bioex3 Flashcards

1
Q

three classical experiments to show DNA is the genetic material

A

1928: Griffith
1944: Avery and McLeod (and McCarty)
1952: Hershey and Chase.

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2
Q

which is the smallest amino acid

describe r group

A

glycine

r group a simple hydrogen

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3
Q

osteogenesis imperfecta, what happens

A

a bigger AA is substituted for the glycine

alpha chains of collagen are braided (TRIPLE HELIX – 3 α chains) with glycine at the core sticking the molecules together more closely

collagen depends on tensile strength. not as tightly bound = not as strong

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4
Q

exact width of double-stranded DNA

A

2nm

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5
Q

two types of aromatic bases

A

purines and pyrimidines

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6
Q

pyrimidines are which bases

A

C, T, and U

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7
Q

what do pyrimidines look like

A

single hex ring (4 C 2 N)

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8
Q

what do purines look like

A

1 hex 1 pent – rings

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9
Q

which bases are purines

A

adenine and guanine

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10
Q

more info about purines?

A

common type of heterocyclic compound
heterocyclic – carbons and nitrogens at corners
one of the rings is a pyrimidine ring

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11
Q

U subs for

A

T

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12
Q

name the base pairs in DNA and RNA

A
adenine
thymine
cytosine
guanine
uracil 

A & T
C & G
A & U (RNA)

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13
Q

what happens in the thymus (2 things)

A

WBCs mature

immune factors learn to ignore self-antigens

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14
Q

which nucleotides bind to which, and is one stronger

A

A binds to T with 2 hydrogen bonds
C binds to G with 3 hydrogen bonds

C and G are bound a bit more tightly

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15
Q

MMP-3, aka:
matrix metalloproteinase-3
Stromelysin-1

A

enzyme which

breaks down ECM proteins
–>during tissue remodelling and pathological processes such as arthritis

degrades collagen types II, III, IV, IX, and X, proteoglycans, fibronectin, laminin, and elastin

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16
Q

ECM glycoprotein which binds to integrins

A

fibronectin

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17
Q

other functions of fibronectin

A

cell adhesion
growth
migration, and differentiation

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18
Q

altered fibronectin associated with pathologies such as

A

cancer, arthritis, fibrosis

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19
Q

laminins

A
proteins
part of basement lamina 
which is a layer of basement membrane
which is a part of the ECM
α β Υ chains
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20
Q

Tight junctions also block lateral movement of lipids and proteins in the plasma membrane

A

Movement of integral membrane proteins is completely blocked

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21
Q

Gap Junctions Allow

A

Direct Electrical and Chemical Communication Between Cells

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22
Q

three types of ECM

A

bone
cartilage
connective tissue

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23
Q

Three Classes of ECM Molecules

A
  1. Structural proteins such as collagens and elastins, which provide strength and flexibility
  2. Protein-polysaccharide complexes, proteoglycans, that provide the matrix
  3. Adhesive glycoproteins, fibronectins and lamins, that allow cells to attach to the matrix
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24
Q

connective tissue: Collagen and Elastin Fibers Are Embedded in a Matrix of Proteoglycans

PROTEOGLYCAN STRUCTURE

proteoglycans integrate into_____

A

gel-like network of proteoglycans, glycoproteins with a lot of glycosaminoglycans (GAGs)

GAGs bound to proteins
core protein, GAG chains

the plasma membrane

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25
Q

glycosaminoglycans (GAGs)

attach to core protein where?

A

large carbohydrates with repeating disaccharide units

serine residues

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26
Q

most common types of GAGs

A

chondroitin sulfate, keratan sulfate, and hyaluronate

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27
Q

Most GAGs in the ECM exist only as components of proteoglycans

_______ is an exception that occurs:

A

Hyaluronate is an exception that occurs both as a backbone of cartilage proteoglycans and as a free molecule

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28
Q

where is hyaluronate most important?

A

joints

It has lubricating properties and is most abundant where friction needs to be reduced, such as in joints

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29
Q

Direct links between the ECM and the plasma membrane are reinforced by a family of adhesive glycoproteins

which are the most common types

A

laminins and fibronectins

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30
Q

list four domains on fibronectin

these are which types of domains

A

BINDING DOMAINS

RGD (cell surface)

collagen

HEPARIN AND FIBRIN

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31
Q

what is interesting about fibronectin binding to both heparin and fibrin

A

heparin is an anticoagulant

fibrin is a key component of clots (insoluble protein – fibrous mesh that impedes blood flow)

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32
Q

clotting factor 1, ________, forms _______-

A

clotting factor I, fibrinogen, forms the fibrin clot

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33
Q

many cancer cells don’t produce fibronectin :(

A

:(

another random fact, fibronectin attaches platelets to fibrin

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34
Q

laminins do what

A

bind cells to basal lamina

distinctive anchor shape

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35
Q

give a quick sketch of what basement membrane comes between

A

EPITHELIUM (top let’s say)
BASEMENT MEMBRANE (of which basal lamina is a part)
underneath, CONNECTIVE TISSUE

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36
Q

basement membrane give basic structure

A

[[epithelium]]

[[basement membrane:

basal lamina
(lamina lucida, lamina densa)

reticular lamina]]

[[connective tissue]]

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37
Q

give 3 properties of basal lamina

A

structural support

permeability barrier

Cells can alter the properties of the basal lamina by secreting enzymes that catalyse changes in the lamina

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38
Q

give one important class of Enzymes That Alter the Basal Lamina

A

metalloproteinases (MMPs) that require metal ions as cofactors

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39
Q

what do MMPs do

A

They degrade the ECM locally, allowing cells to pass through

This is important for leukocytes to invade injured tissues and may be a factor in cancer cell invasiveness

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40
Q

describe integrins

A

transmembrane proteins –anchored in cytoskeleton

cell surface receptors

bind to laminins and fibronectins

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41
Q

1928: Griffith

A

Frederick Griffith, studying a pathogenic bacterial strain that caused pneumonia in animals, found two forms of the bacterium
S-strain caused a fatal infection when introduced into mice
R-strain was unable to do so

When dead S-strain and living R-strain were mixed and used to infect mice, the mice died
Griffith found many live S-strain bacteria in the dead mice

He concluded that the R-strain had been converted into S-strain, a process called genetic transformation

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42
Q

1944: Avery and McLeod (and McCarty)

A

fractionated extracts of the S-strain bacteria and found that only the nucleic acid fraction was able to transform the R-strain

Digesting the DNA from the extract prevented transformation

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43
Q

1952: Hershey and Chase.

A

Phage T2, T4, and T6 are the best studied

==>T2 Phage

to distinguish protein from DNA
They labelled proteins with radioactive sulphur, 35S, and the DNA with radioactive phosphorus, 32P

In two separate experiments, they allowed the labelled phages to infect bacteria

Once the genetic material is injected into the bacteria, the empty phage protein coats (“ghosts”) were removed by agitating cells in a blender

Cells were recovered by centrifugation

They then measured the radioactivity in the supernatant (phage coats) and the cells at the bottom of the tube

DNA and not protein had been injected into the bacterial cells
Therefore, DNA was the genetic material of the phage T2

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44
Q

temperate phages

A

incorporate their dna into bacterial dna

bacterium reproduces normally – both child cells have phage dna incorporated

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45
Q

Infection by T4 Phage

A

Phage DNA and capsid proteins self-assemble into hundreds of new phage particles

The infected cell breaks open and releases the new phage particles into the medium

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46
Q

Chargaff’s Rules Reveal

A

A = T and G = C

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47
Q

DNA basic structure

A

a sugar phosphate backbone with nitrogenous bases attached to each sugar

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48
Q

at physiological pH, the nucleobases would be able to form ______ bonds with each other

A

hydrogen

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49
Q

The Double Helix Model

The critical evidence came from :

A

X-ray diffraction data produced by Rosalind Franklin

It revealed that DNA was a long thin helical molecule

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50
Q

Based on Rosalind Franklin’s structural information, Chargaff’s rules, etc, Watson and Crick used wire modelling which

A

produced the double helix model

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51
Q

Watson-Crick Model

A

ten nucleotide pairs per complete turn, and 0.34 nm per nucleotide pair

The 2-nm diameter of the helix is too small for purines and too large for pyrimidines, but just right for one of each

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52
Q

The two strands of double helix are held together by

A

hydrogen bonding between bases on opposite strands

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53
Q

orientation of the two strands of double helix

A

antiparallel

5’ to 3’ but going opposite ways

5’ 3’
to to
3’ 5’^

(left of the above goes down)

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54
Q

two strands could separate so that each could act as a template to dictate

A

synthesis of a new complementary strand

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55
Q

The ______ bonds that join the 5′ carbon of one nucleotide to the 3′ carbon of the next are oriented _________ in the two DNA strands

A

phosphodiester

in opposite directions (antiparallel)

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56
Q

DNA length is measured in ____________

Larger stretches are measured in:

A

base pairs (bp)

multiples of a single base pair—for example, the kilobase (kb) is 1000 bp

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57
Q

The right-handed helix is called

left-handed helix?

A

B-DNA

Z-DNA

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58
Q

the main chirality of DNA is

A

right

B-DNA

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59
Q

A-DNA is

A

a right-handed helix, shorter and thicker than B-DNA

A-DNA is created artificially; there is very little naturally occurring A-DNA

However, most RNA double helices are of the
A type

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60
Q

Supercoiling occurs in both linear and circular DNA molecules but is more easily studied in circular DNA

A DNA molecule can go back and forth between the supercoiled state and the _________ state

Extensive supercoiling helps make chromosomal DNA _______

A

nonsupercoiled, or relaxed

more compact

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61
Q

___________ can both induce and relax supercoils

A

Topoisomerases

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62
Q

what do topoisomerases basically do

A

break DNA, thereby removing supercoils

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63
Q

Type I topoisomerases: introduce __________ _________ ____________

Type II topoisomerases: introduce __________; one example in bacteria is ________

A

Type I topoisomerases: introduce transient single-strand breaks in DNA

Type II topoisomerases: introduce double-strand breaks

one example in bacteria is DNA gyrase

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64
Q

base stacking (2 aspects)

A

1) stabilizes the double helix by:

2) interactions between adjacent aromatic rings — hydrophobic and van der Waals interactions

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65
Q

DNA renaturation aka**

A

reannealing

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66
Q

Reformation of the DNA double helix is called __________; it is accomplished by:

A

DNA renaturation (or reannealing)

lowering the temperature to permit hydrogen bonds to reform

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67
Q

denaturation of DNA, describe, include temp

A

native DNA breaks into two single strands

it’s ‘native DNA’ – not denatured – up to about 80C

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68
Q

renaturation, describe, include temp

A

nucleation event and ‘zipping up’

temp falls back down to 20C

69
Q

In eukaryotes, there is _____ DNA per cell, and it…

A

more

interacts with more proteins

70
Q

When bound to proteins, DNA is converted into

A

chromatin

71
Q

At the time of division, the ________ condense into a more compact structure:

A

chromatin fibres

the chromosome

72
Q

Lactose is a disaccharide composite of two simple sugars:

A

glucose and galactose.

73
Q

restriction enzyme —

hydrogen bonding —

A

restriction enzyme — cuts DNA

hydrogen bonding — pastes DNA

74
Q

bile does what

A

emulsifies lipids

to facilitate digestion

75
Q

albumin does what

A

pulls water into vessels

76
Q

where is fibronectin found and what type of molecule is it

what does it bind to

A

ECM glycoprotein which binds to integrins

(also binds to membrane-spanning receptor proteins called integrins.[6] Fibronectin also binds to other extracellular matrix proteins such as collagen, fibrin, and heparan sulfate proteoglycans (e.g. syndecans).

77
Q

When bound to proteins, DNA is converted into ________

At the time of division, the chromatin fibers condense into a more compact structure, the _________

A

chromatin

chromosome

78
Q

The mass of _______ in a chromosome is approximately equal to the mass of the DNA

A

histones

79
Q

Histones are a group of small basic ______ with high _______ content

A

proteins

lysine and arginine

80
Q

histones bind to ______. why?

A

dna

The negatively charged DNA binds stably to the positively charged proteins

81
Q

nucleosome shape? structure?

A

“bead”

8 histone
146 bp dna

82
Q

Nucleosomes Are Packed Together
to Form _____________

Nucleosome formation is the first step in ___________

A

Chromatin Fibers and Chromosomes

packaging of nuclear DNA

83
Q
Isolated chromatin (beads on a string) measures about \_\_\_\_\_ in diameter, but chromatin of intact cells measures about \_\_\_\_\_\_\_\_
Histone \_\_\_ facilitates formation of the \_\_\_\_ fibre
A

10 nm
30 nm

H1; 30-nm

84
Q

put DNA packaging structures in order.

A
double helix
nucleosome beads
30-nm chromatin fibre
loops
heterochromatin
chromosome
85
Q

put DNA packaging structures in order. give nm

A
double helix -- 2nm
nucleosome beads --10nm
30-nm chromatin fibre --30nm
loops --300nm
heterochromatin --700nm
chromosome --1400nm
86
Q

between nucleosome “beads” one finds

A

linker DNA

87
Q

DNA loops _______ bp in length, stabilized by _____ protein (in mammals)

A

50,000–100,000

cohesin

88
Q

DNA loops are spatially arranged through attachment to nonhistone proteins that form a ______

A

chromosomal scaffold

89
Q

The extent to which DNA has been folded can be quantified using the ________

A

DNA packing ratio

90
Q

Cells can tightly regulate the portions of chromatin that are active or inactive, through altering ______

A

histones

91
Q

Each histone has a _______ that can be tagged by the addition of methyl, acetyl, phosphate, or other groups

Various combinations of these tags create a _____

A

protruding tail

histone code

92
Q

One tagging reaction is the _______ via histone methyltransferase

A

methylation of lysine

93
Q

One tagging reaction is the methylation of lysine via

A

histone methyltransferase

94
Q

Methylation can serve as a signal for _____________________, depending on the lysine involved

A

activation or repression of transcription

95
Q

Acetylation of histone side chains is accomplished by __________________
The opposite function is catalyzed by ___________

A

histone acetyltransferases (HATs)

histone deacetylase (HDAC)

96
Q
Other proteins, chromatin remodeling proteins, alter the \_\_\_\_\_\_\_\_\_\_\_\_\_
One important class of remodelers is the \_\_\_\_\_\_\_\_\_ which:
A

position of nucleosomes along DNA

SWI/SNF family
These slide nucleosomes or remove them from a region of chromatin, making the DNA more accessible

97
Q

Sections of chromatin so highly compacted that they show up as dark spots in micrographs are called _________

A

heterochromatin

98
Q

More loosely packed, diffuse chromatin is called ________

A

euchromatin

99
Q

After replication, each chromosome is composed of two __________

A

identical chromatids

100
Q

Facultative heterochromatin

A

can be converted to euchromatin, and vice versa

101
Q

Some heterochromatin is permanently compacted; known as ________, it serves structural functions within chromosomes

A

constitutive heterochromatin

102
Q

Two important types of constitutive heterochromatin are

A

centromeres and telomeres

103
Q

Centromeres serve as sites of ______, crucial for attaching spindle microtubules to chromosomes during meiosis and mitosis

A

kinetochores

104
Q

Centromeres are characterized by highly repetitive DNA sequences (____ sequences)

A

CEN

105
Q

centromeres and telomeres both have

A

highly repetitive DNA sequences

106
Q

Telomeres do what

A

protect chromosome ends from degradation during each round of DNA replication

107
Q

There are two categories of repeated DNA:

A

tandemly repeated DNA

interspersed repeated DNA

108
Q

The tandem repeats that are less than 10 bases per repeat comprise a subcategory called :

AKA

A

simple-sequence repeated DNA

satellite DNA

109
Q

give % mammalian genome

tandemly repeated DNA incl satellite DNA
interspersed repeated DNA

A

tandemly repeated DNA incl satellite DNA – 10-15%

interspersed repeated DNA – 20-50%

110
Q

Variable number tandem repeats (VNTRs) refer to _________

give 2 types

A

short repeats

Minisatellites are short, 102 to 105 bp in length
Microsatellites (or short tandem repeats, STRs) are even shorter, 10–100 bp in length, but with numerous sites in the genome

111
Q

interspersed repeated DNA is mostly

A
transposable elements (transposons)
which can move around the genome and leave copies of themselves behind
112
Q

jumping genes

A

transposons

113
Q

% human genome

exons
introns
transposons
(within transposons) Alu
tandem repeated DNA
unique noncoding DNA
A
exons 1.5%
introns 24%
transposons = 50%
(within transposons) Alu - 10%
tandem repeated DNA - 15%
unique noncoding DNA -15%
114
Q

most abundant transposons

A

LINEs

115
Q

most common SINEs

A

Alu sequences

116
Q

Mitochondria and chloroplasts have their own chromosomes, which are devoid of ____ and are usually _____ in shape
Both organelles can encode ____ of their own polypeptides but depend on the nuclear genome to encode _______

A

histones
circular

some
the rest of them

117
Q

do mitochondrial genomes vary among organisms

A

yes

118
Q

oligomer (/əˈlɪɡəmər/ (audio speaker iconlisten)) is:

multimer (/ˈmʌltɪmər/) is used in biochemistry for:

A

a molecule that consists of a few similar or identical repeating units which could be derived, actually or conceptually, from copies of a smaller molecule, its monomer.

multimer: oligomers of proteins that are not covalently bound.

119
Q

Molecules Enter and Exit the Nucleus Through

A

Nuclear Pores

120
Q

Small particles, ______ in diameter, pass through pores at a rate proportional to the size of the particle
The NPC contains tiny ______ channels through which small particles freely move

A

less than 10 nm

aqueous diffusion

121
Q

NPC

transporting large proteins
_______ enable the protein to be recognized and transported by the nuclear pore complex

A

NPC = nuclear pore complex

Nuclear localization signals (NLS)

122
Q

how does NLS work

A

(1) binds to importin (receptor protein)
this complex is transported in by the transporter at the center of the
NPC (2)

123
Q

Inside the nucleus, the importin associates with a GTP-binding protein called ____, causing importin to release the NLS-containing protein (3)

The ___ complex is transported back to the cytoplasm through the NPC (4)

In the cytoplasm, the importin is released as GTP is hydrolyzed (5)

A

Ran

Ran-GTP importin

124
Q

Transport out of the nucleus is used mainly for ____

Some traffic out of the nucleus does not appear to require Ran, for instance ____

A

RNA

mRNAs

125
Q

RNA export is mediated by _____ that bind to the RNA

The adaptor proteins contain sequences called ______, which target the proteins—and the bound RNAs—for export

A

adaptor proteins

nuclear export signals (NES)

126
Q

NES sequences are recognized by _____, which mediate transport of the complexes out of the nucleus

A

exportins

127
Q

Ran-GTP is maintained across membrane, at high levels inside the nucleus by a ______ that promotes Ran to bind GTP

A

guanine-nucleotide exchange factor (GEF)

128
Q

The cytosol contains a _______ that promotes hydrolysis of GTP by Ran

A

GTPase activating protein (GAP)

129
Q

_____ shuttles Ran-GDP back into the nucleus

A

Nuclear transport factor 2 (NTF2)

130
Q

small molecule interactions control gene expression

A

riboswitches

131
Q

riboswitches bind to

and change

A

special sites in mRNA

mRNA’s shape

132
Q

Riboswitches are typically found in the

A

untranslated leader region of mRNAs of bacterial operons

133
Q

The CRISPR/Cas System does what for bacteria

A

Protects Bacteria Against Viral Infection

134
Q

CRISPRs, DNA from

about ____ bp long

A

bacteriophages

~30 bp long, alternating with highly variable spacer sequences, also about 30 bp

135
Q

Cas are

A

CRISPR-associated (Cas) proteins

136
Q

2 functions of cas proteins?

A

help incorporate viral sequences into the CRISPR spacers

help process and target RNAs made from the CRISPR locus

137
Q

Eukaryotic Gene Expression Is Regulated at Five Main Levels

A
GENOME
TRANSCRIPTION
RNA processing and export
TRANSLATION
posttranslational events

The last three categories represent levels of posttranscriptional control

138
Q

give examples of some types of gene regulation

GENOME
TRANSCRIPTION
RNA processing and export
TRANSLATION
posttranslational events
A

GENOME
DNA methylation
chromatin condensation and decondensation
histone modifications (methylation acetylation)

RNA processing and export
RNA splicing
transport of mRNA to cytoplasm

TRANSLATION
(polypeptide synthesis)
initiation factors and translational repressors (microRNA)

posttranslational events
protein folding
polypeptide cleavage
protein degradation

139
Q

Epigenetic Inheritance

A

Epigenetic changes are stable alterations in gene expression transmitted from one generation to the next without any change in DNA sequence

The enzyme for DNA methylation acts preferentially on cytosines in 5′−CG−3′ sequences, paired to complementary 3′−zC−5′ sequences (that are already methylated)
These sequences are said to be hemimethylated

140
Q

Methylation of the complementary sequence allows

A

the methylated pattern of the DNA to be inherited

141
Q

Epigenetic changes also underlie ______ which allows certain genes to differently expressed, depending on the parent from which they are inherited

A

genomic imprinting,

142
Q

small RNA molecules can trigger _______ and _____

this is known as

A

mRNA degradation ; inhibit expressoin

RNAi (RNA interference)

143
Q

_______knocks down the expression of specific genes

First, a cytoplasmic ribonuclease called ____ cleaves the double-stranded RNA into short fragments about 21–22 bp long

The resulting fragments are called

A

Double-stranded RNA (from certain types of viruses or introduced artificially)

Dicer

siRNAs (small interfering or silencing RNAs)

144
Q

in eukaryotes mRNA (genetic) silencing is enacted by

A

miRNA

microRNA

145
Q

Ubiquitin

A

Targets Proteins for Degradation by Proteasomes

146
Q

Internal amino acid sequences called _____ target particular proteins for degradation

A

degrons

147
Q

Protein folding is usually facilitated by proteins called ______; often several are required, acting in sequence

these also bind polypeptide chains during the early stages of folding

A

molecular chaperones

148
Q

Two of the most widely occurring chaperone families are

A

Hsp70 and Hsp60

149
Q

The ribosome reads the mRNA codon by codon in the _____ direction

A

5′ to 3′

150
Q

Missense Mutations, which type

eg (1)

A

A base-pair substitution

eg sickle cell

151
Q

types of dna mutations

A
base pair substitutions
-missense
diff AA
-nonsense
AA becomes stop codon
nonstop (stop codon becomes AA)
-silent
DNA diff but same AA
base pair insertions and deletions
-frameshift mutation
(a) one bp, eg INDELS*
insertion*
deletion*
duplication
inversion
(translocation -- DNA of nonhomologous chromosoems) 
(b) longer DNA segment
152
Q

indel long scale mutations

In an inversion:

A translocation involves

A

, a chromosome section is cut out and reinserted in its original position but in reverse orientation

movement of a segment from one position in the genome to another location

153
Q

nonsense mutations, typically lead to incomplete, nonfunctional polypeptides

These mutations are often lethal but can sometimes be overcome by an independent mutation affecting a tRNA gene
This is called a

A

suppressor tRNA

154
Q

The compartments of eukaryotic cells can be divided into three categories:

A

the endomembrane system; the cytosol; and the mitochondria, chloroplasts, peroxisomes, and interior of the nucleus

155
Q

preproteins destined for

A

ER

156
Q

Protein Folding and Quality Control Take Place

A

Within the ER

An abundant chaperone in the ER lumen is a member of the Hsp70 chaperones called BiP (binding protein)

157
Q

misfolded proteins

A

exported from ER to cytosol

degraded by proteosomes

158
Q

Most proteins synthesized on rough ER are

A

glycoproteins

159
Q

Many important receptor proteins have ____ membrane-spanning domains

A

7

160
Q

Proteins destined for the nuclear interior, mitochondrion, chloroplast, or peroxisome are imported into these organelles after completion of translation

These are synthesized on free ribosomes and released into the cytosol

A

Most mitochondrial and chloroplast polypeptides are synthesized on cytoplasmic ribosome, released into the cytosol, and taken up by the organelle within a few minutes

161
Q

The targeting signal for mitochondrial and chloroplast polypeptides is a :

It is located at the :

A

transit sequence

N-terminus of the polypeptide

162
Q

Mitochondrial transport complexes are called

A

TOM (translocase of the outer mitochondrial membrane) and TIM (translocase of the inner mitochondrial membrane)

In chloroplasts, they are called TOC and TIC

163
Q

Polypeptides Are Transported in:

A

an Unfolded State

164
Q

To maintain an unfolded state, the polypeptides are bound to

A

chaperone proteins

165
Q

DNA helix opens at

pried apart by

which bonds break

A

origin of replication

replication initiator proteins

H bonds between A & T C & G

166
Q

deamination

depurination

A

C becomes U

purine removed (e.g. G). phosphate backbone alone

167
Q

(marked incorr 1-3)

gene expression entails:

A

synthesis of a functional polypeptide

168
Q

post-translational gene editing

A

miRNA

seems he might be wrong about this

169
Q

3 something about RISC (RNA induced silencing complex) ?

A

ask tues