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Biology - MCAT > Class Three > Flashcards

Class Three Flashcards

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1
Q

why is phosphoric acid inorganic

A

doesn’t contain carbon

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2
Q

unique quality of phosphoric acid

A

can donate three protons

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3
Q

how is pyrophosphate formed

A

two orthophosphates (aka normal phosphates) bound together via an anhydride linkage

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4
Q

example of a high energy phosphate bond

A

P-O-P bond in pyrophosphate

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5
Q

hydrolysis of pyrophosphate is..

A

thermodynamically favourable

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6
Q

why is the hydrolysis of pyrophosphate very favourable in the cell

A

cells have higher concentrations of ATP than ADP and P

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7
Q

reasons why phosphate anhydride bonds store a lot of energy (3)

A

when phosphates are linked together, their negative charges repel eachother

orthophosphate has more resonance forms → lower free energy than linked phosphates

orthophosphates have a more favourable interaction with water than linked phosphates

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8
Q

building blocks of nucleic acids

A

nucleotides

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9
Q

nucleotides contain..

A

a ribose (or deoxyribose) sugar group

a purine/pyrimidine base at C1

1 or 2 or 3 phosphate units at C5

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10
Q

RNA precursor

A

ATP

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11
Q

universal short term energy storage molecule

A

ATP

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12
Q

energy extracted from food is..

A

immediately out into the phosphoanhydride bonds of ATP

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13
Q

UTP - glycogenesis

A

activates glucose-1-P

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14
Q

DNA aka

A

deoxyribonucleic acid

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15
Q

RNA aka

A

ribonucleic acid

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16
Q

why are DNA and RNA called nucleic acids

A

found in the nucleus and have many acidic phosphate groups

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17
Q

building block of DNA

A

dNTP

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18
Q

deoxyribose vs ribose

A

deoxyribose is missing an OH

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19
Q

the purines are..

A

guanine and adenine

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20
Q

the pyrimidines are..

A

cytosine and thymine

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21
Q

purine vs pyrimidine

A

purine: double ring structure (6-membered and 5-membered ring)
pyrimidine: single 6-membered ring

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22
Q

can purines and pyrimidines H bond

A

yes

that is why in dilute solutions, they won’t bond to each other (will bond with the water - RNA)

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23
Q

what is a deoxynucleoside composed of

A

deoxyribose and an aromatic base

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24
Q

backbone of a nucleic acid

A

sugar-phosphate portion → invariant

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25
Q
A

adenine

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26
Q
A

guanine

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27
Q
A

cytosine

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28
Q
A

uracil - RNA only

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29
Q
A

thymine - DNA only

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30
Q

nucleotides in nucleic acids are covalently linked by..

A

phosphodiester bonds

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31
Q

phosphodiester bonds are between..

A

the 3’ hydroxyl group and the 5’ phosphate group

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32
Q

why is the polymerization of nucleoside triphosphate energetically favourable

A

pyrophosphate is released & hydrolyzed → drives the polymerization reaction forward

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33
Q

Watson-Crick model

A

DNA is a right-handed double helix held together by H bones and hydrophobic forces between bases

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34
Q

ds-DNA

A

2 polynucleotide chains H-bonded in an antiparallel orientation

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35
Q

A is always H-bonded to..

A

T

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36
Q

G is always H-bonded to..

A

C

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37
Q

H-bonded pair in DNA always contains..

A

a purine + a pyrimidine

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38
Q

GC pair is held together by..

A

3 H-bonds

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39
Q

AT pair is held together by..

A

2 H-bonds

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40
Q

when are two chains of DNA complementary

A

if the bases in each strand can H-bond when the strands are oriented in an antiparallel fashion

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41
Q

annealing/hybridization

A

binding of 2 complementary DNA strands into a double-stranded structure

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42
Q

melting/denaturation

A

separation of DNA strands

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43
Q

Tm - DNA

A

temperature at which a solution of DNA molecules is 50% melted

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44
Q

double helix of DNA is stabilized by..

A

van der Waals foreuse between the bases

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45
Q

hydrophobic interactions between bases..

A

stabilize the double helix

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46
Q

when does the helix pattern repeat itself

A

every 10 base pair (34 angstroms)

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47
Q

what is a genome

A

sum of an organism’s genetic information

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48
Q

how many chromosomes do humans

A

46 chromosomes - 23 from each parent

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49
Q

prokaryotic genomes are composed of..

A

a single circular chromosome

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50
Q

DNA gyrase function

A

only in prokaryotes → makes it more compact & sturdy

enzyme that uses ATP to break DNA and twist the two sides of the circle around each other → creates supercoils

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51
Q

eukaryotic DNA is wrapped around..

A

histones

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52
Q

nucleosomes

A

DNA wrapped around a group of 8 histones

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53
Q

fully packed DNA is called..

A

a chromatin → closely packed nucleosomes

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54
Q

are histones basic or acidic & why

A

they are basic → need to be attracted to the acidic exterior of DNA double helix

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55
Q

basicity of histones come from..

A

arginine & lysine (abundant in histones)

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56
Q

heterochromatin

A

darker, denser regions of chromosomes

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57
Q

euchromatin

A

lighter, less dense regions of chromosomes

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58
Q

why do lighter regions of chromosomes have higher transcription rates

A

higher transcription rates → higher gene activity

this is because the looser packing makes the DNA accessible to enzymes and proteins

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59
Q

what is a centromere

A

region of a chromosome where spindle fibers attach during cell docosopn

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60
Q

spindle fibers attach to centromeres via..

A

kinetochores (anchor attachment sites for spindle fibers)

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61
Q

centromeres are made up of..

A

heterochromatin and repetitive DNA sequences

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62
Q

what determines the ratio between p (short) and q (long) arms

A

position of the centromere

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63
Q

what is a telomere

A

protective caps at the end of DNA that make up chromosomes

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64
Q

repeated units of telomeres

A

6-8 base pairs long & guanine rich → stabilizes the end of chromosomes

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65
Q

function of telomeres

A

prevent chromosome deterioration & prevent fusion with neighbouring chromosomes

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66
Q

do prokaryotes have telomeres

A

no → circular genomes

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67
Q

RNA vs DNA (3)

A

RNA is single-stranded

RNA has uracil instead of thymine

pentose ring in RNA is ribose, not deoxyribose

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68
Q

why is the RNA polymer less stable than DNA

A

the 2’ OH group (only present in ribose) can nucleophilically attack the backbone phosphate of an RNA chain

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69
Q

function of messenger RNA

A

type of coding RNA

carries genetic information to the ribosome → translated into protein

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70
Q

types of non-coding RNA (2)

A

transfer RNA

ribosomal RNA

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71
Q

transfer RNA function

A

translate the genetic code

carries AAs from the cytoplasm → ribosome to be added to a growing protein

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72
Q

ribosomal RNA function

A

major component of ribosome

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73
Q

ribozymes

A

catalytic RNAs → perform specific biochemical reactions

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74
Q

the human genome contains..

A

24 different chromosomes (22 autosomes & 2 sex chromosomes)

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75
Q

what is an intergenic region

A

region composed of noncoding DNA → no known functions

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76
Q

major components of intergenic regions

A

tandem repeats & transposons

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77
Q

what is a gene

A

DNA sequence that encodes a gene product

includes regulatory regions and a region that codes for a protein or a noncoding RNA

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78
Q

single nucleotide polymorphisms

A

single nucleotide changes once in every 1,000 base pairs → essentially a mutation

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79
Q

where do SNPs most commonly occur

A

in noncoding regions → but can also lead to specific traits and phenotypes

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80
Q

copy number variation (CNV)

A

structural variations in the genome that lead to different copies of DNA sections

associated with cancer and other diseases

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81
Q

CNV vs SNP

A

changes with CNVs apply to much larger regions of the genome compared to SNPs

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82
Q

tandem repeats

A

short sequences of nucleotides are repeated one after another

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83
Q

when can tandem repeats be unstable

A

when the repeating unit is very short or very long

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84
Q

unstable tandem repeats..

A

can lead to chromosome breaks and disease

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85
Q

what are rich in tandem repeats

A

heterochromatin, centromeres and telomeres

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86
Q

what is transcription

A

process of reading DNA and writing the information as RNA

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87
Q

outcomes of transcription

A

generation of a final gene product or a messenger molecule (to construct protein)

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88
Q

what is translation

A

the synthesis of proteins using RNA as a template

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89
Q

what is a ribosome

A

massive enzyme composed of many proteins and pieces of RNA

organizes translation

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90
Q

Central Dogma

A

process in which the instructions in DNA are converted into proteins

DNA → RNA → protein

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91
Q

language used by RNA and mRNA to specify the building blocks of proteins

A

genetic code

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92
Q

genetic code is written in __ letter words

A

3

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93
Q

what is a codon

A

a nucleic acid word (3 nucleotide letters)

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94
Q

which nucleic acid actually encodes proteins during translation & what does this mean

A

RNA - has U instead of T

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95
Q

how many stop codons are there

A

3/64

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96
Q

function of a stop codon

A

to notify the ribosome that the protein is complete and cause it to stop reading the mRNA

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97
Q

stop codons aka

A

nonsense codons

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98
Q

switching the third nucleotide in a codon..

A

usually doesn’t have an affect

usually all 4 of the codons with the same first 2 molecules encode the same AA

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99
Q

two or more codons coding for the same AA are..

A

synonyms

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100
Q

when a genetic code has synonyms, it is..

A

degenerate

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101
Q

each codon specifies..

A

only a single AA

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102
Q

how can viruses make DNA from RNA

A

with the use of the enzyme reverse transcriptase

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103
Q

conservative replication theory

A

the parental ds-DNA would remain as-is while an entirely new double-stranded genome was created

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104
Q

dispersive replication theory

A

both copies of the genomes were composed of scattered pieces of new and old DNA

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105
Q

semiconservative replication

A

after replication, one strand of the new double helix is parental and one strand is newly synthesized daughter DNA

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106
Q

DNA replication is..

A

semiconservative

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107
Q

helicase function

A

unwinds the double helix and separates the two strands

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108
Q

origin of replication

A

the place where the helicase begins to unwind

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109
Q

which protein finds the ORI in prokaryotes

A

DnaA

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110
Q

finding the ORI in eukaryotes

A

three proteins find it together (2 of them are destroyed once the S phase begins) → links DNA replication to the cell cycle so DNA replication doesn’t initiate during other phases

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111
Q

topoisomerase function

A

cut one or both of the strands & unwrap the helix to release the excess tension created by the helicases

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112
Q

single-strand binding proteins (SSBPs) function

A

protect DNA that has been unpackaged & help keep the strands separated

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113
Q

importance of RNA primers

A

RNA that initiates DNA synthesis → DNA polymerase can only add not start so RNA primer is needed

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114
Q

how is RNA primer synthesized

A

RNA polymerase called primase (part of a set of proteins aka primosome)

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115
Q

DNA polymerase function

A

catalyzes the elongation of the daughter strand using the parental template → adds dNTPs to the 3’ end

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116
Q

polymerization always occurs in..

A

the 5’ to 3’ direction

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117
Q

DNA pol requires..

A

a primer

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118
Q

template stands are read..

A

3’ to 5’

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119
Q

daughter strands are elongated..

A

5’ to 3’

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120
Q

leading strands

A

elongate continuously right into the widening replication fork

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121
Q

lagging strands

A

must wait until the replication fork widens before beginning to polymerize

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122
Q

Okazaki fragments

A

small chunks of DNA comprising the lagging strand

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123
Q

replication of the leading strand is..

A

continuous

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124
Q

replication of the lagging strand is..

A

discontinuous → resulting in Okazaki fragments

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125
Q

RNA primers are replaced by..

A

DNA

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126
Q

what joins DNA fragments

A

DNA ligase

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127
Q

DNA pol III function

A

found in prokaryotes

responsible for the fast, accurate elongation of the leading strand

can also move backward to chop off newly added nucleotides → proof reading function

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128
Q

DNA pol I function

A

only found in prokaryotes

adds nucleotides at the RNA primer

goes slowly, job gets taken over by DNA pol III

also has exonuclease activity (proofreading)

can also repair damaged DNA

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129
Q

theta replication

A

replication of prokaryotes’ genome

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130
Q

what happens when telomeres become too short

A

chromosome can no longer replicate

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131
Q

Hayflick limit

A

number of times a normal human cell type can divide until telomere length stops cell division

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132
Q

telomere shortening - disease

A

age related diseases are linked to this

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133
Q

what happens when the telomeres’ length is too short

A

cells activate DNA repair pathways or

enter a senescent state (alive but not dividing) or

activate apoptosis

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134
Q

telomerase function

A

enzyme that adds repetitive nucleotide sequences to the ends of chromosomes to lengthen telomeres

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135
Q

what is telomerase composed of

A

it is a ribonucleoprotein

contains an RNA primer and reverse transcriptase enzyme (read RNA templates and generate DNA)

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136
Q

telomerase - cancer

A

cancer cells can express telomerase → helps cells to immortalize

137
Q

how does one get a genetic mutation

A

inherited or acquired through life

138
Q

genetic mutation

A

alteration of the DNA sequence of an organism’s genome

139
Q

germline mutations

A

mutations that can be passed to offspring → occur in germ cells

140
Q

somatic mutations

A

cannot be passed onto offspring, occurs in somatic cells

141
Q

example of a physical mutagen

A

ionizing radiation (X-rays, alpha particles and gamma rays)

142
Q

ionizing radiation can cause..

A

DNA breaks

143
Q

single-strand vs double-strand break

A

single strand: can be easily patched up

double strand break: more difficult to piece back together

144
Q

UV light - physical mutagen

A

causes photochemical damage to DNA

if two pyrimidines are beside each other, can cause them to be covalently linked

distorts the DNA backbone + mutations in DNA replication

145
Q

what are cross-links

A

abnormal covalent bonds between different parts of DNA

146
Q

intercalating agent

A

compounds that insert themselves between base pairs → cause mutations

147
Q

biological agents of mutation (3)

A

DNA polymerase making a mistake in proofreading

viruses

transposons

148
Q

types of mutations (7)

A

point mutations

insertions

deletions

inversions

amplifications

translocations and rearrangements

loss of heterozygosity

149
Q

what is a point mutation

A

single base pair substitution

150
Q

transition vs transversion point mutation

A

transition: substitution for a purine/pyramidine for a correspondent
transversion: substitution of a purine for a pyrimidine & vice versa

151
Q

missense mutation

A

causes an AA to be replaced with a different AA

may not be serious if the AAs are similar

152
Q

nonsense mutation

A

a stop codon replaces a regular codon and prematurely shortens the protein

153
Q

silent mutation

A

a codon is changed into a new codon for the same AA so there is no change in the protein’s AA sequence

154
Q

insertion

A

addition of one or more extra nucleotides into a DNA sequence

155
Q

deletion

A

removal of nucleotides from a sequence

156
Q

frameshift mutations

A

mutations that cause a change in the reading frame

157
Q

inversion

A

when a segment of a chromosome is reversed end to end

158
Q

insertions, deletions and inversions can be caused by..

A

transposons

159
Q

start codon

A

AUG

160
Q

stop codons (3)

A

UAA

UAG

UGA

161
Q

chromosome amplification

A

when a segment of a chromosome is duplicated

162
Q

translocation

A

when recombination occurs between nonhomologous chromosomes → gene fusion

163
Q

balanced and unbalanced translocations

A

balanced: no genetic material is lost
unbalanced: where genetic information is lost or gained

164
Q

_____ is a common occurrence in many types of cancer

A

translocation

165
Q

what is a transposon

A

DNA sequence that can change its position within a genome

166
Q

3 transposons

A

IS element

complex transposon

composite transposon

167
Q

IS element

A

composed of a transposase gene flanked by inverse repeat sequences

168
Q

complex transposon

A

contain additional genes

169
Q

composite transposon

A

two similar/identical IS elements with a central region in-between them

170
Q

transposase

A

has “cut and paste” activity

donor site → new genetic location

171
Q

chromosome with two transposons in the same direction..

A

transposons line up → parallel so they loop around

172
Q

DNA segment between direct transposons is ____

A

deleted

173
Q

if a chromosome has two transposons with inverted orientations..

A

the DNA segment between the two transposons becomes inverted

174
Q

what happens with parallel transposons

A

deletion and chromosomal rearrangements (one transposon and DNA segment leave to integrate into a different genomic site)

175
Q

loss of heterozygosity

A

deletion of the normal copy of a gene and mutated version of the other copy

176
Q

why do mutations on sex chromosomes have greater effects

A

autosomes are present in double copies, sex chromosomes are not

177
Q

hemizygosity

A

haploid expression in a diploid organism → increases effect of mutations on these chromosomes

178
Q

gain-of-function vs loss-of-function mutations

A

gain of function: increases the activity of a certain gene product - gains a new/abnormal function

loss of function: gene product having less or no function

179
Q

haplosufficiency

A

diploid organisms only having a single functional copy of a gene - not enough to support normal state

180
Q

gene dose

A

expressing a gene is not enough - need to express enough of the gene to maintain good health

181
Q

example of beneficial mutation in humans

A

mutation in Hb gene - causes sickle cell anemia BUT makes them more resistant to malaria (important in Africa etc.)

182
Q

inborn errors of metabolism

A

group of genetic diseases that involve disorders of metabolism

183
Q

cause of inborn errors of metabolism

A

single mutation in a single gene that codes for a metabolic enzyme

184
Q

cancer is driven by..

A

mutation accumulation

185
Q

carcinogen

A

mutagen directly involved in causing cancer

186
Q

mutations involved with cancer are usually found in..

A

oncogenes and tumour suppressors

187
Q

oncogene

A

gene that can cause cancer when it is mutated/expressed at high levels

188
Q

tumor suppressors

A

deletion of these or decreased levels can cause cancer

189
Q

direct reversal

A

type of DNA repair

e.g. enzymes can repair UV-induced pyrimidine photodimers using visible light

190
Q

homology dependent repairs

A

dependent on using one strand of DNA to repair the damaged other strand

191
Q

excision repair vs post-replication repair

A

excision: repair that happens before DNA replication

post-replication: repair that happens during and after DNA replication

192
Q

excision repair

A

type of homology dependent repair

removes defective bases/nucleotides + replaces them

193
Q

mismatch repair pathway

A

targets mismatched base pairs that were not repaired by DNA polymerase during replication

194
Q

genome methylation purpose

A

helps bacterial machinery to recognize the older parent chain (will be methylated) and the newer chain that needs to be replaced

195
Q

double strand break repair (2)

A

homologous recombination and nonhomologous end joining

196
Q

goal of double strand break repair

A

reattach and fuse chromosomes that have come apart

197
Q

homologous recombination

A

one sister chromatid helping to repair a DSB in the other

198
Q

purpose of a joint molecule in homologous recombination

A

where damaged and undamaged sister chromatids cross over

199
Q

when is nonhomologous end joining

A

used for cells that don’t have the option of using sister chromatids

common in eukaryotes

200
Q

nonhomologous end joining process

A

broken ends are stabilized + processed → connected by DNA ligase

201
Q

cons of nonhomologous end joining

A

doesn’t care about specificity → just reconnects broken chromosomes (usually gets connected in abnormal ways)

202
Q

what is gene expression

A

process where information contained in genes has effects in the cell

203
Q

mRNA function

A

carries genetic information to the ribosome → translated into protein

204
Q

5’ untranslated region importance of mRNA

A

this part isn’t translated into protein → important in initiation & regulation

205
Q

open reading frame

A

region of mRNA that codes for a protein

start codon to end codon

206
Q

3’ end of mRNA

A

after the stop codon

isn’t translated into protein but contains regulatory regions (influences post-transcriptional gene expression)

207
Q

monocistronic eukaryotic mRNA

A

one gene = one protein

each piece of mRNA encodes only one polypeptide

208
Q

polycistronic prokaryotic mRNA

A

mRNA codes for more than one polypeptide

translation, termination & initiation sequence are found in-between the ORFs

209
Q

how does hnRNA become mRNA

A

addition of a cap & tail

splicing

210
Q

first RNA transcribed from DNA

A

hnRNA (immature precursor)

211
Q

what is transcription

A

synthesis of RNA using DNA as the template

212
Q

what uses template driven polymerization

A

replication and transcription

213
Q

RNA transcript produced in transcription is ___ to the DNA template

A

complementary

214
Q

driving force for replication and transcription

A

removal and hydrolysis of pyrophosphate from each nucleotide added to the chain (existing chain acts as the nucleophile)

215
Q

does transcription need RNA primer

A

no → RNA polymerase

216
Q

does RNA polymerase have exonuclease activity

A

no - does not possess proofreading abilities

217
Q

promoter region

A

sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription

218
Q

upstream nucleotide sequences

A

use negative numbers → toward the 5’

219
Q

downstream nucleotide sequences

A

use positive numbers → toward the 3’

220
Q

characteristics of prokaryotic RNA polymerase

A

5 subunits: two alpha, a beta, a beta’ and an omega subunit

221
Q

core enzyme for rapid elongation of transcript - prokaryotes

A

5 subunits of RNA polymerase

222
Q

what makes up the holoenzyme

A

sigma factor and the 5 subunits of RNA polymerase

223
Q

3 stages of prokaryotic transcription

A

initiation, elongation & termination

224
Q

initiation of transcription in prokaryotes

A

RNA polymerase holoenzyme binds to a promoter

225
Q

primary sequences of a bacterial promoter

A

Pribnow box (-10) and the -35 sequence

226
Q

roles of sigma factor

A

helps the polymerase find promoters

227
Q

how does sigma factor help polymerase find promoters

A

increases RNA polymerase’s ability to recognize promoters

decreases the nonspecific affinity of holoenzyme for DNA

228
Q

termination of prokaryotic transcription

A

termination signal (rho protein) & polymerase falls off the DNA and releases RNA

229
Q

eukaryotic vs prokaryotic transcription (location)

A

p: transcription occurs in the cytoplasm (no nucleus!) - transcription and translation occur simultaneously
e: transcription occurs in the nucleus & then goes to cytoplasm for translation

230
Q

primary transcript in prokaryotes vs eukaryotes

A

mRNA vs hnRNA

in prokaryotes, they are ready for translation right away (starts before transcription even ends)

231
Q

splicing

A

to go from hnRNA → mRNA

introns get removed and axons join togehter

232
Q

splicing occurs with..

A

spliceosome (100+ proteins & 5 small nuclear RNA molecules)

233
Q

how do snRNPs form

A

half of spliceosome proteins bind to the snRNAs to from 3 snRNPs

234
Q

function of snRNPs

A

snRNPS H-bond to nucleotides in the intron

two splicing reactions take place

1: attaches one end of the into to the conserved adenine (forms a loop)
2: joins two axons and releases the loop

235
Q

5 conserved nucleotides necessary for splicing

A

GU, A and AG

236
Q

alternative splicing

A

different options/patterns of splicing

can increase the complexity of gene expression

237
Q

hnRNA → mRNA (3)

A

splicing

5’ cap (methylated guanine)

3’ poly-A tail (100s of adenines)

238
Q

significance of 5’ cap

A

essential for translation

239
Q

significance of cap and poly-A tail

A

prevents digestion of the mRNA by exonucleases free in the cell

240
Q

why do exonucleases float freely in the cell (2)

A

mRNA has a very short lifespan (regulation at the transcription level)

viruses inject RNA into the cell (doesn’t have a cap or tail)

241
Q

RNA polymerase I, II and III function (eukaryotes)

A

RNA polymerase I: transcribes most rRNA

RNA polymerase II: transcribes hnRNA (which becomes mRNA)

RNA polymerase III: transcribes tRNA

242
Q

what is translation

A

synthesis of polypeptides according to the AA sequence by the specific codons in mRNA

243
Q

each tRNA is composed of..

A

a single transcript produced by RNA polymerase III

244
Q

what stabilizes tRNA

A

H bonds

245
Q

anticodon function

A

recognized the mRNA codon to be translation (3 ribonucleotides)

246
Q

tRNA specificity

A

a tRNA for every codon → tRNA is specific for one AA

247
Q

inosine is derived from..

A

adenine

248
Q

Wobble Hypothesis

A

first two codon-anticodon pairs are normal but the third position is more flexible (explains why a smaller number of tRNAs are possible)

249
Q

inosine - Wobble

A

modified inosine base at the 5’ end of an anticodon is very wobbling (can bond to AUC)

250
Q

tRNA loading / AA activation

A

2 high energy phosphate bones are hydrolyzed to provide the energy to attach an AA to its tRNA molecule

251
Q

breaking the aminoacyl-tRNA bond..

A

drives peptide bond formation forward

252
Q

step 1 of AA activation

A

amino acid + AMP → aminoacyl AMP + pyrophosphate

253
Q

step 2 of AA activation

A

pyrophosphate leaving group → hydrolyzed to 2 orthophosphates (very favourable)

254
Q

step 3 of AA activation

A

destruction of the aminoacyl-AMP bond to drive tRNA loading forward

255
Q

amino acid activation requires _ ATP(s)

A

2

256
Q

aminoacyl-tRNA synthetase

A

specific to each AA

joins AA to the tRNA

257
Q

amino acid activation functions (2)

A

specific + accurate AA delivery

thermodynamic activation of the AA

258
Q

ribosomes are composed of..

A

many polypeptides and rRNA chains

259
Q

Svedberg unit

A

sedimentation rate - how quickly something will sink

260
Q

70S ribosome

A

prokaryotic

30S small subunit & 50S large subunit

261
Q

80S ribosome

A

eukaryotic

40S small subunit & 60S large subunit

262
Q

how many rRNA in prokaryotes

A

23S

263
Q

how many rRNA in eukaryotes

A

28S

264
Q

ribozymic activity is found in the __ subunits

A

large

265
Q

rRNA ribozyme function

A

link AAs during protein synthesis via peptidyl transferase activity

266
Q

binding sites on ribosomes (3)

A

A site

P site

E site

267
Q

A site - ribosome

A

where each new tRNA delivers its AA

268
Q

P site - ribosome

A

where the growing polypeptide chain (still attached to tRNA) is located during translation

269
Q

E site - ribosome

A

where the empty tRNA sits before it is released

270
Q

polyribosome arrangement

A

several ribosomes attach to prokaryotic mRNA and translate it simultaneously

271
Q

characteristic of polycistronic mRNA

A

ribosomes can start translation in the middle of the chain

272
Q

Shine-Dalgarno sequence

A

ribosome binding site for prokaryotic translation

located at -10

273
Q

initiation of prokaryotic translation

A

30S (small) subunit binds to 2 initiation proteins (IF1 & IF3)

this entire process then binds to the mRNA transcript

then the aminoacyl-tRNA, IF2 (bound to a GTP) joins

finally, the 50S subunit joins

274
Q

first aminoacyl-tRNA in pro translation initiation

A

initiator tRNA

275
Q

first amino acid in all prokaryotic proteins

A

modified methionine - AUG

276
Q

where does the initiator tRNA sit

A

in the P site of the 70S ribosome (hydrogen bonded with start codon)

277
Q

when does AUG initiate translation

A

when a Shine-Dalgarno sequence comes before

278
Q

what happens before the elongation stage of pro translation

A

initiation factors dissociate from the complex

279
Q

elongation pro translation

A

2nd aminoacyl-tRNA enters the A site & H-bonds with the second codon (done by elongation factor Tu)

peptidyl transferase of the large subunit catalyzes a bond between fMet and the 2nd AA

280
Q

direction of synthesis pro translation

A

N → C

since the N of amino acid 2 bind to the C of amino acid 1

281
Q

translocation pro translation

A

the empty tRNA moves into E site, tRNA #2 (with the growing polypeptide) moves into the P site and the next codon goes into the A site

282
Q

what helps with translocation

A

elongation factor G (EF-G)

283
Q

purpose of EF-Ts

A

removes the remaining GDP from EF-Tu → helps it reset

284
Q

termination pro translation

A

occurs when stop codon appears at the A site

a release facto then enters the A site

causes peptidyl transferase to hydrolyze the bond between the last tRNA and the completed polypeptide

285
Q

RF3 function

A

GTP-binding protein that doesn’t recognize a stop codon but leads to the dissociation of RF1/RF2 after peptide release

286
Q

why can’t eukaryotic transcription and translation occur at the same time

A

needs transport from nucleus → cytoplasm

287
Q

do eukaryotes use Shrine-Dalgarno sequences to initiate translation

A

no

288
Q

how is translation in eukaryotes started

A

with 5’ UTR sequences - common one is the Kosak sequence

289
Q

eukaryotic translation initiation

A

initiation complex forms (40S subunit, Met-tRNAMet and eukaryotic initiation factors (eIFs) → recruited to 5’ cap

once a start codon is found → 60S subunit is recruited and translation can begin

290
Q

eIF proteins & their functions in initiation (4)

A

eIF3 prevents premature association with 60S

eIF4A is a helicase and unwinds mRNA

eIF4E binds the 5’ cap to mRNA

eIF4G is a scaffold protein (regulator)

291
Q

rate limiting step for translation

A

eIF proteins

more of them = more translation

292
Q

eukaryotic translation elongation factors

A

helps with the entry of aminoacyl-tRNA into the A site

and one is a guanine nucleotide exchange factor (releases GDP)

293
Q

eukaryotic translation termination release factors

A

eRF1 recognizes the 3 termination codons

eRF3 helps to release the completed polypeptide

294
Q

cap dependent translation

A

eukaryotic translation starting at the 5’ end of an mRNA

295
Q

cap independent translation

A

eukaryotes can sometimes start translation in the middle of an mRNA molecule

296
Q

what is necessary for cap independent translation

A

transcript must have an internal ribosome entry site

these make sure that cells can make essential proteins under sub-optimal growth conditions

297
Q

principle site of gene expression regulation

A

transcription (in both eu and pro)
amount of protein made is affected by the amount of mRNA that gets transcribed

298
Q

ways of controlling gene expression at the DNA level (4)

A

DNA methylation/chromatin remodelling

gene dose

imprinting

X chromosome inactivation

299
Q

DNA methylation - controlling gene expression

A

prokaryotic & eukaryotic covalently modified by adding a methyl group

300
Q

how does DNA methylation control gene expression (2)

A

physically blocks the gene from transcriptional proteins

certain proteins bing methylate CpG groups & recruit chromatin remodelling proteins to change the winding of DNA around histones

301
Q

gene dose - controlling gene expression

A

increased copy number of a gene by amplification

allows a cell to make large quantities of a protein

gene deletion = opposite

302
Q

genomic imprinting - controlling gene expression

A

when only one allele is expressed

epigenetic process

303
Q

X chromosome inactivation - controlling gene expression

A

females have 2 X chromosomes (one active & one inactive)

different X chromosomes inactivated in different tissues and cells (the cells decide)

304
Q

simple mechanism of bacteria transcriptional regulation

A

some promoters are stronger than others

(this is preset)

305
Q

anabolic and catabolic enzymes - regulation of transcription in prokaryotes

A

anabolic enzymes whose transcription is inhibited in the present of excess products → repressive

catabolic enzymes whose transcription can be stimulated by abundance of substrate → inducible enzymes

306
Q

components of a lac operon (5)

A

P region: promoter site on DNA → RNA polymerase binds here to initiate transcript for Y Z A genes

O region: operator site where Lac repressor binds

Z gene: codes for enzyme beta-galactosidase (cleaves lactose → glucose + galactose)

Y gene: codes for permease (transports lactose into cell)

A gene: codes for tranacetylase (transfers an acetyl group from acetyl-CoA to beta-galactosides

307
Q

crp gene function

A

codes for catabolite activator protein (CAP)

308
Q

I gene fucntion

A

codes for Lac repressor protein

309
Q

in the presence of glucose, lac operon will be __

A

off

310
Q

glucose, adenyl cyclase and cAMP

A

glucose levels control levels of adenyl cyclase

adenyl cyclase converts ATP → cAMP

311
Q

I gene & transcription

A

codes for a repressor protein → prevents RNA pol from binding to the promoter and transcribing Z, Y and A genes

312
Q

lac operon in the presence of glucose and absence of lactore

A

Z, Y and A are not transcribed or translation

low levels of cAMP

313
Q

lac operon in the presence of glucose and lactose

A

Z, Y and A are transcribed at low levels

decreased cAMP levels

314
Q

lac operon in the absence of glucose and presence of lactose

A

Z, Y and A are transcribed at high levels

315
Q

in the presence of tryptophan..

A

trp repressor protein and typotophan bind to the operator together

RNA pol cannot bind to the promoter → trp genes are turned off

316
Q

activator proteins - regulation

A

point of transcriptional regulation in eukaryotes

enhancer sequences in DNA are bound by activator proteins

317
Q

gene repressor proteins - regulation of transcription in eukaryotes

A

these proteins inhibit transcription

318
Q

RNA translocation - transcription regulation in eukaryotes

A

mRNA transcripts aren’t translated into proteins until they are localized properly in the cell

nucleus → cytoplsm

important in cells with a high level of polarity

319
Q

mRNA surveillance - transcription regulation eukaryotes

A

monitoring so only high quality mRNA transcripts are read

defective transcripts are degraded

320
Q

RNA interference - transcription regulation eukaryotes

A

way of silencing gene expression after a transcript has been made

decreases protein expression

321
Q

protein folding: post-translational modification

A

newly synthesized protein is folded into 3D shape by chaperone proteins

322
Q

covalent modification: post-translational modification

A

proteins are covalently modified

e.g. adding acetyl, formyl or alkyl groups

this can change many aspects of a protein (e.g. enzyme affinity for substrate)

323
Q

processing: post-translational modification

A

cleavage (from zymogens → mature protein)

324
Q

why are protein precursors used

A

when the mature protein is dangerous to the organism → allows to control how much there is

325
Q

Doppler ultrasound allows to distinguish between..

A

a stationary and moving object

326
Q

splicing is a…

A

post-transcriptional modification

327
Q

cytochrome C acts as a ___ electron carrier

A

1

328
Q

what makes the best primer for PCR

A

primers with high G and C (esp near the ends)

329
Q

what is PCR

A

polymerase chain reaction

making lots of copies of a specific segment of DNA

330
Q

in what phase of meiosis does nondisjunction occur

A

anaphase I

331
Q

high insulin levels leads to..

A

low blood sugar levels

332
Q

which amino acid is neutral, but zwitterionic at pH 7, despite possessing two nitrogen atoms in its formula

A

glutamine

333
Q

actin is a..

A

microfilament

334
Q

colour weakness is due to..

A

absence/reduction in the number of receptors for the specific colour → fewer signals sent to the brain

335
Q

head of a fatty acid

A

carboxyl group

336
Q

carbonic anhydrase inhibitor to the RBCs would most likely cause an increase in..

A

CO2 in the tissues

337
Q

HCO3– concentration in veins vs arteries

A

higher in the veins

338
Q

lining of the mouth is derived from..

A

ectoderm

339
Q

according to Mead, the spontaneous and autonomous part of our unified self is the..

A

I

Biology - MCAT (11 decks)

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