bioex3 Flashcards
(169 cards)
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.
2
Q
which is the smallest amino acid
describe r group
A
glycine
r group a simple hydrogen
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
4
Q
exact width of double-stranded DNA
A
2nm
5
Q
two types of aromatic bases
A
purines and pyrimidines
6
Q
pyrimidines are which bases
A
C, T, and U
7
Q
what do pyrimidines look like
A
single hex ring (4 C 2 N)
8
Q
what do purines look like
A
1 hex 1 pent – rings
9
Q
which bases are purines
A
adenine and guanine
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
11
Q
U subs for
A
T
12
Q
name the base pairs in DNA and RNA
A
adenine thymine cytosine guanine uracil
A & T
C & G
A & U (RNA)
13
Q
what happens in the thymus (2 things)
A
WBCs mature
immune factors learn to ignore self-antigens
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
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
16
Q
ECM glycoprotein which binds to integrins
A
fibronectin
17
Q
other functions of fibronectin
A
cell adhesion
growth
migration, and differentiation
18
Q
altered fibronectin associated with pathologies such as
A
cancer, arthritis, fibrosis
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
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
21
Q
Gap Junctions Allow
A
Direct Electrical and Chemical Communication Between Cells
22
Q
three types of ECM
A
bone
cartilage
connective tissue
23
Q
Three Classes of ECM Molecules
A
- Structural proteins such as collagens and elastins, which provide strength and flexibility
- Protein-polysaccharide complexes, proteoglycans, that provide the matrix
- Adhesive glycoproteins, fibronectins and lamins, that allow cells to attach to the matrix
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
25
glycosaminoglycans (GAGs)
attach to core protein where?
large carbohydrates with repeating disaccharide units
serine residues
26
most common types of GAGs
chondroitin sulfate, keratan sulfate, and hyaluronate
27
Most GAGs in the ECM exist only as components of proteoglycans
_______ is an exception that occurs:
Hyaluronate is an exception that occurs both as a backbone of cartilage proteoglycans and as a free molecule
28
where is hyaluronate most important?
joints
It has lubricating properties and is most abundant where friction needs to be reduced, such as in joints
29
Direct links between the ECM and the plasma membrane are reinforced by a family of adhesive glycoproteins
which are the most common types
laminins and fibronectins
30
list four domains on fibronectin
these are which types of domains
BINDING DOMAINS
RGD (cell surface)
collagen
HEPARIN AND FIBRIN
31
what is interesting about fibronectin binding to both heparin and fibrin
heparin is an anticoagulant
| fibrin is a key component of clots (insoluble protein -- fibrous mesh that impedes blood flow)
32
clotting factor 1, ________, forms _______-
clotting factor I, fibrinogen, forms the fibrin clot
33
many cancer cells don't produce fibronectin :(
:(
another random fact, fibronectin attaches platelets to fibrin
34
laminins do what
bind cells to basal lamina
distinctive anchor shape
35
give a quick sketch of what basement membrane comes between
EPITHELIUM (top let's say)
BASEMENT MEMBRANE (of which basal lamina is a part)
underneath, CONNECTIVE TISSUE
36
basement membrane give basic structure
[[epithelium]]
[[basement membrane:
basal lamina
(lamina lucida, lamina densa)
reticular lamina]]
[[connective tissue]]
37
give 3 properties of basal lamina
structural support
permeability barrier
Cells can alter the properties of the basal lamina by secreting enzymes that catalyse changes in the lamina
38
give one important class of Enzymes That Alter the Basal Lamina
metalloproteinases (MMPs) that require metal ions as cofactors
39
what do MMPs do
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
40
describe integrins
transmembrane proteins --anchored in cytoskeleton
cell surface receptors
bind to laminins and fibronectins
41
1928: Griffith
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
42
1944: Avery and McLeod (and McCarty)
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
43
1952: Hershey and Chase.
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
44
temperate phages
incorporate their dna into bacterial dna
bacterium reproduces normally -- both child cells have phage dna incorporated
45
Infection by T4 Phage
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
46
Chargaff’s Rules Reveal
A = T and G = C
47
DNA basic structure
a sugar phosphate backbone with nitrogenous bases attached to each sugar
48
at physiological pH, the nucleobases would be able to form ______ bonds with each other
hydrogen
49
The Double Helix Model
| The critical evidence came from :
X-ray diffraction data produced by Rosalind Franklin
It revealed that DNA was a long thin helical molecule
50
Based on Rosalind Franklin's structural information, Chargaff's rules, etc, Watson and Crick used wire modelling which
produced the double helix model
51
Watson-Crick Model
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
52
The two strands of double helix are held together by
hydrogen bonding between bases on opposite strands
53
orientation of the two strands of double helix
antiparallel
5' to 3' but going opposite ways
5' 3'
to to
3' 5'^
(left of the above goes down)
54
two strands could separate so that each could act as a template to dictate
synthesis of a new complementary strand
55
The ______ bonds that join the 5′ carbon of one nucleotide to the 3′ carbon of the next are oriented _________ in the two DNA strands
phosphodiester
in opposite directions (antiparallel)
56
DNA length is measured in ____________
Larger stretches are measured in:
base pairs (bp)
multiples of a single base pair—for example, the kilobase (kb) is 1000 bp
57
The right-handed helix is called
| left-handed helix?
B-DNA
Z-DNA
58
the main chirality of DNA is
right
| B-DNA
59
A-DNA is
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
60
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 _______
nonsupercoiled, or relaxed
more compact
61
___________ can both induce and relax supercoils
Topoisomerases
62
what do topoisomerases basically do
break DNA, thereby removing supercoils
63
Type I topoisomerases: introduce __________ _________ ____________
Type II topoisomerases: introduce __________; one example in bacteria is ________
Type I topoisomerases: introduce transient single-strand breaks in DNA
Type II topoisomerases: introduce double-strand breaks
one example in bacteria is DNA gyrase
64
base stacking (2 aspects)
1) stabilizes the double helix by:
| 2) interactions between adjacent aromatic rings --- hydrophobic and van der Waals interactions
65
DNA renaturation aka**
reannealing
66
Reformation of the DNA double helix is called __________; it is accomplished by:
DNA renaturation (or reannealing)
lowering the temperature to permit hydrogen bonds to reform
67
denaturation of DNA, describe, include temp
native DNA breaks into two single strands
| it's 'native DNA' -- not denatured -- up to about 80C
68
renaturation, describe, include temp
nucleation event and 'zipping up'
| temp falls back down to 20C
69
In eukaryotes, there is _____ DNA per cell, and it...
more
| interacts with more proteins
70
When bound to proteins, DNA is converted into
chromatin
71
At the time of division, the ________ condense into a more compact structure:
chromatin fibres
| the chromosome
72
Lactose is a disaccharide composite of two simple sugars:
glucose and galactose.
73
restriction enzyme —
hydrogen bonding —
restriction enzyme — cuts DNA
hydrogen bonding — pastes DNA
74
bile does what
emulsifies lipids
| to facilitate digestion
75
albumin does what
pulls water into vessels
76
where is fibronectin found and what type of molecule is it
what does it bind to
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
When bound to proteins, DNA is converted into ________
| At the time of division, the chromatin fibers condense into a more compact structure, the _________
chromatin
chromosome
78
The mass of _______ in a chromosome is approximately equal to the mass of the DNA
histones
79
Histones are a group of small basic ______ with high _______ content
proteins
lysine and arginine
80
histones bind to ______. why?
dna
The negatively charged DNA binds stably to the positively charged proteins
81
nucleosome shape? structure?
"bead"
8 histone
146 bp dna
82
Nucleosomes Are Packed Together
to Form _____________
Nucleosome formation is the first step in ___________
Chromatin Fibers and Chromosomes
packaging of nuclear DNA
83
```
Isolated chromatin (beads on a string) measures about _____ in diameter, but chromatin of intact cells measures about ________
Histone ___ facilitates formation of the ____ fibre
```
10 nm
30 nm
H1; 30-nm
84
put DNA packaging structures in order.
```
double helix
nucleosome beads
30-nm chromatin fibre
loops
heterochromatin
chromosome
```
85
put DNA packaging structures in order. give nm
```
double helix -- 2nm
nucleosome beads --10nm
30-nm chromatin fibre --30nm
loops --300nm
heterochromatin --700nm
chromosome --1400nm
```
86
between nucleosome "beads" one finds
linker DNA
87
DNA loops _______ bp in length, stabilized by _____ protein (in mammals)
50,000–100,000
cohesin
88
DNA loops are spatially arranged through attachment to nonhistone proteins that form a ______
chromosomal scaffold
89
The extent to which DNA has been folded can be quantified using the ________
DNA packing ratio
90
Cells can tightly regulate the portions of chromatin that are active or inactive, through altering ______
histones
91
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 _____
protruding tail
histone code
92
One tagging reaction is the _______ via histone methyltransferase
methylation of lysine
93
One tagging reaction is the methylation of lysine via
histone methyltransferase
94
Methylation can serve as a signal for _____________________, depending on the lysine involved
activation or repression of transcription
95
Acetylation of histone side chains is accomplished by __________________
The opposite function is catalyzed by ___________
histone acetyltransferases (HATs)
histone deacetylase (HDAC)
96
```
Other proteins, chromatin remodeling proteins, alter the _____________
One important class of remodelers is the _________ which:
```
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
Sections of chromatin so highly compacted that they show up as dark spots in micrographs are called _________
heterochromatin
98
More loosely packed, diffuse chromatin is called ________
euchromatin
99
After replication, each chromosome is composed of two __________
identical chromatids
100
Facultative heterochromatin
can be converted to euchromatin, and vice versa
101
Some heterochromatin is permanently compacted; known as ________, it serves structural functions within chromosomes
constitutive heterochromatin
102
Two important types of constitutive heterochromatin are
centromeres and telomeres
103
Centromeres serve as sites of ______, crucial for attaching spindle microtubules to chromosomes during meiosis and mitosis
kinetochores
104
Centromeres are characterized by highly repetitive DNA sequences (____ sequences)
CEN
105
centromeres and telomeres both have
highly repetitive DNA sequences
106
Telomeres do what
protect chromosome ends from degradation during each round of DNA replication
107
There are two categories of repeated DNA:
tandemly repeated DNA
interspersed repeated DNA
108
The tandem repeats that are less than 10 bases per repeat comprise a subcategory called :
AKA
simple-sequence repeated DNA
satellite DNA
109
give % mammalian genome
tandemly repeated DNA incl satellite DNA
interspersed repeated DNA
tandemly repeated DNA incl satellite DNA -- 10-15%
| interspersed repeated DNA -- 20-50%
110
Variable number tandem repeats (VNTRs) refer to _________
give 2 types
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
interspersed repeated DNA is mostly
```
transposable elements (transposons)
which can move around the genome and leave copies of themselves behind
```
112
jumping genes
transposons
113
% human genome
```
exons
introns
transposons
(within transposons) Alu
tandem repeated DNA
unique noncoding DNA
```
```
exons 1.5%
introns 24%
transposons = 50%
(within transposons) Alu - 10%
tandem repeated DNA - 15%
unique noncoding DNA -15%
```
114
most abundant transposons
LINEs
115
most common SINEs
Alu sequences
116
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 _______
histones
circular
some
the rest of them
117
do mitochondrial genomes vary among organisms
yes
118
oligomer (/əˈlɪɡəmər/ (audio speaker iconlisten)) is:
multimer (/ˈmʌltɪmər/) is used in biochemistry for:
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
Molecules Enter and Exit the Nucleus Through
Nuclear Pores
120
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
less than 10 nm
aqueous diffusion
121
NPC
transporting large proteins
_______ enable the protein to be recognized and transported by the nuclear pore complex
NPC = nuclear pore complex
Nuclear localization signals (NLS)
122
how does NLS work
(1) binds to importin (receptor protein)
this complex is transported in by the transporter at the center of the
NPC (2)
123
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)
Ran
Ran-GTP importin
124
Transport out of the nucleus is used mainly for ____
| Some traffic out of the nucleus does not appear to require Ran, for instance ____
RNA
mRNAs
125
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
adaptor proteins
nuclear export signals (NES)
126
NES sequences are recognized by _____, which mediate transport of the complexes out of the nucleus
exportins
127
Ran-GTP is maintained across membrane, at high levels inside the nucleus by a ______ that promotes Ran to bind GTP
guanine-nucleotide exchange factor (GEF)
128
The cytosol contains a _______ that promotes hydrolysis of GTP by Ran
GTPase activating protein (GAP)
129
_____ shuttles Ran-GDP back into the nucleus
Nuclear transport factor 2 (NTF2)
130
small molecule interactions control gene expression
riboswitches
131
riboswitches bind to
and change
special sites in mRNA
mRNA's shape
132
Riboswitches are typically found in the
untranslated leader region of mRNAs of bacterial operons
133
The CRISPR/Cas System does what for bacteria
Protects Bacteria Against Viral Infection
134
CRISPRs, DNA from
| about ____ bp long
bacteriophages
~30 bp long, alternating with highly variable spacer sequences, also about 30 bp
135
Cas are
CRISPR-associated (Cas) proteins
136
2 functions of cas proteins?
help incorporate viral sequences into the CRISPR spacers
help process and target RNAs made from the CRISPR locus
137
Eukaryotic Gene Expression Is Regulated at Five Main Levels
```
GENOME
TRANSCRIPTION
RNA processing and export
TRANSLATION
posttranslational events
```
The last three categories represent levels of posttranscriptional control
138
give examples of some types of gene regulation
```
GENOME
TRANSCRIPTION
RNA processing and export
TRANSLATION
posttranslational events
```
GENOME
DNA methylation
chromatin condensation and decondensation
histone modifications (methylation acetylation)
TRANSCRIPTION
--
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
Epigenetic Inheritance
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
Methylation of the complementary sequence allows
the methylated pattern of the DNA to be inherited
141
Epigenetic changes also underlie ______ which allows certain genes to differently expressed, depending on the parent from which they are inherited
genomic imprinting,
142
small RNA molecules can trigger _______ and _____
this is known as
mRNA degradation ; inhibit expressoin
RNAi (RNA interference)
143
_______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
Double-stranded RNA (from certain types of viruses or introduced artificially)
Dicer
siRNAs (small interfering or silencing RNAs)
144
in eukaryotes mRNA (genetic) silencing is enacted by
miRNA
| microRNA
145
Ubiquitin
Targets Proteins for Degradation by Proteasomes
146
Internal amino acid sequences called _____ target particular proteins for degradation
degrons
147
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
molecular chaperones
148
Two of the most widely occurring chaperone families are
Hsp70 and Hsp60
149
The ribosome reads the mRNA codon by codon in the _____ direction
5′ to 3′
150
Missense Mutations, which type
eg (1)
A base-pair substitution
eg sickle cell
151
types of dna mutations
```
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
indel long scale mutations
In an inversion:
A translocation involves
, 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
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
suppressor tRNA
154
The compartments of eukaryotic cells can be divided into three categories:
the endomembrane system; the cytosol; and the mitochondria, chloroplasts, peroxisomes, and interior of the nucleus
155
preproteins destined for
ER
156
Protein Folding and Quality Control Take Place
Within the ER
An abundant chaperone in the ER lumen is a member of the Hsp70 chaperones called BiP (binding protein)
157
misfolded proteins
exported from ER to cytosol
| degraded by proteosomes
158
Most proteins synthesized on rough ER are
glycoproteins
159
Many important receptor proteins have ____ membrane-spanning domains
7
160
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
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
The targeting signal for mitochondrial and chloroplast polypeptides is a :
It is located at the :
transit sequence
N-terminus of the polypeptide
162
Mitochondrial transport complexes are called
TOM (translocase of the outer mitochondrial membrane) and TIM (translocase of the inner mitochondrial membrane)
In chloroplasts, they are called TOC and TIC
163
Polypeptides Are Transported in:
an Unfolded State
164
To maintain an unfolded state, the polypeptides are bound to
chaperone proteins
165
DNA helix opens at
pried apart by
which bonds break
origin of replication
replication initiator proteins
H bonds between A & T C & G
166
deamination
depurination
C becomes U
purine removed (e.g. G). phosphate backbone alone
167
(marked incorr 1-3)
| gene expression entails:
synthesis of a functional polypeptide
168
post-translational gene editing
miRNA
| seems he might be wrong about this
169
#3 something about RISC (RNA induced silencing complex) ?
ask tues
