease saturation)

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57
Q

what is total lung capacity, vital lung capacity, residual volume, and tidal volume?

A

vital capacity is the maximum amount of air that can be moved in one respiratory cycle (the tidal volume + inspiratory and expiratory reserve volumes)

tidal volume is the amount of air exchanged in a normal breath

total lung capacity is the total amount of air the lungs can hold

residual volume is the minimum air left in the lungs at all times

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58
Q

what enantiomer of AA are found in the human body?

A

L!!!

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59
Q

what does an enhancer accomplish?

in an enhancer, what is the differences between signal molecules, TFs and response elements?

A
  • increases the activity of RNA polymerase at a single promoter site

signal molecules are hormones or secondary messengers (cortisol, cAMP, estrogen) that bind to their receptors

their receptors are transcription factors that bind to specific DNA sequences in the promoter, the activation domain of these TF’s will bind response elements to increase transcription

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60
Q

-CH2CH(CH3)2

A

leucine

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61
Q

postranslational processing - what is glycosylation/prenylation?

A

glycos - add oligonucleotides

prenylation - add lipid groups

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62
Q

how do the structures of flagella centrioles differ?

A

flagella - 9 pairs of microtubules forming outside ring with 2 in the middle

centrioles - 9 triplets of microtubules forming outside ring with a hollow center

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63
Q

what is a zwitterion

A

when a molecule has a negative and positive charge - hybrid

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64
Q

-CH2OH

A

serine

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65
Q
A
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66
Q

primary structure of a protein includes what kind of bonds and structure?

A

peptide bonds - linear sequence

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67
Q

what is a solvation shell

A

it is the layer of solvent around the protien

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68
Q

what is mixed inhibition of enzymes?

what causes a lower Km? higher?

A

inhibitor binds to either enzyme allosteric site or enzyme- complex

  • binding to enzyme will increase Km (lower enzyme affinity)
  • binding to complex will decrease Km (increase affinity)
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69
Q

4 major points about enzymes

1._________ rate of reaction forward and reverse 2. _______ the activation energy 3. they _______ the equilibrium concentrations of the reactants and products 4. they _____ consumed during a reaction

A
  1. increase rate of reaction forward and reverse 2. lower the activation energy 3. they do not alter the equilibrium concentrations of the reactants and products 4. they are never consumed during a reaction
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70
Q

why is glycine considered a special AA?

A
  • no chiral carbon because the side chain is just an H –> very flexible - ALPHA HELIX BREAKER
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71
Q

catalytic efficiency equation?

A

Kcat/Km

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72
Q

which direction does DNA polymerase read DNA to add nucleotides?

A

reads DNA in the 3 to 5 direction in order to add nucleotides in the 5’ to 3’ direction

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73
Q

what is the difference between cofactors and coenzymes?

similarities?

A

cofactors - ingested in diet, usually metal ions or inorganic molecules

coenzymes - organic molecules, mostly vitamins or derivatives of vitamins (NAD, FAD, coenzyme A)

  • both will bind to enzymes to make conformational changes to active them
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74
Q

what is the difference between infection stage of viral life cycle of enveloped viruses compared to bacteriophages?

A

bacteriophages fuse to cell membrane and inject genetic info in

enveloped viruses fuse and virions can enter the cell intact

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75
Q

what are the post-transcriptional processing that occurs to hnRNA to form mRNA? and what are they for?

A
  1. intron/exon splicing - getting rid of non coding regions
  2. 5’ mRNA cap - ribosomal recognition site and prevents degradation
  3. 3’ poly-A tail - protects message from degradation (time bomb after leaving the nucleus)
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76
Q

what are the alkyl AAs?

A

giraffes and vets make less impressive pets

glycine

alanine

methionine

leucine

isoleucine

proline

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77
Q
A

glycine

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78
Q

what are the three stop codons

A

UAA, UGA, UAG

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79
Q

what is histone protein 1’s function?

A

seals off DNA as it enters and leaves nucleosome

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80
Q

what happens to the affinity of hemoglobin for oxygen as the pH decreases (environment becomes more acidic)?

A

the affinity will decrease

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81
Q

what kind of sequences do you restriction enzymes usually target?

A

ds DNA palindromic sequences

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82
Q

competitive inhibition and non-competitive inhibition effects on Km and vmax?

A

competitive - same Vmax, smaller Km

noncompetitive - same Km, smaller Vmax

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83
Q

what are the neutral AAs?

A

STAG CT scan (all have either a sulfur or oxygen)

Serine

threonine

asparagine

glutamine

cysteine

tyrosine

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84
Q

difference between coding and template strand as compared to mRNA?

A

coding (sense)- is not transcribed - is sense to mRNA

template (antisense)- is transcribed - is antisense and complementary to mRNA

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85
Q

what does histone acetylator acetylate? what does DNA methylase methylate?

A

lysine residues (to reduce positive charge and cause open chromatin conformation from histones)

DNA methylates cytosine and adenine residues to silence genes

86
Q

what are the acidic AAs?

A

aspartate (unprotonated form), aspartic acid

glutamate (unprotonated form), glutamic acid

87
Q

three things a vector requires

A

restriction enzyme site, orgin of replication and antiboitic resistance gene

88
Q

what does high frequency of recombination (Hfr) mean?

A

when sex factor plasmid is conjugated, the plasmid can be transformed into host genome. When this happens, the next cell that this bacterium conjugates will try to transfer entire copy of its genome into the recipient

89
Q

what is an episome?

A

plasmids that can be integrated into the bacterium to increase bacterial genetic recombination to aid genetic diversity

via - transformation, conjugation, transduction

90
Q

-CH2(CH2)2NH(NH)(NH2)

A

arginine

91
Q
  • CH2SHCH3
A

methionine

92
Q

-CH2SH

A

cysteine

93
Q

what is the steady state assumption?

A

that formation of ES is equal to the loss of ES, or rate1 + rate-2 = rate-1 + rate 2

94
Q

-CH2(COOH)

A

aspartic acid

95
Q

what is a southern blot?

A

used to detect the presence and quantity of various DNA strands in a sample

  • DNA cut by restriction enzymes then separated by gel electrophoresis
  • fragments are moved to a membrane retaining their separation
  • the membrane with separated fragments is probed with a specific DNA sequence
  • probes will bind to these specific sequences in the membrane with radioisotopes/indicator proteins to indicate desired sequence
96
Q

histones:

5 histone proteins in eukoryotes?

what is the histone core made of?

how many bp wrap around each histone?

what does a histone core with DNA wrapped around it called?

A

H1, H2A, H2B, H3, H4

two copies of 2A/B, 3 and 4

200

nucleosomes

97
Q
A

tyrosine

98
Q

when is cysteine in cysteine form and when is it in cystine form?

A

cysteine - reduced - intracellular (because antioxidants inside cell) cystine - oxidized - extracellular

99
Q

what direction do you read DNA? what direction are nucleotides added onto the strand?

what charge does DNA have?

A

5 –> 3

5 C of the sugar is added onto the 3 C of the sugar that is already on the strand

negative!

100
Q

huckel’s rule?

A

stability of aromatic structures because 4n + 2 pi electrons

101
Q
A

histidine

102
Q
  • CH2(CH2)2NH2
A

lysine

103
Q

difference between apoenzyme, holoenzyme and prosthetic groups?

A

apoenzyme - enzyme without its cofactor/coenzyme

holoenzyme - contains cofactor/coenzyme

prosthetic group - cofactor/coenzyme that is necesaary for enzyme function

104
Q

RNA polymerase (what number?) binds to what on the DNA strand? aided by what?

what direction does RNA polymerase travel along template strand?

what direciton is transcription formation?

A

II

promoter region at the TATA box (around -25)

TF’s

3’ to 5’ direction

5’ to 3’ - just like replication

105
Q

are human AA’s d or l? S or R?

A

all human AA’s are l (except glycine, because glycine is not chiral)

all are S (except cysteine is R)

106
Q

are genomic libraries or cDNA used for sequencing genes, identifying disease-causing mutations, producing recombinant proteins, and producing transgenic animals?

A

cDNA - because they lack the non-coding regions (unlike genomic libraries) because they are directly reverse transcribed from the active mRNA in the tissue

107
Q

why is cysteine considered a special AA?

A
  • the thiol groups will form a disulfide bond of other AA with thiol groups (redox rxn)
108
Q

what kind of bonds are in play in a tertiary structure protein?

A

H bonds

  • van der waal
  • hydrophobic packagin
  • disulfide bonds
109
Q

what structure do proteins lose when denatured?

what does heat do?

what does a solute do?

A

3-D

heat - increases KE so much that the motion will overcome the H bonds and cause the protein to unfold

directly interfere with forces that hold the protein together (breaking disulfide bridges by reducing cystine to cysteine, can break H bonds, noncovalent bonds)

110
Q

what happens during termination of translation?

A

stop codon will recruite RF, which will add water molecule to hydrolyze mRNA from tRNA

111
Q

chiral carbon

A

a carbon with 4 different groups attached

112
Q

why is proline considered a special AA?

A

-it forms a ring with its side chain making the amino group into a secondary a-amino group - this will modify secondary protein structure - ALPHA HELIX BREAKER

113
Q

what is this structure?

A

dihydroxyacetone - the simplest ketone monosaccharide

114
Q

what is this structure?

A

glyceraldehyde - the simplest aldose monosaccharide

115
Q

what is this structure?

A

D-fructose

116
Q

what is this structure?

A

D-glucose

117
Q

what is this structure?

A

D-galactose

118
Q

what is this structure?

A

D-mannose

119
Q

fischer projections:

all D-sugars have the _________ of their highest numbered chiral center on left or right?

L-sugars?

A

hydroxide

D- RIGHT

L - LEFT

120
Q

what is an epimer?

A

diastereoisomer that differs at one chirality center

121
Q

what is an anomeric carbon?

how do a and B anomers differ?

does a-anomer of glucose have its hydroxyl group cis or trans to CH2OH?

A

when a monosaccharide goes from linear to cyclic and the carbonyl carbon becomes chiral

differ with the anomeric carbon hydroxyl group in relation to CH2OH group

-trans

(a is axial and B is equitorial)

122
Q

any substituent on the right side of a fischer projection will point which way in a haworth projection?

A

DOWN

123
Q

what is mutarotation of hemiacetals?

which anomer (B or a) is more prevalent at equilbrium of hemiacetals in water and why?

A

mutarotation – when hemiacetals are exposed to water, they will spontaneously cycle between open and closed formation

  • C1 will either be in a-anomer or B-anomer conformation when ring is reclosed (because free rotation around single bond)
  • this is called mutarotation
    • since B-anomer is conformationally more stable than a (because hydroxyl group is equatorial rather than axial), there is more a higher percentage of B-anomer in a mixture of hemiacetals with water at equilibrium
124
Q

why are monosaccharides considered reducing sugars?

what does oxidation of a cyclic monosaccaride yield

A

because they are oxidized (either to a carboxylic acid or lactone - which is a cyclic ring with a ketone)

125
Q

when testing to detect whether an aldose _________ is present, tollens and benedicts reagents are used. what will you see with tollens reagent vs benedicts reagent?

can ketone sugar be detected in this way?

A

reducing sugar

tollens - silvery in presence of aldehyde group

benedicts - red percipitate in presence of aldehyde group, which will be oxidized to carboxylic acid

yes, but must be tautomorized first into aldose form, or -enol first (a double bond with hydroxyl group at the end instead of ketone group)

126
Q

what kind of bond is between the oxygen of an anomeric hydroxyl group of an aldose and an alcohol? what is the products?

A

glycosidic bond

a and B glycosides (monosaccharide + alcohol = acetal)

and water

127
Q

what are pyranosides/furanosides?

A

glycosides derived from pyranose/furanose rings, respectively

128
Q

what monosaccharides and a/B anomers comprise sucrose, lactose and maltose disaccharides?

A

sucrose - glucose-a-1,2-fructose

lactose - galactose-B-1,4-glucose

maltose- glucose-a-1,4-glucose

129
Q

what is this monosaccharide?

A

fructose

130
Q

what is this monosaccharide?

A

galactose

131
Q

what is this monosaccharide?

A

glucose

132
Q

where does B-amylose cleave vs a-amylose and what do they produce?

A
  • B-amylose will cleave at nonreducing end of amylose to produce maltose
  • a-amylase will cleave randomly along amylose to produce glucose, maltose and smaller polysaccharide chains
133
Q

difference between starch (amylopectin) and glycogen?

A

amylopectin and glycogen are both homopolysaccharides of a-1,4- D-glucose BUT amylopectin has a-1,6 branches LESS OFTEN than glycogen does

glycogen has many more branches

134
Q

what does glycogen phosphorylase do to glycogen?

A

will cleave glucose off the nonreducing ends and phosphorylate it for metabolism

135
Q

is a very branched substance like glycogen more or less soluble than a less branched polysaccharide?

A

MORE- because branching increases interaction with solution

136
Q

GLUT 2 vs GLUT 4:

location?

order of kinetics and why?

how does GLUT 4 deal with saturation?

A

2 - pancreatic/liver - will uptake glucose mainly for storage

4 - muscle and adipose tissue

2 - first order because Km is so high that these transporters do not become saturated

4 - zero order because Km is only slightly above blood glucose concentration so transporters easily become saturated

GLUT4 will increase GLUT 4 at the membranes of adipose tissue/skeletal muscle via insulin to increase uptake

137
Q

similarities and differences between hexokinase and glucokinase?

A

similarities - both convert glucose –> glucose-6-P to ‘trap’ glucose inside cytoplasm

differences: glucokinase is restricted to liver/pancreas and has similar properties to GLUT 2 (high Km, insulin induced)

hexokinase is widely distributed and not sensitive to insulin

138
Q

what is phosphofructose kinase inhibited/activated by?

why is this enzyme so important?

A

it is the rate limiting enzyme of glycosis

induced by low energy (AMP) and F-2,6-P (produced by PFK-2), insulin

inhibited by high energy (ATP/citrate) - and indirectly by glucagon which inhibites PFK-2

139
Q

what is PFK-2 important for and where is it located?

A

located in the liver mostly and is important for overriding the inhibition of PFK-1 by ATP in order to produce excess ATP in the liver for other processes

produces F-2,6-P (which activates PFK-1) from F-6-P

140
Q

glyceraldehyde-3-P accomplishes what?

A

G-3-P –> 1,3 - BPG

oxidation rxn

  • will reduce NAD+ to NADH for the ETC
  • inorganic P is added
141
Q

what two enzymes facilitate substrate phosphorylation in glycolysis?

A

3-phosphoglycerate kinase (1,3-BPG –> 3- phosphoglycerate)

pyruvate kinase (phosphoenolpyruvate –> pyruvate)

142
Q

what is pyruvate kinase activated by?

what kind of ‘activation’ is this?

A

fructose-1,6-biphosphate

  • feedforward activation where an intermediate at the beginning of the pathway stimulates/activates a later reaction
143
Q

what is fermentation in mammalian cells?

enzyme involved?

what is fermentation in yeast cells?

A
  • in the absence of oxygen, fermentation will occur: pyruvate –> lactate

lactate dehydrogenase – oxidizes NADH to NAD+ (which will be reduced by 3-phosphogyclerate kinase)

  • this prevents glycolysis from being halted when NAD+ is used up

yeast cells: pyruvate –> CO2 + ethanol

  • oxidizes NADH to NAD+
144
Q

what are three important intermediates of glycolysis?

A
  1. DHAP (dihydroxyacetone phosphate)
  • used in adipose and hepatic tissue for triacylglycerol synthesis
  • formed from F-1,6-BP  Glyceraldheyde-3P + DHAP by aldolase
  • DHAP isomerized into glycerol-3-phosphate  glycerol (backbone of TAGs)
  1. 1,3- biphosphoglycerate and phosphoenolpyruvate
    * high energy intermediates used to generate ATP by substrate-level phosphorylation
145
Q

which 4 enzymes are irreversible in glycolysis?

A
  1. hexokinase
  2. glucokinase
  3. PFK-1
  4. pyruvate kinase
146
Q

what does bisphosphoglycerate mutase do for erythrocytes?

A

: 1,3-BPG 2,3-BPG

  • 2,3-BPG will bind allosterically to B-chains of hemoglobin to reduce its affinity to oxygen
  • useful because it will regulate oxygen affinity at high altitudes when oxygens affinity for hemoglobin is increased
147
Q

hexokinase regulated by?

glucokinase regulated by?

A

inhibited by G-6-P

induced by insulin

148
Q

what are the two important enzymes to know for galactose metabolism and what do they catalyze?

A

galactokinase: galactose –> galactose-1-P

gal-1-P uridyltransferase: galactose-1-P –> glucose 1-P

149
Q

what are the two important enzymes in fructose metabolism and what do they catalyze?

A

fructokinase: fructose –> fructose-1-P

aldolase B: fructose-1-P –> DHAP + glyceraldehyde

150
Q

why are high-fructose drinks able to supply a quick source of energy in both aerobic and anaerobic cells?

A

fructose metabolism produces DHAP and glyceraldehyde from fructose-1-P, bypassing the regulatory PFK1 step of glycolysis

151
Q

pyruvate dehydrogenase - what does it produce and what is it inhibited by?

A

pyruvate –> acetyl CoA + CO2

  • reduces NAD+ to NADH
  • inhibited by high acetyl coA (opposite of pyruvate carboxylase)

activated by high pyruvate

152
Q

how does glycogen synthase work?

activated/inhibited by?

how dose the branching enzyme work?

A

glucose-1-P + UTP –> UDP-glucose + PPi

glycogen synthase: UDP-glucose –> glycogen (adds glucose linearly in a-1,4 fashion)

  • activated by glucose-1-P and insulin
  • inhibited by epinephrine (liver and muscle), glucagon (liver) and AMP (muscle)

will take oligoglucose chain from linear chain and attach it back on in a-1,6 fashion - where glycogen synthase will continue to add glucose on

153
Q

how does glycogen phosphorylase work? activated by what?

how does debranching enzyme work? what kind of complex is it?

A

glycogen phosphorylase: breaks a-1,4 bonds to release single glucose molecules from peripheral granules

  • cannot break a-1,6 bonds
  • activated by glucagon in the liver (to distribute glucose to rest of body), AMP and epinephrine

Debranching enzyme (two enzyme complex): glycogen phosphorylase will break a-1,4 bonds until close to the branching a-1,6 point

  • debranching enzyme will come in an cleave the oligoglucoses at the nearest glucose beside the initial branch point
  • will place the oligoglucoses at the end of another chain

will come in and cleave and release SINGLE glucose at a-1,6 branch

154
Q

glucagon and epinephrine work to _____ blood sugar levels

insulin works to ______ blood sugar levels

A

raise

lower

155
Q

pyruvate carboxylase - what does it catalyze?

what is it activated by and where does its substrate come from?

A

ACTIVATED BY ACETYL COA FROM B-OXIDATION of FA

  • produces OAA from pyruvate
  • important because high acetyl CoA indicates the cell is energetically satisfied and that acetyl coA can be redirected into producing glucose
  • fatty acids must be burned in order to produce glucose in the liver
156
Q

phosphoenol pyruvate carboxykinase (PEPK)

  • what does it do and what is it activated by?
A

converts OAA to PEP

  • requires GTP
  • activated by glucagon and cortisol to raise blood glucose levels
157
Q

fructose-1,6-BP - what is important about this enzyme in gluconeogenesis?

what is it activated by and what is it inhibited by?

A

RATE LIMITING STEP

  • reverses PFK-1 (the rate limiting step of glycolysis)
  • activated by ATP
  • inhibited by AMP and F-2,6- BP
158
Q

where is glucose-6-P found?

A

liver cells

159
Q

what are the three substrates for gluconeogenesis?

what is gluconeogenesis activated by? (hormone wise)

where does the energy source for gluconeogenesis come from?

how does acetyl-coA shift the metabolism of pyruvate/

A

lactate, glucogenic AA, and glycerol-3-P (DHAP) -which are all converted to pyruvate

glucagon, cortisol, epinephrine

B-oxidation of fatty acids which will activate pyruvate carboxylase which links all three substrates into the same gluconeogenesis pathway

high acetyl coA will inhibit pyruvate dehydrogenase and will activate pyruvate carboxylase, shifting the cells from burning pyruvate into energy into building pyruvate back into glucose for the rest of the body

160
Q

what enzymes are involved in the PPP?

what does PPP accomplish?

A

forms ribose-5-P for nucleotide synthesis and generates NADPH

glucose-6-P dehydrogenase

transketolases and transaldolases

161
Q

glucose-6-P dehydrogenase: what does it catalyze?

activated by?

inhibited by?

A

glucose-6-P –> Ribulose -5-P

  • reduces NADP+ to NADPH
  • activated by insulin and NADP+
  • inhibited by NADPH
162
Q

DIFFERENCES BETWEEN NAD+ AND NADP+

A

NAD+ - high-energy electron acceptor for reactions, potent oxidizing agent

NADPH - acts as electron donor, potent reducing agent

  • works in biosynthesis, immune system and antioxidant
163
Q

what is mixed inhibition of enzymes?

A
  • binds to either enzyme or enzyme- substrate complex, but has different affinity for each – binds at allosteric site
    • alters Km depending on preference for enzyme or complex
      • if preference is the enzyme, increases Km (decreases enzyme affinity)
      • if preference is complex, decreases Km (increases enzyme affinity)
164
Q

what is uncompetitive inhibition? effects on km and vmax?

A
  • bind only to complex and essentially locks substrate in enzyme
    • decreases both Km and Vmax
165
Q

what is B-DNA?

A

right- handed helix with major and minor grooves for regulatory protein binding

Z- DNA – left-handed helix, with no biological activity

166
Q

what do centromers and telomeres have in common?

A

repeated TAGGG sequences to prevent unravelling of DNA

167
Q

what kind of dsDNA do restriction enzymes target?

A

recognize specific dsDNA sequences (usually palindromic)

168
Q

what is rRNA? where is it synthesized?

what polymerase transcribes rRNA strands in the nucleolus (except 5S)

what polymerase transcribes 5S

A

rRNA – synthesized in the nucleolus

  • is part of ribosomal machinery used during protein assembly in cytoplasm
  • function as ribozymes (proteins made from RNA)
    • catalyzes peptide bond formation
    • splices introns in nucleus

RNA polymerase I transcribes these strands in the nucleolus (except 5S)

RNA polymerase III transcribes 5S

169
Q

ribosomes contain how many strands of rRNA?

A

Ribosomes contain four strands of rRNA: 28S, 18S, 5.8S, 5S

170
Q

pyruvate dehydrogenase - what are the three components and what happens in each component?

besides through pyruvate dehydrogenase, what other molecules can produce acetyl coA?

A

pyruvate dehydrogenase (PDH) – TPP + pyruvate  TPP + 2 C molecule + CO2

  • lipo arm disulfide bond (oxidizing agent) will reach into this enzyme and OXIDIZE 2 carbon molecule into acetyl
  • acetyl will be attached to this arm

dihydrolipoyl transacetyl – acetyl group from lipo arm + CoA  acetyl coA

dihydrolipoyl dehydrogenase – reduced lipo arm + FAD+  oxidized lipo arm + FADH

  • B-oxidation, AA catabolism, ketone bodies, alcohol
171
Q

B-oxidation to form acetyl coA?

A

B-oxidation to form acetyl coA

  • in cytosol, thioester bond is made via acyl group (fatty acid) + CoA-SH  FA-CoA
  • FA-CoA cant cross membrane so acyl group is attached to carnitine (FA-carnitine)
  • FA-carnitine can cross the membrane from cytosol into mitochondria
  • acyl group is transferred back onto CoA-SH where B-oxidation occurs in mitochondria
172
Q

amino acid catabolism to form acetyl coA?

A

amino acid catabolism to form acetyl coA

  • ketongenic AA  transanimation to remove amino group  carbon skeleton made into ketone bodies  acetyl coA
173
Q

alcohol to form acetyl coA?

A

alcohol to form acetyl coA

  • alcohol dehydrogenase and acetylaldehyde dehydrogenase convert alcohol into acetyl coA
174
Q

enzymes of krebs cycle?

A

A – cis-aconitase: -> citrate -> isocitrate

I – isocitrate dehydrogenase: isocitrate -> a-ketoglutarate + CO2

  • NAD+ -> NADH
  • RATE LIMITING STEP

k – a-ketoglutarate dehydrogenase: a-ketoglutarate -> succinyl coA + CO2

  • similar to PDH (requires TPP, lipoic acid, Mg2+)
  • NAD+ -> NADH

sc – succinyl Co-A synthetase: succinyl coA -> CoA-SH + GTP + succinate

  • GTP phosphate transferred to ADP to form ATP (the only step ATP is formed in krebs cycle)

s – succinate dehydrogenase: succinate -> fumarate

  • FAD -> FADH2 (which is a flavoprotein attached to inner membrane of mitochondria – as compared to the matrix)
    • FAD is used vs NAD+ because succinate does not have as high of reducing power as other substrates

f – fumarase: fumarate -> malate

m – malate dehydrogenase: malate -> oxaloacetate

  • NAD+  NADH

cs – citrate synthase: OAA + acetyl- coA -> citrate + CoA-SH

175
Q

what is the rate limiting step of the krebs cycle?

what two steps of the citric acid cycle produces CO2?

what step produces GTP?

what step reduces FAD? why?

what step produces ATP?

what steps produce CoA-SH?

what enzyme is similar to PDH?

A

isocitrate dehydrogenase

isocitrate dehydrogenase and a-ketoglutarate dehydrogenase

succinyl coA synthetase (synthetases require energy)

succinate dehydrogenase (because succinate is a weak reducing agent and FAD doesnt require as much energy)

succinyl coA synthetase (from GTP)

succinyl coA synthetase and citrate synthase

a-ketoglutarate dehydrogenase (TPP, lipo arm, Mg2+)

176
Q

net results of PDH and citric acid cycle?

net ATP per 1 glucose molecule just from krebs cycle?

net ATP per 1 glucose from krebs cycle + glycolysis?

A

net results of PDH and citric acid cycle:

PDH: pyruvate + NAD+ CoA-SH -> acetyl coA + CO2 + NADH + H+

kreb’s: acetyl coA + 3 NAD+ + GDP + 2 H20 + FAD -> 2 CO2 + CoA-SH + GTP + 3 NADH + 3 H+ + FADH2

4 NADH x 2.5 ATP each = 10 ATP

1 FADH2 x 1.5 ATP each = 1.5 ATP

1 GTp -> 1 ATP

= 12.5 ATP per pyruvate = 25 ATP per glucose

2 ATP from glycolysis + 2 NADH (5 ATP) = 7 ATP

25 ATP + 7 ATP = 30-32 ATP per glucose molecule

177
Q

pyruvate dehydrogenase kinase?

pyruvate dehydrogenase phosphatase?

A

pyruvate dehydrogenase kinase -> phosphorylates pyruvate dehydrogenase which inactivates it

  • activated by high ATP

pyruvate dehydrogenase phosphatase -> dephosphorylates pyruvate dehydrogenase which activates it

  • activated by high AMP
178
Q

three control points of citric acid cycle?

A

citrate synthase

  • inhibited by high ATP, NADH, succinyl coA, citrate
  • activated by nothing
    • isocitrate dehydrogenase
  • inhibited by high ATP, NADH
  • activated by high ADP, NAD+

a-ketoglutarate dehydrogenase

  • inhibited by high ATP, NADH, succinyl coA
  • activated by ADP, Ca2+
179
Q

ETC - when there are two molecules with different reduction potentials, which molecule will be reduced and which will be oxidized?

A

** keep in mind that when there are two molecules with different reduction potential, the one with the higher reduction potential will be reduced, and the other molecule will be oxidized

180
Q

ETC - complex 1 reactions?

how many protons are pumped?

A

complex I

  1. NADH -> NAD+

FMN -> FMNH2

  1. Fe-S -> Fe-SH

FMNH2 -> FMN

  1. Q -> QH2

Fe-SH -> Fe-S

4 protons pumped into intermembrane space from matrix

181
Q

ETC - complex II rxns?

how many protons are pumped?

A

complex II

  1. succinate -> fumarate

FAD -> FADH2

  1. FADH2 -> FAD

Fe-S -> Fe-SH

  1. Fe-SH -> Fe-S

Q -> QH2

no protons are pumped

182
Q

ETC - complex III?

  • how many protons are pumped?
A

complex III (cytochrome reductase)

  • facilitates transfer of e- from Coenzyme Q to cytochrome c
  • two steps – one QH2 will reduce to cytochrome c’s
    • cytochrome c: proteins with heme groups where Fe3+ is reduced to Fe2+

CoQH2 + 2 cytochrome c oxidized (Fe3+)-> CoQ + 2 cytochrome c reduced (Fe2+) + 2H+

2 protons pumped

183
Q

ETC - complex IV

how many protons?

A

complex IV (cytochrome oxidase)

  • oxidizes 4 cytochrome c to reduce oxygen (4 e-)
  • oxygen is reduced + 4 H+ -> 2 H20 + 2H+
184
Q

what are the NADH shuttles – to get NADH into cell because cant cross membrane?

A

NADH shuttles – to get NADH into cell because cant cross membrane

  1. glycerol -3 -phosphate dehydrogenase
  • will convert NADH to FADH2 (through DHAP -> G-3-P)
  • one molecule of NADH -> 1 FADH2 = 1.5 ATP
  1. malate-aspartate shuttle
  • will convert NADH to NADH = 2.5 ATP
  • OAA -> malate in order to cross the membrane, then malate -> OAA
185
Q

Chemiosmotic Coupling:

where do the protons flow and what sections of ATP synthase do what ?

A

Chemiosmotic Coupling

ETC will pump protons into the intermembrane space, creating a electrochemical gradient. When the protons flow back into the matrix

  • protons will travel through F0 of ATP synthase
  • as they do this, F1 will use the energy in this electrochemical gradient to couple Pi to ADP to form ATP
186
Q

two main regulators of oxidative phosphorylation?

A

Regulators of oxidative phosphorylation

think of O2 and ADP as main regulators

  • low O2 will decrease rate of oxidative phosphorylation
    • levels of NADH and FADH2 will increase, which inhibits Krebs cycle

these coordinated regulation of these pathways is known as respiratory control

With adequate O2, rate of oxidative phosphorylation is dependent on ADP

  • ADP allosterically activates isocitrate dehydrogenase to increase production of NADH and FADH2
    • this increases the ETC, which increases ATP
187
Q

standard free energy ??

A

standard free energy: ΔG = ΔG° + RTIn(Q)

  • Standard free energy is the energy change that occurs at standard concentrations of 1 M, pressure of 1 atm, and the temperature 25 degrees
188
Q

what does ΔG°’ mean?

A

standard free energy that fixes pH at 7 (unlike ΔG°)

189
Q

spontaneous oxidation-reduction reactions have a _____ value of ΔG and ______ E (electromotive force)

A

spontaneous oxidation-reduction reactions have a negative value of ΔG and positive E (electromotive force)

190
Q

postabsorptive state: catabolism > anabolism

what 4 hormones oppose the actions of insulin?

A

postabsorptive state: catabolism > anabolism

glucagon, cortisol, epinephrine, growth hormone opposes the actions of insulin

191
Q

T3 onset and duration?

T4 ?

A

T3 causes rapid increase in metabolic rate and is short lived

T4 has latent effects but may last for days

192
Q

liver: well fed – ? fasting – F?

resting skeletal muscle:

cardiac muscle:

adipose tissue

brain:

RBC:

A

liver: well fed – glucose and AA; fasting – FA

resting skeletal muscle: well fed – glucose; fasting – FA, ketones

cardiac muscle: well fed – FA; fasting – ketones, FA

adipose tissue: well fed – glucose; fasting – FA

brain: well fed – glucose; fasting – glucose

RBC: well fed – glucose; fasting – glucose

193
Q

glucose will be taken up in the liver for glycogen stores. excess glucose will do what

A

glucose will be taken up in the liver for glycogen stores. excess glucose will be converted to acetyl coA and made into FA in the liver

FA converted to triacylglycerol, which is released into blood as VLDL

194
Q

phospholipid bilayer is made of both unsaturated and saturated phospholipids

unsaturated will make up the _____ portions of the membrane why?

A

phospholipid bilayer is made of both unsaturated and saturated phospholipids

  • unsaturated will make up the fluid portions of the membrane since the double bonds will make it hard to stack and solidify
195
Q

sphingolipids – 4 subclasses

  1. ceramide –
  2. sphingomyelin –
  3. glycosphingolipids

cerebrosides –

globosides –

  1. gangliosides –
A

sphingolipids – have sphingosine or sphingoid backbone

  1. ceramide – single hydrogen atom as its head group
  2. sphingomyelin – contain phosphodiester bond (are phospholipids)
    * major component of myelin
  3. glycosphingolipids – sphingolipids with head groups composed of sugars bonded by glycosidic linkages

cerebrosides – have a single sugar

globosides – have two or more

  1. gangliosides – glycolipids that have a polar head group composed of oligosaccharides with one or more N-acetylneuraminic acid (NANA)
196
Q

WAXES – esters of _______ with _________

A

WAXES – esters of long chain fatty acids with long chain alcohols

197
Q

Fat-soluble vitamins? what are their main function

A

Fat-soluble vitamins (A, D, E, K)

vitamin A – unsaturated and important for growth, vision and immune function

  • important for retinal (light-sensing) and retinoic acid

vitamin D – consumed or activated by UV

  • increases calcium and phosphate uptake from intestines (increase bone production)

vitamin E – substituted aromatic rings – hydrophobic

  • biological antioxidants

vitamin K – posttranslational modifications required to form prothrombin

198
Q

structure of a steroid?

A

Steroids – 4 cycloalkane rings fused together; 3 cyclohexane and 1 cyclopentane

  • NON-POLAR
199
Q

triacylglycerols – composed of ?

A

triacylglycerols – composed of three FAs (usually varying length and saturation) bonded by ester linkages to glycerol

  • non polar and hydrophobic
200
Q

free fatty acids –bonded to what in blood?

saponification – what bonds are broken?

A

free fatty acids – unesterified FAs with a carboxylate group

  • bonded to serum albumin in the blood

saponification – ester hydrolysis of triacylglycerols using a strong base (lye)

  • forms glycerol and soap
201
Q

what is it called when there is a signalling cascade in development which changes the structure of function of developing tissues through chemical mediators?

A

induction

202
Q

GAP JUNCTIONS – allow adjacent cells to communicate

  • formed by what?
A

GAP JUNCTIONS – allow adjacent cells to communicate

  • formed by 6 molecules of connexin that permit water and solutes to move through
203
Q

desmosomes –?

hemidesmosomes ?

A

desmosomes – bind adjacent cells to their cytoskeletons (usually epithelial tissue)

hemidesmosomes – binds epithelial cells to underlying structures

204
Q

osmotic pressure: ?

A

osmotic pressure: = iMRT

i = number of particles obtained from the molecule when in solution and dissociated

205
Q
  1. facilitated diffusion ?

includes what type of proteins?

A
  1. facilitated diffusion – simple diffusion for molecules that are impermeable to membrane (large, polar, charged)
    * require transmembrane proteins (transporters, channels)

carriers – open to one side of cell membrane at a time

channels – open or closed conformation

206
Q

Nernst equation:?

A

Nernst equation: E = 61.5/z ln [ions inside]/[ions outside]

z = charge

207
Q

inner mitochondrial membranes – many cristae involved in ATP synthesis and ETC

  • inner membrane encloses the mitochondrial matrix

lacks what?

A

inner mitochondrial membranes – many cristae involved in ATP synthesis and ETC

  • inner membrane encloses the mitochondrial matrix
  • lacks cholesterol
208
Q

Functionalism – ?

conflict theory –?

symbolic interactionism?

social constructionism – ?

A

Functionalism – focuses on function of each component of society and how the components fit together

  • manifest functions: deliberate actions that serve to help a given system
  • latent functions: unexpected, unintended positive consequences of manifest functions

conflict theory – power differentials are created and how they dictate social order

  • anger based off inequality

symbolic interactionism – the way individuals interact through a shared understanding of words, gestures, and other symbols

  • thumbs up is approval in America, but offensive in other cultures

social constructionism – individuals and groups make decisions to agree upon concepts and principles

  • the concept that paper model holds value to people
209
Q

rational choice theory –?

exchange theory –?

A

rational choice theory – people will make decisions that maximize their potential benefit and minimize potential harm (pros and cons)

exchange theory – rational choice theory applied to group setting

  • ppl will continue to behave in ways that are praised and avoid behavior that is not
210
Q
A

MCAT (6 decks)

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