exam 2 Flashcards
(173 cards)
1
Q
What are the most diverse macromolecules
A
proteins
2
Q
what does an enzyme do and what are some examples
A
catalyzes covalent bond breakage or formation
anything that ends with -ase like polymerase or protein kinase
3
Q
what does a structural protein do and what are some examples
A
provides mechanical support to cells and tissues
collagen elastin actin tubulin keratin
4
Q
what does a transport protein do and what are some examples
A
carry small molecules or ions
hemoglobin, glucose transporters
5
Q
what does a motor protein do and what are some examples
A
generate movement in cells and tissues
myosin kinesin
6
Q
what does a signal protein do and what are some examples
A
carry extracellular signals from cell to cell
insulin, nerve growth factor, epidermal growth factor
7
Q
what does a storage protein do and what are some examples
A
store amino acids or ions
ferritin, ovalbumin, casein
8
Q
what does a receptor protein do and what are some examples
A
detects signals and transmits them to the cell’s response machinery
rhodopsin, acetylcholine receptor, insulin receptor,
9
Q
what is a transcription regulator and what are some examples
A
binds to DNA to switch genes on or off
lac repressor, DNA-binding proteins
10
Q
what are some special purpose proteins
A
antifreeze proteins, green fluorescent proteins, glue proteins
11
Q
what is the general protein structure
A
a polymer of amino acids in a polypeptide sequence
12
Q
what determines a protein’s structure
A
the sequence of amino acids
13
Q
what are the parts of protein
A
central carbon with one hydrogen, amino group, R-group, carboxyl group
14
Q
how many polar/nonpolar amino acids are there
A
10 polar, 10 nonpolar
15
Q
how many amino acids are there
A
20
16
Q
what types of noncovalent bonds help proteins fold
A
electrostatic attractions, hydrogen bonds, van der Waals attractions
17
Q
T/F denatured proteins cannot return to their natural shape
A
false, they often can :)
18
Q
what happens to proteins when there is a high concentration of them, and they’re all being denatured
A
they start to clump together
19
Q
how many levels of protein structures are there, and what are they called
A
4;
primary; secondary; tertiary; quaternary
20
Q
what is the primary structure of protein
A
the sequence of amino acids
21
Q
what are common secondary structures
A
alpha helix and beta sheet
22
Q
what shape would a protein take if it needed to cross the lipid bilayer (like a cell membrane or nuclear membrane) and why
A
alpha helix because this usually keeps the hydrophobic amino acids on the inside and hydrophilic amino acids surrounding on the outside of the helices
23
Q
what is a coiled coil
A
a protein structure where the amino acids stay in the center line between the two wrapped alpha helices and it becomes very strong
24
Q
what does it mean to be a parallel beta sheet
A
secondary structure where each row of amino acids go from left to right, and then loops back over without anything important
25
what does it mean to be an antiparallel beta sheet
secondary structure where each row goes from left to right then right to left in a snake pattern
26
what is a tertiary structure
a long strand of amino acids with multiple secondary structures connecting
27
what is a quaternary structure
multiple polypeptide chains of amino acids coming together
28
what other forces help proteins fold
hydrophobic forces
29
what helps guide the folding of a newly synthesized polypeptide chain
chaperone proteins
30
T/F many proteins are composed of separate functional domains (secondary structures)
True :)
31
what connects multiple secondary structures (domains)
unstructured areas are between these domains
32
T/F many proteins contain multiple copies of the same protein subunit
True, this means that many of the exact same tertiary structures come together to form the quaternary structure
33
T/F proteins cannot be two different protein subunits
false, they can and sometimes are two subunits symmetrically assembled into 4 (2 of one tertiary structure, 2 of the other tertiary structure)
34
what is a dimer
two identical protein molecules linked together
35
what other shapes can be formed with identical protein subunits
dimer (2 proteins connected)
helix (fit like a puzzle piece bc two binding sites)
ring (also like puzzle piece bc two binding sites)
36
what is an actin filament made of
identical protein subunits that form 2 strands that wrap around each other
37
what are some common subunit shapes
filaments, spherical, hollowed tubes
38
what shape is collagen
triple helix
39
what shape is elastin
when not stretched, it looks like curled worms connected, but when it is stretched, it forms rows of fibers connected like ladders
40
what bonds help stabilize the protein shape
disulfide bonds
41
T/F all proteins bind to other molecules
TRUE
42
what can proteins bind to
little proteins (ligands)
43
T/F binding sites can interact with all ligands
False they are designed for specific ligands
44
what are antibodies
proteins produced by immune system in response to foreign molecules
45
what is an antibody's target ligand
antigen
46
T/F antibody binding sites have extreme specificity
true
47
what are the common uses of antibodies in the lab
purify smthg to get a single protein by binding to their protein while everything else falls out, then changing pH with another liquid to remove those bindings to get that ligand
48
how does the immune system make anitbodies
the immune system makes B cells, which then each make their own antibody
49
what is a monoclonal antibody
specific B cell is immortalized with a tumor cell so that antibody can be made infinitely
50
what is a polyclonal antibody
make antibodies through the B cells in mice, goats, and other mammals
51
what are the three ways that an enzyme could make a reaction happen
1. bind 2 molecules together to make them interact
2. rearrange electrons
3. bend/force molecules to favor reaction
52
what is lysozyme
an enzyme that cleaves (breaks apart) a polysaccharide chain
53
what is kinase
an enzyme that does phosphorylation
54
what is phosphorylation
adding a phosphate
55
what is phosphotase
an enzyme that dephosphorylates (removes phosphate)
56
what is competitive inhibition
a drug blocks substrate binding by binding to an active site itself
57
what is noncompetitive inhibition
drug bind to side site which changes shape so nothing else can bind
binds to one active site but changes the shape of another binding site so the normal substrates can't bind there
58
what happens when a regulatory ligand binds
the equilibrium between 2 protein conformations can be altered
59
what is feedback inhibition
this is the drug/molecule that does the competitive/noncompetitive inhibition
60
why is feedback inhibition needed
to regulate the flow through biosynthetic pathways and regulate metabolic pathways
61
T/F phosphorylation can control protein activity by causing a conformational change
True, the adding/subtracting of the phosphate molecules can change the protein shape while decides if the function will work or not
62
how can a protein walk, and what would it walk across
conformation changes would let it walk (changing shape) across the cytoskeleton filament
63
what makes the protein walking irreversible
they are coupled to the hydrolysis of ATP so the energy was used to get to the next shape and can't go back
64
what is an example of conformation changing
GTP to GDP changes the shape of the protein which turns it on or off (turning it on happens really fast bc favorable)
65
T/F small protein complexes function as machines
false, LARGE protein complexes function as machines
66
what is a proteosome
a large protein complex that breaks down old or misfolded proteins
67
what is a ribosome
a multi RNA and large protein complex that synthesizes proteins
68
what is a condensate and what produces them
large biochemical sub-compartments created by macromolecular interactions --- they are not membrane bound but just groupings of macromolecules
69
what is the nucleolus
biomolecular condensate that brings RNA and proteins together that will assemble ribosomes
70
what is homogenization
the outer membrane of cells are ruptured so that the organelles can be released in a resulting thick soup (homogenate)
71
what are the four homogenization techniques
ultrasound, detergent, pressure, plunger
72
what is column chromatography
a technique used to separate proteins by putting sample in gel tube and each protein size/shape travels down at a different rate so you can collect the specific one you want
73
what are the three type of chromatography
ion exchange
gel filtration
affinity
74
what is ion exchange chromatography
small beads with pos or neg charge will hold onto specific proteins
75
what is gel filtration chromatography
beads with small holes catch smaller proteins so bigger ones go out
76
what is affinity chromatography
antibodies bind to some proteins to separate them and others go out
77
what is used to separate proteins by size
SDS polyacrylamide gel electrophoresis
78
what is the benefit of 2D gel electrophoresis
this provides greater protein separation bc it separates by charge first then isoelectric point
79
what is the isoelectric point
a pH in 2D gel electrophoresis where the molecules have no net charge
80
what are three ways of determining a protein's structure
1. x-ray crystallography
2. NMR
3. cryo electron microscopy
81
was is xray crystallography
certain conditions can make proteins into crystals that can reveal things about structures
82
what is NMR
nuclear magnetic resonance spectroscopy used to determine structure in smaller proteins
83
what is cryo electron microscopy
freezes proteins to see with electron microscopy the structure
84
what is DNA made of
sugar phosphate backbone, and four nucleotide building blocks (bases A G C T)
85
what shape is DNA
double stranded helix
86
what bonds are used in the DNA backbone
phosphodiester
87
what bonds are formed between DNA bases
hydrogen bonds
88
what direction do the strands of DNA run
antiparallel
89
what atom in DNA have a negative charge
one of the oxygens on the phosphate group on the backbone has a neg charge
90
How many hydrogen bonds does CG have
3
91
how many hydrogen bonds does AT have
2
92
which two bases are purines and what does this mean
this is double ring structure and is ga
93
what bases are pyrimidines and what does this look like
single ring structure and is CUT
94
T/F base pairs are perpendicular rungs of the ladder that lay flat
true, they stack on top of one another
95
why are the bases stacked horizontally flat
so that only specific flat molecules can get in to affect replication and transcription
96
T/F all grooves of DNA are the same size
False, there are major grooves and minor grooves
97
what does the sequence of bases in DNA determine
this is the genetic information to making RNA and proteins
98
what is the sequence called that makes RNA or protein
gene
99
what is a chromosome
a double stranded DNA molecule with thousands of genes
100
T/F all genes code for proteins
false, sometimes, the gene will only produce RNA and not get translated into protein
101
what is central dogma
DNA - RNA - protein
replication - transcription - translation
102
do yeast or human chromosomes have genes closer together?
yeast genes are closely packed together along chromosomes
human genes are much farther apart
103
when can chromosomes be seen under a microscope
during cell division when they group and condense
104
draw the process of condensing chromosomes in the cell (uncondensed to condensed)
DNA wraps around histone making nucleosome, which bundles up to make chromatin and forms chromosome
105
how many chromosomes does a human have
23 pairs so 46
106
what is reciprocal chromosomal translocation
a top of one chromosome has been switched with the top of another
107
what are the noncoding base pair sequences called
introns
108
when are introns removed from the DNA
after inscription, the RNA removes the introns and turns into mRNA
109
what is mitosis
cell duplication where the cell copies all of its chromosomes to two daughter cells
110
what are the three elements on the DNA strand that are needed for mitosis to happen
telomere, replication origin, centromere
111
when do chromosomes have their own distinct area within the nucleus
during interphase, there are specific territories for the interphase chromosomes to live
112
what is the nucleolus
in the nucleus and is the site for ribosome assembly
113
are interphase or mitotic chromosomes more compact
chromosomes are most compact during mitosis, so during the inter phases the chromatins relax and spread out
114
how long is the DNA strand that is wrapped around a histone
147 base pairs long by wrapping around twice
115
how does the chromatin stay on the helix
the histones are positively charged which binds with the negatively charged backbone
116
how are the chromatin loops formed (before reaching shape of chromosome)
the SMC Ring Complex using ATP to form loops by connecting to two sides and walking to make loop bigger
117
what do clamp proteins do (draw this with cohesin)
these tell the cohesin (SMC complex) when to stop making the loop bigger
118
what is the difference between cohesion and condensin (draw both in one picture)
cohesion is used to make individual loops and condensin is used to make big loops with little loops in them
119
what shape does condensin make the chromatin loop into
this makes the many smaller loops turn into one big loop that spirals up
120
what holds together the two fully condensed chromatins
centromere
121
how are the genes on the DNA wrapped around histones accessed
there are chromatin remodeling complexes that locally reposition the wrapped DNA to allow access to any part of DNA
122
what is heterochromatin
chromatin that is tightly packaged and make it hard to read the gene expression
123
what is euchromatin
chromatin that is loosely packaged which makes it easy to read the gene expressions
124
what helps determine if a stretch of chromatin should be hetero or euchromatin
the histone tails that come off of the histones help determine how the cell should handle the chromatin
125
T/F there are various stretches of euchromatin and heterochromatin along a single chromosome
true, there can be lots of switching between the types on the chromosome
126
what is the difference between constitutive and facultative heterochromatin
constitutive means that the chromatin is permanently condensed and doesn't need to have gene expression (like in telomere and centromere)
facultative means that the chromatin has been condensed temporarily
127
what is the difference between quiescent and active euchromatin
quiescent means that the euchromatin is inactive and doesn't have any genes to be read
active means that the euchromatin has gene expression and are stretched out even further to be read
128
what happens if heterochromatin spreads too far when chromatin is being condensed
this would make certain genes unreadable and possible cause disease
129
what cell is inactivated in female mammals
one of the two X chromosomes
the active one stays uncondensed and the inactive one curls up and condenses so as not to be read
130
how does a parent cell pass down which chromatins should be hetero or euchromatin
the heterochromatins are marked and then spread until hit barrier DNA sequence to switch to euchromatin
131
what did scientists use to find genetic material
they used the Strep pneumonia bacteria (living and dead) to see when a mouse died by it, and worked with different macromolecules to see when the killed living strand made the mouse sick. they found only DNA could transform the R bacteria into the S bacteria
other scientists used protein and DNA attached to e coli and colored, and saw which color would the e coli turn out to be with the genetic material going to it. DNA won obviously
132
why cant other base pairs work like CA AG CT TG
CA would not be able to form any hydrogen bonds
AG is two purines so too wide
CT is two pyrimidines so too narrow
TG would make one hydrogen bond, but would repel everywhere else
133
T/F DNA replication is nonconservative
false, it's semiconservative because one template parent strand is given to the each daughter cell
134
where does DNA synthesis begin
at the replication origin
135
what does an initiator protein do
pulls apart the replication origin
136
what direction does DNA replication occur
5' to 3'
137
what are replication forks
the replication origin opens into forks into both directions
138
what protein synthesizes the DNA
DNA polymerase
139
how are bases added to DNA
a sugar-phosphate-base group is brought to the strand and the nucleoside triphosphates break two phosphates off to produce energy to create phosphodiester bonds
140
leading vs lagging strand
the leading strand is synthesized continuously while the lagging strand is in pieces called okazaki fragments
141
draw the picture of directions of replication within DNA fork
leading and lagging strands, 5' to 3' directions
142
T/F DNA polymerase doesn't correct wrong bases
FALSE! the DNA polymerase will cleave the incorrect base and try another
143
T/F DNA polymerase uses the same site for polymerizing and proofreading
False, there are two different sites for the synthesis and editting
144
what does RNA primase do
the primer starts base chain without starting point (no previous double strand needed to) which helps the DNA polymerase start it's binding
145
where are RNA primers needed
at the beginning of the leading strand, and at each starting point of lagging strands
146
what is DNA ligase
this is what seals up the nicks and empty space made by the RNA primers
147
what proteins are needed to carry out DNA synthesis
sliding clamp
clamp loader
RNA primase
DNA polymerase
DNA helicase
single strand DNA binding protein
DNA topoisomerase
DNA ligase
telomerase
148
what does the clamp loader do
during DNA synthesis, this holds the DNA polymerases close together to the helicase
149
what does DNA helicase do
during DNA synthesis, the helicase is what unwinds the DNA so each strand can be synthesized
150
what does DNA topoisomerase do
during DNA synthesis, it relieves the torsional tension that the helicase is creating in front of it by creating a single strand break and then resealing it
151
what does DNA polymerase do
catalyzes the adding of bases to the newly created strand with polymerizing and proofreading spots
152
what does single-strand DNA binding protein do
this binds to the open DNA strands to prevent bases from repairing
153
what do the clamp loader and sliding clamp do
the clamp loader locks the sliding clamp onto the DNA
the sliding clamp keep the DNA polymerase attached
154
what does telomerase do
this adds multiple copies of a random sequence to the end so that the lagging strand can prime and then finish synthesizing the full strand
155
T/F telomeres are long repeated sequences and are always the same
false, they are SHORT repeated sequences and vary in every cell and with age
156
T/F DNA damage happens rarely
FALSE DNA Damage occurs continually in cells
157
what are the two most frequent chemical reactions causes of DNA damage
depurination and deamination
158
what is depurination
this removes guanine or adenine (the purines) from DNA
159
what is deamination
changes cytosine to uracil
160
how can UV light cause DNA damage
this makes thymine dimers between two bases
161
what is a mutation
any change in the nucleotide sequence
162
what happens if DNA damage is not fixed
depurination or deamination could lead to permanent mutations
depurination because one daughter strand would completely miss the base
deamination because one daughter strand would get a different base pair like U-A instead of C-G
163
what are the three steps to DNA repair
excision, resynthesis, ligation
164
what is excision
step one of the DNA repair where the damage is cut out
165
what is resynthesis
step two of DNA repair where a DNA polymerase gets in there and fixes the base that was just cut out
166
what is ligation
step three of DNA repair where DNA ligase seals the break in the backbone
167
what are the two ways to repair a double stranded DNA break
homologous and nonhomologous recombination
168
what is homologous recombination (draw picture)
the break is cut more to be staggered, then another strand is opened to get the correct order, then the rest are filled in through normal synthesis of complimentary base pairs
this doesn't lose any nucleotide info
169
what is nonhomologous end joining
strands are cut until they are straight, then ligase joins the ends
this loses some nucleotides
170
what causes sickle cell anemia
a single nucleotide change from A to T
171
why does sickle cell anemia persist in some communities
it helps prevent the body from malaria as any cell that gets infected will sickle and die before it can spread, which is why this mutation is passed down sometimes
172
T/F Cancer rates increase with age
true because more mutations are prone to happen when age increases
173
what causes genetic diversity
mutations during DNA replication
