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BIOCHEM Flashcards

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1
Q

Which reactions within the citric acid cycle are considered stereospecific

A

production of (intermediates) D-isocitrate and L-malate

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2
Q

Do synthases require energy/consume ATP to break/form new bonds

A

No
- synthases do not use ATP (use flow of protons)

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3
Q

what is a hydrolysis reaction

A

the breaking apart of molecules using water
- release energy

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4
Q

what is a condensation reaction

A

the building of molecules with a loss of water
- require energy

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5
Q

what is conformational stability

A

the ability of a protein to maintain its three-dimensional fold
- can be measured by melting temperature
- a lower Tm indicates decreased conformational stability bc less thermal energy is required to denature the protein

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6
Q

what is melting temperature (Tm)

A

the temperature at which half the proteins in solution are folded and half are denatured

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7
Q

what is kcat

A

the turnover number of an enzyme
- represents the number of reactions catalyzed per second
- represents ability of an enzyme to catalyze a reaction

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8
Q

what is apo vs holoenzyme

A

apoenzyme - enzyme’s catalytically inactive component (without cofactor)
holoenzyme - enzyme’s catalytically active form

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9
Q

all flavoproteins use ______ as their coenzyme

A

FAD

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10
Q

lysine
- abbreviations, qualities, and key structure

A

Lys - K
positively charged
4 CH2 groups in a chain
protonated amine at the end

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11
Q

arginine
- abbreviations, qualities, and key structure

A

Arg - R
positively charged
3 CH2 groups in a chain
NH-C=NH2+(-NH)

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12
Q

histidine
- abbreviations, qualities, and key structure

A

His - H
positively charged
CH2 followed by an imidazole (five-membered ring containing two nitrogens)

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13
Q

aspartate
- abbreviations, qualities, and key structure

A

Asp - D
negatively charged
1 CH2 group followed by COO- (carboxylate)

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14
Q

glutamate
- abbreviations, qualities, and key structure

A

Glu - E
negatively charged
2 CH2 groups followed by COO- (carboxylate)

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15
Q

describe the Na+ - H+ exchanger

A

an antiporter in which the transport of one Na+ is coupled with the transport of one H+ in the opposite direction
- no net translocation of charge

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16
Q

describe the Na+ - Cl- cotransporter

A

cotransporter that transports one Na+ and one Cl- in the same direction
- no net movement of charge, electroneutral process

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17
Q

describe the Na+ - glucose cotransporter

A

transports Na+ cations and glucose into the cell
- electrogenic process
- results in net movement of positive ions into the cell

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18
Q

what is glycosylation

A

the attachment of carbohydrates to the back of a protein
- crucial for the structural conformation of a protein

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19
Q

insulin is released in response to ____________ by ___________

A

high blood glucose levels ; pancreatic beta cells

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20
Q

glucagon is released in response to ___________ by __________

A

low blood glucose levels ; pancreatic alpha cells

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21
Q

what is an ionophore

A

compound that binds to an ion and moves it across the cell membrane
- degrades ion gradient in process

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22
Q

diaphragm contraction results in _________ thoracic volume and _________ intrathoracic pressure, which causes _________

A

increased ; decreased ; inhalation

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23
Q

what are colonocytes

A

epithelial cells that line the colon

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24
Q

in an enzyme-catalyzed reaction where enzyme concentration is constant and substrate concentration is relatively low, which kinetic parameter will increase with the addition of more substrate

A

Vo (initial velocity)

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25
Q

what are enterocytes

A

intestinal cells that produce enzymes that digest disaccharides (like lactase)

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26
Q

what are parietal cells

A

stomach cells that produce HCl

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27
Q

why would some DNA sequences be conserved among species

A

they are vital to an organism’s life

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28
Q

what are lyases

A

enzymes that catalyze the cleavage of a single molecule into two products
- do not require water as a substrate
- can also catalyze the reverse of their specific reactions (synthesis of two molecules into one) but referred to as synthases

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29
Q

what are isomerases

A

enzymes that restructure the chemical formula of a compound
- rearrangement of bonds within a molecule
- do not break down chemical bonds
- catalyze reactions between stereoisomers and constitutional isomers
- can be classified as other kinds of enzymes based on their reaction-

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30
Q

what are transferases

A

enzymes that transfer chemical groups between compounds
- example: kinases (transfer a phosphate group, generally from ATP, to another molecule)

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31
Q

what are oxidoreductases

A

enzymes that catalyze oxidation-reduction reactions; the removal of hydrogen atoms and transfer of electrons
- often have a cofactor that acts as an electron carrier like NAD+
- enzymes with names like dehydrogenase or reductase are usually oxidoreductases
- enzymes where oxygen is the final electron acceptor are called oxidases

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32
Q

what are hydrolases

A

enzymes that catalyze hydrolysis (breaking of bonds) using the addition of water
- usually named for their substrate
- example: phosphatases, peptidases, nucleases, lipases

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33
Q
A
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34
Q

mutations to what regions of genes most specifically alter gene expression over gene function

A

promotor and enhancer regions

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35
Q

exocrine glands secrete substances through _______ while endocrine glands secrete substances __________

A

ducts onto your body’s surfaces ; directly into your bloodstream

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36
Q

what is transformation

A

the process that transfers genetic material from the environment into bacteria

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37
Q

what is transduction

A

process by which nucleic acids are transferred from viruses to cells

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38
Q

what is conjugation

A

the exchange of nucleic acids between bacteria

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39
Q

what is the induced fit model

A

the theory that an active site changes its form when it comes into contact with a substrate in order to make the enzyme-substrate complex
- process of changing shape requires energy/is endergonic
- process of releasing product is exergonic

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40
Q

what is a prosthetic group

A

cofactor that is tightly bound to the enzyme

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41
Q

compare cofactors vs coenzymes

A

cofactors - inorganic molecules or metal ions that are often ingested as dietary minerals (example: Mg2+)
coenzymes - small, organic groups, usually vitamins or derivatives of vitamins like NAD+, FAD, and CoA

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42
Q

what are the fat-soluble vitamins

A

A,D,E, and K

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43
Q

what are the water-soluble vitamins

A

B complex and C

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44
Q

what does the Michaelis-Menten plot of enzyme kinetics tell you

A

as the amount of substrate increases, the enzyme is able to increase its rate of reaction until it reaches a maximum enzymatic reaction rate (saturation)

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45
Q

what is the Michaelis-Menten equation (when enzyme concentration is constant)

A

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

when v = 1/2vmax –> Km = [S]

at very low substrate concentrations, you can take out the + [S] in the denominator

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46
Q

what is Km

A

the Michaelis constant
- the substrate concentration at which half of the enzyme’s active sites are full
- also a measure of affinity (higher Km means lower affinity)

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47
Q

what is the equation relating max velocity to kcat

A

Vmax = [E]kcat

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48
Q

what is the catalytic efficiency of the enzyme

A

ratio of kcat / Km
- a large kcat (high turnover) or small Km (high affinity) will result in a greater catalytic efficiency

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49
Q

what is the value of the x-intercept of a lineweaver-burk plot

A
  • 1 / Km
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50
Q

what is the value of the y-intercept of a lineweaver-burk plot

A

1 / vmax

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51
Q

what is T vs R state of an enzyme

A

T state = low-affinity tense state
R state = high-affinity relaxed state

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52
Q

what is Hill’s coefficient

A

numerical value that quantifies cooperativity
- if Hill’s > 1, positive cooperativity
- if Hill’s < 1, negative cooperativity
- if Hill’s = 1, no cooperative binding

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53
Q

the anaerobic process that replenishes NAD+ levels occurs in the

A

cytosol

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54
Q

what is the most important start codon for amino acids and which amino acid does it code for

A

AUG
methionine

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55
Q

how do you find the percent decrease of something

A

(old value - new value) / old value

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56
Q

lipid rafts tend to be rich in _________ and poor in ___________

A

sterols ; phospholipids

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57
Q

what are prostaglandins

A

nonhydrolyzable lipids that are involved in inflammatory responses
- not found in cell membranes

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58
Q

what are triglycerides

A

molecules in which 3 fatty acids are each linked to a glycerol molecule
- used for energy storage not structure, not found in cell membranes

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59
Q

what are waxes

A

lipid molecules that typically form soft solids that are malleable at room temperature
- composed of two sets of long chain hydrocarbons linked together through an ester group

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60
Q

which functional group is most common in waxes

A

ester groups

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61
Q

glycolysis uses ATP with which two enzymes

A

hexokinase and phosphofructokinase-1

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62
Q

are L or D amino acids degraded more quickly

A

L amino acids are more common in nature –> more easily recognized by proteins –> get degraded faster

63
Q

T or F: for a reversible reaction, the same enzyme catalyzes both forward and reverse reactions

A

T

64
Q

which metabolic process provides the necessary energy for sustained gluconeogenesis

A

fatty acid oxidation

65
Q

which amino acids contain alkyl side chain groups

A

alanine, proline, leucine, isoleucine, valine

66
Q

which amino acids contain branched alkyl side chain groups

A

isoleucine, leucine, valine

67
Q

what are isoprene units and terpenes

A

isoprene units are branched 5-carbon molecules that are the basis for cholesterol synthesis
terpenes are at least 2/3 isoprene units linked together

68
Q

sugars with the anomeric carbon at position 1 are called __________

A

aldoses

69
Q

sugars with the anomeric carbon at position 2 are called ________

A

ketoses

70
Q

how to distinguish which carbon is the anomeric carbon?

A

carbon bound to 2 oxygens
- if one of the oxygens is an OH, it is a hemi

71
Q

what’s the difference between a hemiacetal and hemiketal

A

hemiacetal - when an alcohol adds to an aldehyde (resulting product has 2 R groups and 2 H atoms)

hemiketal - when an alcohol adds to a ketone (resulting product has 3 R groups and 1 H)

72
Q

which reactions of glycolysis are energy-investment and which are energy-payoff

A

the first 5 are energy-investment and the remaining 5 are energy-payoff

73
Q

preincubation with an inhibitor enzyme allows for what to occur

A

covalent linkages

  • typical of irreversible inhibitors
74
Q

is an amino acid positive or negatively charged when the pH is below its pI

A

positive

75
Q

what different information does boiling point vs heat of combustion tell you

A

boiling point measures the energy required to overcome intermolecular forces
heat of combustion tells you energy needed to break bonds (thermodynamic stability)

76
Q

T or F: post-transcriptional modifications occur before translation

A

T
after transcription, before translation

77
Q

what are transposons

A

DNA sequences that can insert and remove themselves from the genome, can exist in both prokaryotic and eukaryotic cells (no known active ones in humans)
- in prokaryotes, can act as a ‘stress response’ system, allowing for rapid inactivation of genes in response to environmental changes
- can regulate transcription (if they occur in the middle of a coding sequence, that gene will no longer be transcribed)

78
Q

where does a repressor bind to an operon?

A

the operator

79
Q

what is the structure of GPCRs?

A

a single subunit consisting of seven membrane-spanning a helices

80
Q

what is the structure of enzyme-linked receptors

A

a single transmembrane protein with an extracellular ligand-binding domain and an intracellular catalytic domain

81
Q

what is the structure of a ligand-gated channel

A

multiple subunits arranged around a central channel with a ligand-binding site on the subunits

82
Q

competitive inhibitors increase _______

A

Km
- vmax stays the same

83
Q

uncompetitive inhibitors do what to Km and vmax

A

decrease them both

84
Q

noncompetitive inhibitors do what to Km and vmax

A

Km is unaffected
vmax is reduced

85
Q

what does helicase do

A

enzyme responsible for unwinding DNA during replication, generating two single-stranded template strands ahead of the polymerase
- breaks the hydrogen bonds between nitrogenous bases

86
Q

what do DNA topoisomerases do

A

alleviate torsional stress and reduce the risk of strand breakage by introducing negative supercoils
- work ahead of helicase, nicking one or two strands and then resealing them

87
Q

how can you tell if a sugar is reducing or nonreducing

A

reducing if they contain a free anomeric carbon that can be oxidized

nonreducing if the anomeric carbon is linked to another molecule

88
Q

adjacent sugars in RNA and DNA are joined by what bonds

A

phosphodiester bonds at the 5’ and 3’ carbon

89
Q

the nitrogenous bases in RNA and DNA are bound to their sugar by what bond

A

glycosidic bonds (covalent)

90
Q

what functional groups does cytosine have attached to its aromatic ring

A

amino group attached to carbon 4 and carbonyl at carbon 1

91
Q

what functional groups does uracil have attached to its aromatic ring

A

carbonyl attached to carbon 4 and carbonyl at carbon 1

92
Q

what functional groups does thymine have attached to its ring

A

carbonyl at carbon 4, carbonyl at carbon 1, amine branch, and methyl group at carbon 3

93
Q

what functional groups does adenine have

A

amine group at carbon 4

94
Q

what functional groups does guanine have

A

amine at carbon 1 and carbonyl at carbon 4

95
Q

what is differential scanning calorimetry

A

technique that shows the rate at which proteins denature
- peak in the curve is the Tm (melting temperature)

96
Q

what is palmitic acid

A

free fatty acid synthesized by cells
- can be incorporated into phospholipids

97
Q

what is sphingomyelin

A

a phospholipid with a sphingosine backbone

98
Q

the best competitive inhibitors are molecules that _____

A

bind tightly and resemble most closely the transition state
- have small Kd values

99
Q

what is a futile cycle

A

when anabolic and catabolic metabolism occurs at the same rate, so there is no overall energy gain
- active or proliferating cells usually prefer one over the other

100
Q

what is the rate-limiting enzyme of fatty acid oxidation

A

carnitine palmitoyltransferase I

101
Q

what are anabolic hormones

A

generally stimulate anabolic processes and inhibit catabolic processes
- insulin, growth hormone, testosterone, estrogen

102
Q

what are catabolic hormones

A

generally stimulate catabolic processes
- glucagon, cortisol, epinephrine

103
Q

NADPH is used in fatty acid _______ not _________

A

synthesis ; oxidation

104
Q

each PCR cycle amplifies DNA by how much?

A

doubles it

105
Q

what is the rate-limiting enzyme of glycolsis

A

phosphofructokinase-1

106
Q

what is the rate-limiting enzyme of fermentation

A

lactate dehydrogenase

107
Q

what is the rate-limiting enzyme of glycogenolysis

A

glycogen phosphorylase

108
Q

what is the rate-limiting enzyme of glycogenesis

A

glycogen synthase

109
Q

what is the rate-limiting enzyme of gluconeogenesis

A

fructose-1,6-biphosphotase

110
Q

what is the rate-limiting enzyme of the pentose phosphate pathway

A

glucose-6-phosphate dehydrogenase

111
Q

how does the reaction rate of enzyme kinetics change with substrate concentration

A

michaelis-menten kinetics : reactions are approximately first-order at low substrate concentrations ; under saturating concentrations it reaches zero-order kinetics (rate does not increase with increasing concentration)

112
Q

what does it say about the substrate if the enzyme is operating at vmax

A

the substrate is bound to every enzyme active site in solution

113
Q

how can molecules that pertain to the citric acid cycle be easily identified

A

with the exception of succinyl-CoA and acetly-CoA, they are all flanked by carboxylate ions on both ends of the main carbon chain

114
Q

How does prokaryotic DNA differ from eukaryotic DNA?

I. Prokaryotic DNA lacks nucleosomes.
II. Eukaryotic DNA has telomeres.
III. Prokaryotic DNA is replicated by a different DNA polymerase.
IV. Eukaryotic DNA is circular when unbound by centromeres.

A

I, II, and III only

Prokaryotic DNA is circular and lacks histone proteins, and thus does not form nucleosomes. Both prokaryotic and eukaryotic DNA are replicated by DNA polymerases, although these polymerases differ in identity. Eukaryotic DNA is organized into chromatin, which can condense to form linear chromosomes; only prokaryotes have circular chromosomes. Only eukaryotic DNA has telomeres.

115
Q

T or F: the light emitted by fluorescence is always lower in energy than the light that was absorbed

A

True

116
Q

what is the equation for glucose combustion

A

C6H12O6 + 6O2 –> 6CO2 + 6H2O

117
Q

an isotopic substitution requires ______

A

a radioactive 15N

118
Q

what is the basic central dogma

A

DNA –>(transcription)–> RNA –>(translation)–> protein

119
Q

what is reverse transcription

A

making of DNA from RNA
- reverse transcriptase: enzyme that generates complementary DNA (cDNA) from an RNA template

120
Q

retroviruses like HIV use what kind of transcription

A

reverse transcription
- use reverse transcriptase to reverse transcribe their RNA genome into DNA so it can be integrated into the host genome and replicated

121
Q

what are RNA viruses

A

viruses that only use RNA as their genetic information
- the RNA can be used as is for translation or used as a template for transcription and then translation
- example: coronavirus, influenza, paramyxo (measles)

122
Q

what is noncoding RNA (ncRNA)

A

a functional RNA molecule that skips the last step of being translated into a protein and can directly perform functions within the cell
- example: transfer RNA (tRNA) and ribosomal RNA (rRNA) - both used in translation

123
Q

what is epigenetics and what are some ways it happens

A

the study of heritable changes in gene activity that are not caused by changes in DNA sequence ; mechanisms where the same DNA sequence can be modified in a way that results in different phenotypes without changes to the underlying DNA sequences
- examples: DNA methylation, histone modification
- explains why each cell in your body has the same DNA but doesn’t perform the same function (only certain genes are expressed)

124
Q

what’s the structural difference between deoxyribsoe and ribose

A

deoxyribose - has OH group on 3’ carbon and H group on 2’ carbon

ribose - has OH groups on both 2’ and 3’ carbon

125
Q

what does RNA polymerase II do

A

uses a DNA template to make a complementary RNA strand (mRNA transcript)

126
Q

what are the two phases of mRNA processing

A

protection
- nucleotide sequences are added to each end of the transcript to protect it from degradation
- 5’ cap: 5’ end of a single G nucleotide is attached ot the 5’ end
- poly-A tail : a long sequence of A nucleotides are attached to the 3’ end
- protect from exonuclease attacks

splicing
- removal of introns from RNA using spliceosomes
- parts that remain are called exons
- pre-mRNA (before splicing) and primary or mature RNA (after splicing)

127
Q

what are exonucleases

A

enzymes that specifically target RNA molecules with exposed 5’ ends

128
Q

what are introns and exons

A

introns - sequences of RNA that don’t contain any information on how to construct a protein

exons - sequences of RNA that do contain information

129
Q

what are spliceosomes

A

enzyme that locates introns in mRNA, cuts them out, and fuses the remaining parts together

130
Q

what is the idea of RNA interference

A

promising class of medical therapy that disrupt the production of harmful proteins by intercepting and incapacitating mRNA transcripts before they make it to the ribosomes
- used in Ebola treatment
- siRNA (short interfering RNA) - class of engineered molecules that capture and destroy harmful mRNA transcripts

131
Q

what are the three germ layers formed by gastrulation

A

ectoderm (outermost layer) ; mesoderm ; endoderm (innermost layer)

132
Q

what does the ectoderm differentiate into

A

form epithelial cells/tissues and neuronal tissues (neuronal plate and tube)
- neural tube will later give rise to brain and spinal cord
- stimulated by growth factors
- epidermis; cornea and lens of eye; nervous system; sensory receptors in skin; adrenal medulla; teeth enamel

133
Q

what does the mesoderm differentiate into

A

develops into the circulatory system (blood cells, vessels, heart) and various connective tissues (bone, muscles, tendons, and dermal layer) and kidney
- reorganized into groups of cells called somites which have spaces in between them and develop into the ribs, lungs, and spine muscles
- notochord ; skeletal system ; muscular layer of stomach ; excretory system ; reproductive system (except germ cells)

134
Q

what does the endoderm differentiate into

A

forms the epithelial lining of the whole of the digestive tube (except part of mouth and pharynx) and the end part of the rectum
- forms internal organs like stomach, colon, liver, pancreas, bladder, lungs, intestines, thyroid glands

135
Q

a nucleotide contains ______

A

a phosphate group, a pentose sugar, and a nitrogenous base

136
Q

why are the nitrogenous bases called bases

A

the electronegative N has an extra lone pair that can take up protons if needed

137
Q

what are phosphodiester linkages

A

ester bonds that connect phosphate groups to sugars and make up the DNA backbone
- phosphate is connected to 5’ carbon of sugar below it and 3’ carbon of sugar above it (for 5-3’)
- opposite way for 3’-5’ strand

138
Q

what’s the difference between the 5’ and 3’ end of DNA

A

5’ end - has free phosphate group attached to 5’ carbon

3’ end - has free hydroxyl group attached to 3’ carbon

139
Q

what are telomeres and what do they do

A

little caps at the end of chromosomes that protect them from degradation
- act as a buffer zone (very tips of chromosomes cannot be reached by replication enzymes so telomeres are there to ensure all the important genes are replicated)
- prevent chromosomes from sticking to each other

140
Q

what does telomerase do

A

enzyme that lengthens telomeres and brings them back to their original length
- telomeres shorten each time DNA gets replicated

141
Q

what is single copy vs repetitive DNA

A

single copy DNA
- one sequence of DNA that does not repeat itself
- usually contains the most important genes
- gets highly translated and transcribed with low rates of mutation

repetitive DNA
- found mainly near the centromeres (centers) of DNA
- contains both genes and sequences that are not genes
- higher rate of mutation
- highly repetitive DNA has no genetic information and is not transcribed/translated (telomeres are an example of this highly repetitive DNA - TTAGGG)

142
Q

you can only add nucleotides to DNA in which direction

A

5’ –> 3’
- can only add nucleotides on to 3’ end

143
Q

what is leading vs lagging strand of DNA

A

leading is 3’-5’ end (so its complementary sequence is 5’ - 3’ and bases can easily be added in the same direction

lagging is opposite direction so bases cannot be directly added on
- DNA primase puts RNA primers on small sections of DNA so they can be transcribed at a time (gives you Okazaki fragments)

144
Q

what does DNA primase do

A

adds RNA primers (usually around 10 nucleotides) so that transcription can begin

145
Q

what does DNA ligase do

A

seals up all the Okazaki fragments on the lagging strand

146
Q

what does DNA polymerase I do

A

uses its 5’-3’ exonuclease activity to remove RNA primers and replace them with DNA

147
Q

western blotting detects _______ while southern blotting detects ________

A

specific proteins ; specific DNA sequences

148
Q

the stereochemical designators a and B distinguish between

A

epimers at an anomeric carbon

149
Q

which ideal solution exhibits the greatest osmotic pressure

0.1 M MgCl2
0.2 M NaCl
0.2 M CaCl2
0.5 M glucose

A

0.2 M CaCl2

this would dissociate into 3 ions so concentration becomes 0.6 M

150
Q

what kind of mutation is necessary for a southern blot to be useful

A

the mutation needs to create or eliminate a restriction site (palindromes usually 4-6 bases long)

151
Q

proteolytic cleavage is a _________ reaction

A

hydrolysis

152
Q

what is native vs SDS page

A

native page - electrophoresis method of analyzing proteins ; keeps them in their native shape ; results are limited bc mass-to-charge ratio can get in the way

SDS page - electrophoresis method that compares proteins ONLY based on molecular mass
- denatures proteins through addition of a detergent which disrupts the non-covalent interactions and masks the charge (only size matters)
- functional protein cannot be regained

153
Q

what is isoelectric focusing electrophoresis

A

separates proteins by their isoelectric point (pI)
- the protein migrates toward an electrode in a pH gradient until it reaches a region of the gel where pH = pI of the protein. Positively (+) charged proteins will move towards the cathode and negatively (-) charged proteins will move towards the anode.

MCAT (7 decks)

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