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Cell & Molecular Biology > DNA (lectures 1-5) > Flashcards

DNA (lectures 1-5) Flashcards

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1
Q

What are the 3 domains of organism classification?

A
  • Bacteria
  • Archaea
  • Eukaryotes
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2
Q

What is the cell theory?

A

This suggests that all living organisms are made up off cells that are derived from pre-existing cells.

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3
Q

What are the 3 general characteristics of a cell?

A
  • Can obtain energy (light or chemical)
  • Able to use available chemicals (to grow & multiply)
  • Contains hereditary information (stored & passed on)
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4
Q

What are the main physical characteristics of a cell?

A
  • Enclosed by plasma membrane
  • nucleus
  • mitochondria
  • the ER (endoplasmic reticulum)
  • the Golgi
  • lysosomes
  • peroxisomes
  • chloroplasts
  • cytoskeletal structure
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5
Q

Where is all hereditary information stored in a cell?

A

DNA

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6
Q

Can human DNA transcribe human proteins in bacteria?

A

No

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7
Q

Describe the transition from DNA to protein

A

DNA - Transcription - RNA - Translation - Protein

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8
Q

What is the polymer of a nucleotide?

A

Polynucleotide

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9
Q

What is the polymer of an amino acid?

A

Protein

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10
Q

What is the polymer of a monosaccharide?

A

Polysaccharide

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11
Q

What is the polymer of Acetyl coA?

A

Fatty acid

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12
Q

What is a hormone?

A

Small proteins that travel in the blood stream & bind to specific receptors elsewhere in the body

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13
Q

What are antibodies?

A

Recognize foreign material, allowing the immune system to respond

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14
Q

What are DNA binding proteins?

A

Proteins that bind to specific DNA sequences & affect gene expression

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15
Q

What is the role of porin? (clue in the name)

A

On the outer layer of bacteria & allows diffusion of certain molecules in the cell

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16
Q

What is the role of ferritin?

A
  • Stores, transports & releases ions.
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17
Q

What is the main structure in the cytoskeleton (protein)

A

Microtubules

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18
Q

What is a microtubule made up of?

A

Alpha & Beta tubulin subunits

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19
Q

Describe the role of microtubules

A
  • Separation of chromosomes during mitosis
  • Specific structures at base of cilia & flagella
  • Strong yet dynamic
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20
Q

What are enzymes?

A

Proteins that accelerate the rate of chemical reactions by reducing the activation energy needed.

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20
Q

How does an enzyme-substrate complex form?

A

An enzyme has an active site that binds the substrate & yields a product.

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21
Q

What differences do proteins have?

A
  • Shape
  • Size
  • Electrical charges
  • Polarity (charge isn’t even ly distributed (no overall charge)
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22
Q

How many amino acids are there?

A

20

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23
Q

What tens to be the pH of proteins?

A

7.4

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24
Q

Describe the primary structure of a protein

A

Order of amino acids

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25
Q

What joins amino acids (residues) together?

A

Peptide bonds

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26
Q

Describe the formation of a peptide bond

A

Loss of a water molecule (condensation) causes the formation of a peptide bond between a carbon & nitrogen.

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27
Q

Which way do polypeptide chains read? (Think terminus)

A

N(Nitrogen) terminus to C (carbon) terminus

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28
Q

What is another word for an unfolded protein?

A

Denatured

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29
Q

What is another word for a folded protein?

A

Native

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30
Q

What is sometimes required for a protein to become folded (native)?

A

Chaperones

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31
Q

What is formed on the backbone of DNA & stabilizes DNA?

A

Hydrogen bonds

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32
Q

What type of charge is the oxygen end of water?

A

Negative

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33
Q

What type of charge is the hydrogen end of water?

A

Positive

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34
Q

What 2 types of secondary structure are there?

A
  • Alpha helix
  • Beta sheet
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35
Q

In a alpha helix, what 2 substances does the Hydrogen bond form between?

A

Nitrogen group (positive) & Carboxyl group (negative)

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36
Q

How many residues are there between the Nitrogen group & Carboxyl group in an alpha helix?

A

4 residues

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37
Q

What type of structure does an alpha helix have?

A

Helical (spiral) structure, with side chains on the outside

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38
Q

What is the difference between the H bonds on an alpha helix & a beta sheet?

A

Beta sheet has bonds with residues further away on the primary sequence (e.g. on different strands)

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39
Q

What determines tertiary structure?

A
  • Non-covalent interactions between side chains
  • Electric charges
  • Size & shape of side chains also constrains
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40
Q

What are the 2 types of side chains?

A
  • Hydrophilic side chains
  • Hydrophobic side chains
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41
Q

What type of bonds can hydrophilic side chains form?

A

Hydrogen bonds/ionic interactions

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42
Q

What type of chains do hydrophobic side chains form?

A

Non polar bonds

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43
Q

On what part of the proteins do polar residues end up on?

A

Outside of the protein

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44
Q

What is the purpose of the polar residues being on the outside of the protein?

A

Can interact with polar water molecules

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45
Q

Where do the nonpolar residues end up in a protein?

A

Centre of the proteins

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46
Q

Between what residues do the sulfide bridges form in the tertiary structure?

A

Cysteine

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47
Q

What is the purpose of the disulfide bonds between the cysteine residues?

A

To strengthen the tertiary structure

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48
Q

What can control how compact protein domains are?

A

The flexible regions within proteins

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49
Q

What determines whether a polypeptide has quaternary structure?

A

The number of subunits it has - 2+ subunits = a complex with quaternary structure.

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50
Q

What is the names given to proteins with 2, 3, & 4 subunits?

A

Dimer (2), Trimer (3), Tetramer (4)

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51
Q

What are 2 examples of post-translational modification & targeting?

A
  • removal of parts of the sequence
  • addition of molecules
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52
Q

What are 3 specific types of post-translation modification?

A
  • Methylation
  • Glycosylation
  • Ubiquitination
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53
Q

What is methylation?

A

Addition of methyl group (-CH3) to histones, which control which parts of the genome is expressed.

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54
Q

What is glycosylation?

A

Addition of various sugars - especially on the cell surface & secreted proteins.

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55
Q

What is ubiquitination?

A

Addition of 76-aa polypeptide. Ubiquitin polymers mark out a protein for degradation

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56
Q

What is phosphorylation?

A

Reversible addition of phosphate (PO3) groups

57
Q

What types of enzymes are used to allow phosphorylation to occur?

A

Kinases

58
Q

Why is phosphorylation’s function in post-translational modification?

A

It is an important way of regulating enzyme function

59
Q

What are Gregor Mendel’s 3 laws of inheritance?

A

Segregation - genes come in pairs (individuals only pass on one to offspring.
Independent assortment - different genes are passed on separately.
Dominance - an individual with 2 alleles of a gene will express the dominant form.

60
Q

What 4 features about DNA was known previously?

A

There was:
- replication of information
- storage of information
- expression of information
- variation by mutation

61
Q

What did Sutton-Boveri theory look into?

A

Chromosomal inheritance

62
Q

What animal did Sutton do research in to?

A

Grasshoppers

63
Q

What animal did Boveri do research into?

A

Ascaris worms

64
Q

Why did Sutton-Boveri use grasshoppers & worms?

A

Because they have chromosomes that are large and few in number.
As a result they noticed that destruction of chromosomes will lead to prevention of the development of an embryo.

65
Q

What 3 conclusions were drawn about chromosomes from Sutton-Boveri’s experiment?

A
  • chromosomes are required for embryonic development.
  • chromosomes carry “factors” (genes)
  • chromosomes are linear structures with genes along them
66
Q

What microorganism can cause pneumonia in humans & in mice?

A

Streptococcus pneumoniae

67
Q

What are the 2 strains of neumonia?

A

S strain & R strain

68
Q

Describe the 2 differences in the 2 strains of Streptococcus pneumoniae

A

S strain (pathogenic) - smooth bacteria - polysaccharide coats
R strain (non-pathogenic) - rough bacteria - no polysaccharide coats

69
Q

How does the polysaccharide coats on the S strain cause it to be virulent?

A

The polysaccharide coat forms a capsule that protects some strains from the host immune system.

70
Q

Does dead S bacteria & live R bacteria establish an infection? (WHY)

A

Yes - as the R cells have undergone a ‘transformation’. The hereditary material has been passed down and the bacteria has changed the genotype.

71
Q

What was Griffin’s principle?

A

The transformation principle

72
Q

What did Avery, MacLeod & McCarthy research?

A

Research into what molecules caused the transformation seen in Griffin’s experiment

73
Q

How did Avery & McCarthy find out what molecule was responsible for causing the transformation to occur?

A
  1. Systematically destroyed each component of the S strain using enzymes to specifically digest each type of molecule.
  2. They then recombined the S strain with live R bacteria and watched what happened.
  3. Whatever compnent led to the S strain not living, meant that it was responsible for it being passed on.
74
Q

What were the result of Avery & McCarthy’s experiment?

A

DNA encoding was required to make the polysaccharide coat.

75
Q

What is the host for bacteriophage T2?

A

E. coli

76
Q

What is the life cycle of bacteriophage T2?

A
  1. Destruction of host cell’s chromosome.
  2. Transcription & translation of viral genes & replication
  3. Assembly of new virus particles
77
Q

What is the outline of Hershey’s experiment?

A
  1. Label bacteriophage DNA or protein with a radioactive isotope.
  2. Infect unlabeled bacteria with radioactive phage.
  3. Separate phage ghosts from infected bacteria.
  4. Test bacteria & phage ghosts for radioactivity.
78
Q

What molecule does DNA contain that Hershey tested for?

A

Phosphate

79
Q

What molecule does protein contain that Hershey tested for?

A

Sulphur

80
Q

How did Hershey label the bacteriophages?

A

Grew bacteriophages in 1 of 2 medias - either containing 32P or 35S.
32P - bacteriophage would contain radioactively labelled DNA.
32S - bacteriophage would contain radioactively labelled protein.

81
Q

How did Hershey remove the “phage ghosts” from the infected cell?

A

Agitated them in a blender

82
Q

What did Hershey do to separate the phage & bacteria?

A

Centrifuge to separate them. The bacteria was heavier (pellet) and the phage was lighter (supernatant).

Both was tested for radioactivity/

83
Q

What results were found in Hershey’s experiment?

A

DNA is being injected which leads to the formation of a new phage.

32P (DNA):
Phage ghost - no label
Bacteria - labelled

35S (protein):
Phage ghost - Label
Bacteria - no label

84
Q

What is DNA composed of?

A
  • Nucleotides
  • Base sugar (deoxyribose)
  • Phosphate
85
Q

What way is DNA read?

A

5’ to 3’

86
Q

What carbon (3 or 5) is joined to phosphate?

A

Carbon 5

87
Q

What are the 2 purines?

A
  • Adenine
  • Guanine
88
Q

What are the 2 pyramidines?

A
  • Cytosine
  • Thymine
89
Q

What joins the chain of nucleotides?

A

Covalent bonds - bond created is called phosphodiester bonds.

90
Q

What was Chargaff’s experiment?

A
  • Isolate the nucleobase components of DNA from a number of species (USING PAPER CHROMATOGRAPHY)
91
Q

What are Chargaff’s rules?

A

% Purine = %pyrimidines
%AT = %GC
%A = % T
%G = %C

92
Q

What is X-ray crystallography structure of DNA?

A
  1. X-ray put through a crystalline solid.
  2. X-ray interacts with the solid.
  3. They will either be blocked, bounce-off or refract from the solid.
  4. Because its crystal, shaped-patterns with be formed.
93
Q

Why is X-ray crystallography useful?

A

It allows you to gain information about the structure of a molecule.

94
Q

What does an X pattern in X-ray crystallography signify?

A

Helical structure

95
Q

What does a regular pattern in X-ray crystallography signify?

A

Repeating, even structure

96
Q

What does the distance between spots mean in X-ray crystallography?

A

Distance of one turn (3.5nm)

97
Q

What were the main features of the Watson & Crick Model?

A
  • AT & GC hydrogen bonded pairs
  • Antiparallel strands
  • Right-handed double helix
  • One helical turn every 10.5bp
  • Major & minor grooves
98
Q

How many hydrogen bonds are there between T-A nucleotides?

A

2

99
Q

How many hydrogen bonds are there between G-C nucleotides?

A

3

100
Q

The presence of which 2 nucleotides makes DNA more stable?

A

A higher ratio of C-G = more stable DNA

101
Q

What is the difference between purines & pyrimidines?

A

Purines (A & G) = 2 carbon rings
Pyrimidines (C & T) = 1 carbon ring

102
Q

What type of strands does DNA have?

A

Antiparallel & complementary

103
Q

What type of helical structure does DNA have?

A

Double, right-handed helices

104
Q

How long is one complete turn including a major & minor groove?

A

10.5 base pairs

105
Q

What is a chromosome?

A

A long DNA molecule with part of all the genetic material of an organism.

106
Q

What are histones?

A

Packaging proteins involved in chromosomes

107
Q

How many chromosomes do humans have?

A

46 (23 pairs)

108
Q

What is a centromere?

A

The specialized chromosomal region where spindle microtubules assemble.

109
Q

Are histones conserved?

A

Yes

110
Q

What are telomeres?

A

Repetitive DNA at the end of linear chromosomes

111
Q

Describe prokaryotic genomes

A

Singular, circular chromosome (usually a few million bp)

112
Q

How can plasmids be passed between cells?

A

Conjugation

113
Q

What is an example of an advantageous gene that a plasmid could have?

A

Antibiotic resistance

114
Q

What is a difference between DNA-binding proteins?

A
  • Some have a general affinity for DNA, whereas some are sequence-specific.
  • Some prefer single-stranded, whereas some prefer double-stranded DNA.
115
Q

What are the 3 roles of DNA-binding proteins?

A
  1. Regulate gene expression
  2. Cut DNA at specific sequences
  3. Protect DNA
116
Q

What are transcriptional regulators?

A

Proteins that bind regulatory sequences near the promotors of genes, to either stimulate or block transcription. This can bend DNA into a favorable or unfavorable shape.

117
Q

What is an example of a transcriptional regulator?

A

Lac operon - E.coli (contains enzymes for breaking down lactose sugar)

118
Q

How does the Lac operon regulate transcription?

A
  1. Lac repressor binds to DNA & blocks transcription (when lactose is absent)
  2. Catabolic activator protein binds to DNA & increases transcription (when glucose is absent).
119
Q

What are restriction endonucleases?

A

Enzymes that cut DNA at specific, normally palindromic sequences 6-10bp.

120
Q

Where do restriction endonucleases originate?

A

In bacteria, to restrict the action of viruses.

121
Q

What were the 3 possible models for DNA replication?

A
  • conservative
  • semi-conservative
  • dispersive
122
Q

What did Meselson aim to find out?

A

What mechanism is used for DNA replication:
- conservative
- semi-conservative
- dispersive

123
Q

How Meselson research into how DNA replication occurs?

A
  • Used isotopes of nitrogen in DNA.
  • Centrifuged caesium chloride.
  • Separated the DNA by molecular weight.
  • E.coli is grown in 15N (nitrogen) then transferred to 14N medium.
  • It is then separated by heavy & light molecules by ultracentrifugation.
124
Q

What type of replication was discounted as a result of Meselson’s experiment?

A

Conservative

125
Q

Describe what semi-conserved DNA looks like

A
  • One original strand
  • One new strand
126
Q

What type of direction are replication forks?

A

BIdirectional

127
Q

Describe the enzymatic activities neccesary for DNA replication

A
  • Primase
  • DNA polymerase
  • DNA ligase (Okazaki fragments)
  • Single-strand binding protein
  • Helicase
  • Topoisomerase
128
Q

What is the role of primase?

A

Enzyme that synthesizes RNA sequences called primers

129
Q

What is the role of DNA polymerase

A
  • Add nucleotides on at a time, in a 5’ to 3’ direction
130
Q

What is the role of DNA ligase?

A

Enzyme that facilitates the joining of DNA strands together by catalyzing the formation of phosphodiester bond

131
Q

What is single-strand binding protein?

A

SSB binds to separated strands, separating them.

132
Q

What is the role of DNA helicase?

A

Used to unwind DNA (break hydrogen bonds)

133
Q

What is the role of topoisomerase

A

Relieves pressure from overwinding around the replication bubble, by making & revealing breaks in the DNA.

134
Q

Describe the leading strand

A

5’ - 3’ DNA synthesis points towards the replication fork can process continuously.

135
Q

Describe the lagging strand

A

5’ - 3’ DNA synthesis points away from the replication fork and therefore is discontinuous (primed numerous times).

136
Q

What is Okazaki fragments

A

The pieces of DNA that are stuck together to make up the lagging strand of replication.

137
Q

Describe semi-continuous replication

A

Continuous replication of the leading strand & discontinuous replication of the lagging strand

138
Q

What is the problem with telomeres?

A

Primer removal at the end of chromosomes leave a gap that can’t be filled in. This means a piece is lost from the end of the chromosomes.

139
Q

What enzyme can replenish telomeres from an RNA template in some cell types?

A

Telomerase

140
Q
A

Cell & Molecular Biology (20 decks)

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