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LS3 > Midterm 1 > Flashcards

Midterm 1 Flashcards

Ace this midterm!

1
Q

Central Dogma

A

The flow of genetic information goes from DNA to RNA to Proteins

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2
Q

Beadle and Tatum

A

They worked with bread mold and showed that each gene controlled a single protein (one gene: one enzyme hypothesis)

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3
Q

Griffith Experiment

A

The lethal strain S has a smooth capsule that allows it to evade the host’s immune system. The nonlethal strain was called the R strain. Griffith showed that the genetic material from the heat killed S strain turned the R strain into lethal cells.

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4
Q

Griffith’s conclusion

A

The S strain was able to transform the R strain into a virulent strain.

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5
Q

Avery, Macleod, and McCarty

A

They took Griffith’s experiment and did it in vivo. Then, they treated cells with DNase, RNase, and Proteinase to see which would affect the transforming ability. Since DNase prevented transformation, they concluded that DNA is responsible.

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6
Q

Hershey Chase Experiment

A

Used S and P radioisotopes to label the protein capsid and DNA of bacteriophage. They saw that most of the P was in the pellet where the cells are while the S was in the supernatant. This concluded that bacteriophages inject their DNA into the host cell and only this genetic info directs the creation of more progeny. DNA = genetic info!

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7
Q

Building blocks of DNA

A

Nucleotides!
Purines: Adenine and Guanine
Pyrimidines: Cytosine and Thymine

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8
Q

Polarity of DNA

A

Polarity comes from phosphodiester linkages, and has a net negative charge.

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9
Q

Chargaff’s rules

A

G and C are in same amount and A and T are in same amount

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10
Q

Rosalind Franklin and Maurice Wilkins

A

Performed X-ray diffraction studies on DNA and their data showed that DNA was in helical form with “ladder-like” rungs connecting parts of it

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11
Q

Watson and Crick

A

They proposed 3D structure of DNA to be double helix

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12
Q

Structural characteristics of DNA

A

Has sugar phosphate backbone, bases project inwards, one turn is about 10.5 bp, has major and minor grooves.

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13
Q

Mica experiment

A

DNA has about 10.5 bp per turn in solution

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14
Q

Gel Electrophoresis

A

Separates DNA molecules according to their weight. DNA travels to positive side because it is negatively charged

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15
Q

Ethidium Bromide

A

Intercalates between bases and can be seen under UV light

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16
Q

B form of DNA

A

Represents an ideal form of DNA with about 10 bp per turn. But DNA is not perfectly regular like this

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17
Q

Z form DNA

A

DNA is more elongated and slim, about 12 bp per turn. It is also left handed

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18
Q

Why is DNA so stable?

A

Large number of weak h-bonds, and also stacking interactions

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19
Q

Why is major groove rich in chemical information?

A

Proteins can tell by the order of hydrogen bonds/acceptors which base pairs are there. AADH = GC and ADAM = AT

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20
Q

Denaturation

A

Can be done with high heat or changing pH (the OH- concentration). Separates the double helix into single strands

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21
Q

Conditions for denaturation

A

high temp, lower salt concentration, high pH because they break the h-bonds

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22
Q

GC content and denaturation

A

The more GC present in DNA, the more stable it is and therefore the more heat is required for denaturation.

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23
Q

Wavelength that DNA absorbs

A

260nm

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24
Q

DNA sequence homology

A

similarity between the sequences of two DNA molecules

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25
Q

DNA hybridization

A

the pairing between complementary ssDNA or RNA. Only occurs when the strands have homology. (Used in southern blots)

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26
Q

Southern vs. Northern vs. Western blots

A 
Southern = DNA size
Northern = RNA probed with DNA probe
Western = proteins probed with antibodies
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27
Q

DNA supercoiling

A

relaxed circular DNA has about 10.5 bp per turn but supercoiled has more. It is caused by some sort of structural strain on the DNA, like underwinding

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28
Q

Linking number

A

The number of times that each strand winds around the other. L = Twist + Writhe, when there are no supercoils, L=T

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29
Q

Topoisomerases (general)

A

Enzymes that increase or decrease the linking number by underwinding the DNA. They break one strand, allowing the DNA to unwind and then religate

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30
Q

Type 1 and 2 topoisomerases

A

Type 1 relax supercoiled DNA without ATP

Type 2 need ATP to relax the DNA or to introduce supercoils

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31
Q

Topoisomerase inhibitors

A

They are used in chemotherapy to stop fast cell division, and stop topoisomerases from doing their jobs

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32
Q

Pulse-Chase

A

In the pulse, we expose the cells to labeled precursors which the cell will use when making macromolecules like DNA, RNA or proteins. In the chase, we wash out the label and let cell grow. Then, we use x-ray imaging to see where the labels end up

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33
Q

What labels are used in Pulse-chase experiments?

A 
Protein = 35S-methionine
DNA = 3H-thymine
RNA = 3H-uracil
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34
Q

Conclusion of Pulse-chase experiments

A

RNA is synthesized in the nucleus and then migrates to the cytoplasm where it partakes in protein synthesis. Confirms central dogma

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35
Q

RNA characteristics

A
  • Has ribose instead of deoxyribose
  • Uracil instead of thymine
  • Single stranded and has secondary structure
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36
Q

Why is RNA less stable in alkali?

A

Since the ribose sugar has a hydroxyl group, it can be deprotonated and this O- can attack the phosphodiester bond and degrade the RNA

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37
Q

Types of RNA

A

mRNA, tRNA, rRNA, miRNA, siRNA, and ribozymes

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38
Q

Secondary structures for RNA

A

Stem-loop, bulge, loop, RNA tends to fold on itself where there are complementary sequences

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39
Q

What form of helix does RNA take?

A

A form rather than B form like DNA

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40
Q

Does RNA follow Watson-Crick base pairing? Why or why not?

A

No, you can find GU and GA very commonly in RNA. Triple base-pairing is also possible for stabilization

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41
Q

Uses for Mg2+ and K+ in RNA

A

Since they are positively charged, they shield the negative charge of the backbone and provide stability. Also helps RNA pack more tightly

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42
Q

RNase P

A

Its an endoribonuclease that cleaves off a leader segment from 5’ end of precursor tRNA and changes it into functional mature tRNA

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43
Q

Hammerhead Ribozyme?

A

Another ribonuclease that is self-cleaving RNA

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44
Q

Primary structure of proteins

A

Chain of amino acids called a polypeptide

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45
Q

Protein homology

A

Either an identical amino acid, or an amino acid with similar properties. If an amino acid is similar enough, it shouldn’t change the protein function or structure that much

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46
Q

Secondary structure of proteins

A

Beta sheets, alpha helices, random coils, and turns

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47
Q

Protein tertiary structure

A

Stable 3D structure

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48
Q

Protein quaternary structure

A

The number of polypeptide subunits together

Ex) hemoglobin has 4 subunits

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49
Q

What interactions are occurring in protein secondary structure?

A

Secondary structures are stabilized by H-bonds between the peptide bonds in the backbone

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50
Q

Homodimer

A

Both polypeptides are identical

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51
Q

Heterodimer

A

Non-identical polypeptides (2) could be more if it wasn’t a dimer

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52
Q

Oligomer

A

Composed of multiple polypeptide chains

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53
Q

Protomer

A

Individual polypeptide chains

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54
Q

Structural domain of a protein

A
  • A part of a single polypeptide chain that has folded onto itself.
  • Domains can have independent functions, or all be used for one function
  • Protein function is usually based on the combination of different domains
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55
Q

Dimerization region

A

The region where two different polypeptides interact

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56
Q

Antibodies

A

Their quaternary structure creates an extremely specific antibody-antigen interaction
-contain disulfide linkages for added stability

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57
Q

Motif

A

A combination of secondary structures found in many proteins

EX) Beta barrel, coiled coil, and helix loop helix motif

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58
Q

4 Different types of protein folding

A

1) Spontaneous
2) Chaperone assisted folding
3) denaturing
4) renaturing

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59
Q

How does major groove information?

A

Through its pattern of h-bond donor and acceptor groups. Bases can be read by this characteristic pattern

60
Q

Do protein H-bonds interfere with base-pair bonding?

A

Nope!

61
Q

Protein to protein interactions

A
  • hydrophobic

- may be affected by post-translational modifications like methylation or acetylation

62
Q

Enzymes

A

Very specific catalyst that provides an environment for a reaction to occur rapidly
(Lower the activation energy of the reaction)

63
Q

Protein levels modified by…

A
  • Transcriptional regulation
  • Post-transcriptional (RNA)
  • Translational
  • Post-translational (modifications)
  • Allosteric regulation
64
Q

Proteolytic modification

A

Removes certain peptide segments in order to produce usable insulin. It’s activated in response to specific conditions

65
Q

Def of Phosphorylation

A

Adds phosphate using ATP

66
Q

Def of Adenylylation

A

Adds adenine using ATP

67
Q

Def of Acetylation

A

Adds acetyl group from Acetyl-CoA

68
Q

Def of Methylation

A

Adds methyl group from S methionine

69
Q

Kd

A

Represents the dissociation constant and is the concentration of the ligand at which half of all the ligand binding sites on the protein are occupied

70
Q

What does a high Kd mean?

A

It means the protein has a low affinity for the ligand

71
Q

Ways to purify protein

A

Separation, detection using immunological techniques, and sequence or structural analysis

72
Q

Protein separation

A

1) Lyse cells
2) Centrifuge
3) Chromatography
4) Gel electrophoresis

73
Q

What does detergent do to cells?

A

Makes holes in the plasma membrane

74
Q

Ion exchange chromatography

A

Separates molecules according to their charge. Positively charged particles will come through column first and negatively charged particles are bound to the beads (can be eluted later). The opposite will happen if you use negatively charge beads

75
Q

Gel filtration chromatography

A

Large proteins come out first because the smaller proteins go through the beads and can get stuck.

76
Q

Affinity chromatography

A

Use a competing molecule, salt or change in pH to remove the protein of interest from the column

77
Q

Antibody affinity chromatography

A

Separated molecules according to their affinity for a specific ligand like an antibody. The beads have the antibody so the protein will stick to the beads. The antibody-binding proteins can be eluted by lowering the pH

78
Q

Immunoprecipitation

A

Antibody is again coupled to the bead and this makes the protein heavier for centrifugation

79
Q

Epitope

A

A sequence of 7-10 amino acids recognized by an antibody

80
Q

What wavelength do we measure for proteins?

A

280nm

81
Q

How can we measure beta-galactosidase activity?

A

Instead of giving the cell lactose, we give it ONPG. Bgal will also recognize this fake sugar and will cleave it to create galactose and ONP which turns yellow

82
Q

What does SDS do?

A

It linearizes the protein and coats it with a negative charge

83
Q

Beta-mercaptoethanol

A

Reduces disulfide bonds

84
Q

What does SDS-PAGE separate by?

A

It separates proteins according to their molecular weights. Low MW will travel farther down and high MW will travel through the gel more slowly.

85
Q

2D gel electrophoresis

A

The first gel separates the proteins by their IEP. While the second separates by size.

86
Q

IEP

A

Stands for the isoelectric point. It is the pH at which the protein no longer has any charge.

87
Q

Western blot

A

Transfer the proteins from SDS PAGE gel to a nitrocellulose membrane. Then add an antibody that will bind tightly to the antigen. Next, add a secondary antibody that contains a marker that will bind to the primary antibody.

88
Q

ELISA

A

Wells are coated with an antigen. Next add plasma from the subject and if they have the antibody, it will bind to the antigen. Then add a secondary antibody to bind to that first one. Finally, if that secondary antibody binds, it should chnge the color of the solution

89
Q

Edman degradation

A

A type of protein sequencing that takes off one amino acid at a time and can identify which amino acid it was through column chromatogrpahy.

90
Q

What is mass spectrometry used for?

A

It’s a fast an accurate way to measure the molecular weight of a protein. It can also determine the sequence of proteins

91
Q

Proteomics

A

The main goal is to identify the full set of proteins produced by a cell under a certain set of conditions

92
Q

G

A

Glycine

93
Q

A

A

Alanine

94
Q

V

A

Valine

95
Q

I

A

Isoleucine

96
Q

W

A

Tryptophan

97
Q

F

A

Phenylalanine

98
Q

P

A

Proline

99
Q

M

A

Methionine

100
Q

L

A

Leucine

101
Q

D

A

Aspartate

102
Q

E

A

Glutamate

103
Q

K

A

Lysine

104
Q

R

A

Arginine

105
Q

H

A

Histidine

106
Q

S

A

Serine

107
Q

T

A

Threonine

108
Q

Y

A

Tyrosine

109
Q

N

A

Asparagine

110
Q

Q

A

Glutamine

111
Q

X-ray crystallography

A

An x-ray beam is shot through a crystallized protein and from the diffraction pattern, we can determine the protein’s structure.

112
Q

EMSA

A

Stands for the Electrophoretic mobility shift assay. The protein is mixed with radio-labeled DNA and if the protein sticks to a certain binding site, it will produce a different band in western blot than the rest of the DNA

113
Q

DNA footprinting

A

Another way of finding out where the protein is binding to the DNA. Put a radio-labelon end of DNA and allow protein to bind. Then cute DNA at different sites and see where the DNA wasn’t cut. This is usually the location of the protein.

114
Q

ChIP

A

Chromatin Immunoprecipitation.

1) Proteins are attached to DNA.
2) Antibody against the protein of interest is added
3) Precipitate the sample with the primary antibody attached
4) Take off protein and antibody and amplify the sequence of DNA using PCR

115
Q

Restriction enzymes

A

Bacterial enzymes that recognize specific, symmetric (palindromes) sequences in DNA and cleave at these sites

116
Q

Homologous genes

A

Genes with similar sequences that indicate a common ancestor

117
Q

What year was the human genome finally sequenced?

A

2003

118
Q

DNA in bacteria

A

They have circular chromosomes and extrachromosomal elements like plasmids

119
Q

What causes lower chromosomal gene density?

A

As an organism’s complexity increases, it’s gene density decreases because the DNA is filled with repeating sequences and introns rather than the actual gene

120
Q

What happens to introns?

A

They are removed form the RNA after transcription during RNA splicing

121
Q

Intergenic vs. Intragenic

A

Intergenic is within the gene itself while intragenic is between different genes

122
Q

Pseudogenes

A

They are integrated into the genome after reverse transcription but can’t be expressed because they lack the right regulatory sequences to direct their expression

123
Q

Transposable elements

A

Sequences that can move form one place in the genome to another. (Transposition)

124
Q

Paralogs

A

Homologous genes within a species

125
Q

Orthologs

A

Homologous genes between two species

126
Q

Synteny

A

Conserved linear order of the genes. It’s a good illustration of common ancestry. We have quite a bit of synteny with the mouse genome

127
Q

Protein families

A

Proteins related in amino acid sequence and 3D structure

128
Q

Single nucleotide polymorphism

A

A difference in one nucleotide

129
Q

The four main factors that drive evolution

A

1) Mutation rate
2) Natural selection
3) Genetic drift
4) Migration

130
Q

Chromatin

A

DNA mixed with protein

131
Q

Number of nucleotides between nucleosomes

A

20 to 60 bp

132
Q

How many base pairs per nucleosome?

A

200 base pairs per nucleosomes

133
Q

Structure of nucleosome

A

Has 2 copies of each H2A, H2B, H3, and H4. Only one copy of H1. H2A and H2B form a dimer and H3 and H4 come together as a tetramer

134
Q

What charge do nucleosomes carry?

A

They are positively charged

135
Q

Histone motif

A

Has three alpha helices and two loops connecting them

136
Q

Where do histone interact with the DNA?

A

They interact between the histone fold and the phosphide ester backbone of the minor groove

137
Q

Function of histone tails

A

They stick out of the histone and are sites of post-translational modifications like methylation, acetylation, and phosphorylation. They aren’t needed for nucleosome formation though. They also interact with adjacent nucleosomes to further pack the DNA tightly together

138
Q

Function of H1

A

It binds to the linker DNA at the end of the nucleosome and also the middle of the associated 147 bp. It leads to more compact defined structure.

139
Q

Order of DNA packing

A

DNA ➡ nucleosomes ➡ 30nm filament ➡ extended form of chromosome ➡ condensed section of chromosome ➡ the mitotic chromosome!

140
Q

Nucleosome remodelers

A

They are enzymes that loosen the interactions between the DNA and the nucleosomes in order to increase its accessibility

141
Q

A sliding

A

Slides the DNA off the nucleosome to expose the genes needed

142
Q

B transfer

A

Transfers nucleosomes to a different DNA so that that strand is now free

143
Q

H2A and H2B exchange

A

The third form of unwrapping DNA exchanges the subunits in a nucleosome in order to loosen up the DNA

144
Q

Signal of acetylation

A

It tells cells to start transcription of this gene. It is done by adding an acetyl group from acetylcoA to a lysine or other amino acid

145
Q

Signal from Methylation

A

It’s usually tells the cells that this gene is not needed and signals the nucleosome to bind more tightly to the DNA. It is done by adding a methyl group to arginine

146
Q

Method of DNA replication

A

Semi-conservative!

147
Q

Meselson and Stahl 1958

A

They did an experiment to prove that DNA replicates semi-conservatively. They grew the cells in a medium containing 15N and then transferred the cells to media containing 14N. If the DNA is conservative, we should see 2 bands (HL HH) while the semi conservative should only have HL. They observed only one band. In the next doubling, they saw two bands HL and LL. this further proved that this was a semi-conservative process

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