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exam 2 Flashcards

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1
Q

What are the most diverse macromolecules

A

proteins

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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

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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

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4
Q

what does a transport protein do and what are some examples

A

carry small molecules or ions
hemoglobin, glucose transporters

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5
Q

what does a motor protein do and what are some examples

A

generate movement in cells and tissues
myosin kinesin

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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

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7
Q

what does a storage protein do and what are some examples

A

store amino acids or ions
ferritin, ovalbumin, casein

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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,

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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

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10
Q

what are some special purpose proteins

A

antifreeze proteins, green fluorescent proteins, glue proteins

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11
Q

what is the general protein structure

A

a polymer of amino acids in a polypeptide sequence

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12
Q

what determines a protein’s structure

A

the sequence of amino acids

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13
Q

what are the parts of protein

A

central carbon with one hydrogen, amino group, R-group, carboxyl group

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14
Q

how many polar/nonpolar amino acids are there

A

10 polar, 10 nonpolar

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15
Q

how many amino acids are there

A

20

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16
Q

what types of noncovalent bonds help proteins fold

A

electrostatic attractions, hydrogen bonds, van der Waals attractions

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17
Q

T/F denatured proteins cannot return to their natural shape

A

false, they often can :)

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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

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19
Q

how many levels of protein structures are there, and what are they called

A

4;
primary; secondary; tertiary; quaternary

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20
Q

what is the primary structure of protein

A

the sequence of amino acids

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21
Q

what are common secondary structures

A

alpha helix and beta sheet

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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

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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

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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

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25
Q

what does it mean to be an antiparallel beta sheet

A

secondary structure where each row goes from left to right then right to left in a snake pattern

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26
Q

what is a tertiary structure

A

a long strand of amino acids with multiple secondary structures connecting

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27
Q

what is a quaternary structure

A

multiple polypeptide chains of amino acids coming together

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28
Q

what other forces help proteins fold

A

hydrophobic forces

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29
Q

what helps guide the folding of a newly synthesized polypeptide chain

A

chaperone proteins

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30
Q

T/F many proteins are composed of separate functional domains (secondary structures)

A

True :)

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31
Q

what connects multiple secondary structures (domains)

A

unstructured areas are between these domains

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32
Q

T/F many proteins contain multiple copies of the same protein subunit

A

True, this means that many of the exact same tertiary structures come together to form the quaternary structure

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33
Q

T/F proteins cannot be two different protein subunits

A

false, they can and sometimes are two subunits symmetrically assembled into 4 (2 of one tertiary structure, 2 of the other tertiary structure)

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34
Q

what is a dimer

A

two identical protein molecules linked together

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35
Q

what other shapes can be formed with identical protein subunits

A

dimer (2 proteins connected)
helix (fit like a puzzle piece bc two binding sites)
ring (also like puzzle piece bc two binding sites)

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36
Q

what is an actin filament made of

A

identical protein subunits that form 2 strands that wrap around each other

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37
Q

what are some common subunit shapes

A

filaments, spherical, hollowed tubes

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38
Q

what shape is collagen

A

triple helix

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39
Q

what shape is elastin

A

when not stretched, it looks like curled worms connected, but when it is stretched, it forms rows of fibers connected like ladders

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40
Q

what bonds help stabilize the protein shape

A

disulfide bonds

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41
Q

T/F all proteins bind to other molecules

A

TRUE

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42
Q

what can proteins bind to

A

little proteins (ligands)

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43
Q

T/F binding sites can interact with all ligands

A

False they are designed for specific ligands

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44
Q

what are antibodies

A

proteins produced by immune system in response to foreign molecules

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45
Q

what is an antibody’s target ligand

A

antigen

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46
Q

T/F antibody binding sites have extreme specificity

A

true

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47
Q

what are the common uses of antibodies in the lab

A

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

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48
Q

how does the immune system make anitbodies

A

the immune system makes B cells, which then each make their own antibody

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49
Q

what is a monoclonal antibody

A

specific B cell is immortalized with a tumor cell so that antibody can be made infinitely

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50
Q

what is a polyclonal antibody

A

make antibodies through the B cells in mice, goats, and other mammals

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51
Q

what are the three ways that an enzyme could make a reaction happen

A
  1. bind 2 molecules together to make them interact
  2. rearrange electrons
  3. bend/force molecules to favor reaction
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52
Q

what is lysozyme

A

an enzyme that cleaves (breaks apart) a polysaccharide chain

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53
Q

what is kinase

A

an enzyme that does phosphorylation

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54
Q

what is phosphorylation

A

adding a phosphate

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55
Q

what is phosphotase

A

an enzyme that dephosphorylates (removes phosphate)

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56
Q

what is competitive inhibition

A

a drug blocks substrate binding by binding to an active site itself

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57
Q

what is noncompetitive inhibition

A

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

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58
Q

what happens when a regulatory ligand binds

A

the equilibrium between 2 protein conformations can be altered

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59
Q

what is feedback inhibition

A

this is the drug/molecule that does the competitive/noncompetitive inhibition

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60
Q

why is feedback inhibition needed

A

to regulate the flow through biosynthetic pathways and regulate metabolic pathways

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61
Q

T/F phosphorylation can control protein activity by causing a conformational change

A

True, the adding/subtracting of the phosphate molecules can change the protein shape while decides if the function will work or not

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62
Q

how can a protein walk, and what would it walk across

A

conformation changes would let it walk (changing shape) across the cytoskeleton filament

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63
Q

what makes the protein walking irreversible

A

they are coupled to the hydrolysis of ATP so the energy was used to get to the next shape and can’t go back

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64
Q

what is an example of conformation changing

A

GTP to GDP changes the shape of the protein which turns it on or off (turning it on happens really fast bc favorable)

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65
Q

T/F small protein complexes function as machines

A

false, LARGE protein complexes function as machines

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66
Q

what is a proteosome

A

a large protein complex that breaks down old or misfolded proteins

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67
Q

what is a ribosome

A

a multi RNA and large protein complex that synthesizes proteins

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68
Q

what is a condensate and what produces them

A

large biochemical sub-compartments created by macromolecular interactions — they are not membrane bound but just groupings of macromolecules

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69
Q

what is the nucleolus

A

biomolecular condensate that brings RNA and proteins together that will assemble ribosomes

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70
Q

what is homogenization

A

the outer membrane of cells are ruptured so that the organelles can be released in a resulting thick soup (homogenate)

71
Q

what are the four homogenization techniques

A

ultrasound, detergent, pressure, plunger

72
Q

what is column chromatography

A

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
Q

what are the three type of chromatography

A

ion exchange
gel filtration
affinity

74
Q

what is ion exchange chromatography

A

small beads with pos or neg charge will hold onto specific proteins

75
Q

what is gel filtration chromatography

A

beads with small holes catch smaller proteins so bigger ones go out

76
Q

what is affinity chromatography

A

antibodies bind to some proteins to separate them and others go out

77
Q

what is used to separate proteins by size

A

SDS polyacrylamide gel electrophoresis

78
Q

what is the benefit of 2D gel electrophoresis

A

this provides greater protein separation bc it separates by charge first then isoelectric point

79
Q

what is the isoelectric point

A

a pH in 2D gel electrophoresis where the molecules have no net charge

80
Q

what are three ways of determining a protein’s structure

A
  1. x-ray crystallography
  2. NMR
  3. cryo electron microscopy
81
Q

was is xray crystallography

A

certain conditions can make proteins into crystals that can reveal things about structures

82
Q

what is NMR

A

nuclear magnetic resonance spectroscopy used to determine structure in smaller proteins

83
Q

what is cryo electron microscopy

A

freezes proteins to see with electron microscopy the structure

84
Q

what is DNA made of

A

sugar phosphate backbone, and four nucleotide building blocks (bases A G C T)

85
Q

what shape is DNA

A

double stranded helix

86
Q

what bonds are used in the DNA backbone

A

phosphodiester

87
Q

what bonds are formed between DNA bases

A

hydrogen bonds

88
Q

what direction do the strands of DNA run

A

antiparallel

89
Q

what atom in DNA have a negative charge

A

one of the oxygens on the phosphate group on the backbone has a neg charge

90
Q

How many hydrogen bonds does CG have

A

3

91
Q

how many hydrogen bonds does AT have

A

2

92
Q

which two bases are purines and what does this mean

A

this is double ring structure and is ga

93
Q

what bases are pyrimidines and what does this look like

A

single ring structure and is CUT

94
Q

T/F base pairs are perpendicular rungs of the ladder that lay flat

A

true, they stack on top of one another

95
Q

why are the bases stacked horizontally flat

A

so that only specific flat molecules can get in to affect replication and transcription

96
Q

T/F all grooves of DNA are the same size

A

False, there are major grooves and minor grooves

97
Q

what does the sequence of bases in DNA determine

A

this is the genetic information to making RNA and proteins

98
Q

what is the sequence called that makes RNA or protein

A

gene

99
Q

what is a chromosome

A

a double stranded DNA molecule with thousands of genes

100
Q

T/F all genes code for proteins

A

false, sometimes, the gene will only produce RNA and not get translated into protein

101
Q

what is central dogma

A

DNA - RNA - protein
replication - transcription - translation

102
Q

do yeast or human chromosomes have genes closer together?

A

yeast genes are closely packed together along chromosomes
human genes are much farther apart

103
Q

when can chromosomes be seen under a microscope

A

during cell division when they group and condense

104
Q

draw the process of condensing chromosomes in the cell (uncondensed to condensed)

A

DNA wraps around histone making nucleosome, which bundles up to make chromatin and forms chromosome

105
Q

how many chromosomes does a human have

A

23 pairs so 46

106
Q

what is reciprocal chromosomal translocation

A

a top of one chromosome has been switched with the top of another

107
Q

what are the noncoding base pair sequences called

A

introns

108
Q

when are introns removed from the DNA

A

after inscription, the RNA removes the introns and turns into mRNA

109
Q

what is mitosis

A

cell duplication where the cell copies all of its chromosomes to two daughter cells

110
Q

what are the three elements on the DNA strand that are needed for mitosis to happen

A

telomere, replication origin, centromere

111
Q

when do chromosomes have their own distinct area within the nucleus

A

during interphase, there are specific territories for the interphase chromosomes to live

112
Q

what is the nucleolus

A

in the nucleus and is the site for ribosome assembly

113
Q

are interphase or mitotic chromosomes more compact

A

chromosomes are most compact during mitosis, so during the inter phases the chromatins relax and spread out

114
Q

how long is the DNA strand that is wrapped around a histone

A

147 base pairs long by wrapping around twice

115
Q

how does the chromatin stay on the helix

A

the histones are positively charged which binds with the negatively charged backbone

116
Q

how are the chromatin loops formed (before reaching shape of chromosome)

A

the SMC Ring Complex using ATP to form loops by connecting to two sides and walking to make loop bigger

117
Q

what do clamp proteins do (draw this with cohesin)

A

these tell the cohesin (SMC complex) when to stop making the loop bigger

118
Q

what is the difference between cohesion and condensin (draw both in one picture)

A

cohesion is used to make individual loops and condensin is used to make big loops with little loops in them

119
Q

what shape does condensin make the chromatin loop into

A

this makes the many smaller loops turn into one big loop that spirals up

120
Q

what holds together the two fully condensed chromatins

A

centromere

121
Q

how are the genes on the DNA wrapped around histones accessed

A

there are chromatin remodeling complexes that locally reposition the wrapped DNA to allow access to any part of DNA

122
Q

what is heterochromatin

A

chromatin that is tightly packaged and make it hard to read the gene expression

123
Q

what is euchromatin

A

chromatin that is loosely packaged which makes it easy to read the gene expressions

124
Q

what helps determine if a stretch of chromatin should be hetero or euchromatin

A

the histone tails that come off of the histones help determine how the cell should handle the chromatin

125
Q

T/F there are various stretches of euchromatin and heterochromatin along a single chromosome

A

true, there can be lots of switching between the types on the chromosome

126
Q

what is the difference between constitutive and facultative heterochromatin

A

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
Q

what is the difference between quiescent and active euchromatin

A

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
Q

what happens if heterochromatin spreads too far when chromatin is being condensed

A

this would make certain genes unreadable and possible cause disease

129
Q

what cell is inactivated in female mammals

A

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
Q

how does a parent cell pass down which chromatins should be hetero or euchromatin

A

the heterochromatins are marked and then spread until hit barrier DNA sequence to switch to euchromatin

131
Q

what did scientists use to find genetic material

A

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
Q

why cant other base pairs work like CA AG CT TG

A

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
Q

T/F DNA replication is nonconservative

A

false, it’s semiconservative because one template parent strand is given to the each daughter cell

134
Q

where does DNA synthesis begin

A

at the replication origin

135
Q

what does an initiator protein do

A

pulls apart the replication origin

136
Q

what direction does DNA replication occur

A

5’ to 3’

137
Q

what are replication forks

A

the replication origin opens into forks into both directions

138
Q

what protein synthesizes the DNA

A

DNA polymerase

139
Q

how are bases added to DNA

A

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
Q

leading vs lagging strand

A

the leading strand is synthesized continuously while the lagging strand is in pieces called okazaki fragments

141
Q

draw the picture of directions of replication within DNA fork

A

leading and lagging strands, 5’ to 3’ directions

142
Q

T/F DNA polymerase doesn’t correct wrong bases

A

FALSE! the DNA polymerase will cleave the incorrect base and try another

143
Q

T/F DNA polymerase uses the same site for polymerizing and proofreading

A

False, there are two different sites for the synthesis and editting

144
Q

what does RNA primase do

A

the primer starts base chain without starting point (no previous double strand needed to) which helps the DNA polymerase start it’s binding

145
Q

where are RNA primers needed

A

at the beginning of the leading strand, and at each starting point of lagging strands

146
Q

what is DNA ligase

A

this is what seals up the nicks and empty space made by the RNA primers

147
Q

what proteins are needed to carry out DNA synthesis

A

sliding clamp
clamp loader
RNA primase
DNA polymerase
DNA helicase
single strand DNA binding protein
DNA topoisomerase
DNA ligase
telomerase

148
Q

what does the clamp loader do

A

during DNA synthesis, this holds the DNA polymerases close together to the helicase

149
Q

what does DNA helicase do

A

during DNA synthesis, the helicase is what unwinds the DNA so each strand can be synthesized

150
Q

what does DNA topoisomerase do

A

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
Q

what does DNA polymerase do

A

catalyzes the adding of bases to the newly created strand with polymerizing and proofreading spots

152
Q

what does single-strand DNA binding protein do

A

this binds to the open DNA strands to prevent bases from repairing

153
Q

what do the clamp loader and sliding clamp do

A

the clamp loader locks the sliding clamp onto the DNA
the sliding clamp keep the DNA polymerase attached

154
Q

what does telomerase do

A

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
Q

T/F telomeres are long repeated sequences and are always the same

A

false, they are SHORT repeated sequences and vary in every cell and with age

156
Q

T/F DNA damage happens rarely

A

FALSE DNA Damage occurs continually in cells

157
Q

what are the two most frequent chemical reactions causes of DNA damage

A

depurination and deamination

158
Q

what is depurination

A

this removes guanine or adenine (the purines) from DNA

159
Q

what is deamination

A

changes cytosine to uracil

160
Q

how can UV light cause DNA damage

A

this makes thymine dimers between two bases

161
Q

what is a mutation

A

any change in the nucleotide sequence

162
Q

what happens if DNA damage is not fixed

A

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
Q

what are the three steps to DNA repair

A

excision, resynthesis, ligation

164
Q

what is excision

A

step one of the DNA repair where the damage is cut out

165
Q

what is resynthesis

A

step two of DNA repair where a DNA polymerase gets in there and fixes the base that was just cut out

166
Q

what is ligation

A

step three of DNA repair where DNA ligase seals the break in the backbone

167
Q

what are the two ways to repair a double stranded DNA break

A

homologous and nonhomologous recombination

168
Q

what is homologous recombination (draw picture)

A

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
Q

what is nonhomologous end joining

A

strands are cut until they are straight, then ligase joins the ends
this loses some nucleotides

170
Q

what causes sickle cell anemia

A

a single nucleotide change from A to T

171
Q

why does sickle cell anemia persist in some communities

A

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
Q

T/F Cancer rates increase with age

A

true because more mutations are prone to happen when age increases

173
Q

what causes genetic diversity

A

mutations during DNA replication

biology (4 decks)

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