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L 211 > exam 1 info > Flashcards

exam 1 info Flashcards

1
Q

what functions do proteins carry out

A 
catalyze reactions
form cellular structures
transmit signals 
carry oxygen
repair damaged DNA
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2
Q

why are enzymes used

A

to speed up reactions

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3
Q

“ase” means what

A

enzyme

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4
Q

what is the the cytoskeleton and its purpose

A

network of filaments and helps regulate a cell’s shape

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5
Q

what is the primary level of structure

A

linear sequence of amino acids joined covalent peptide bonds. Disordered and folded string

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6
Q

what is the second level of structure

A

hydrogen bonds of nearby amino acids

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7
Q

what is the tertiary level of structure

A

entire 3D structure of a protein. non-covalent bonds

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8
Q

what is the quaternary level of structure

A

multiple smaller proteins interacting to form one large protein

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9
Q

how does the identity change by the varying structure levels

A
  • straight chain
  • beta sheet
  • jumbled protein
  • several proteins jumbled
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10
Q

what are the components of an amino acid structure

A

amino group
alpha carbon
carboxyl group
r group/ side chain

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11
Q

why does the acidity of proteins matter?

A

many proteins act as enzymes

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12
Q

what is pepsin

A

stomach enzyme that is very acidic

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13
Q

what is salivary amylase

A

saliva, neutral, slightly acidic

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14
Q

what is alkaline phosphatase

A

bones, very basic

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15
Q

what is the primary protein structure

A

linear sequence of amino acids, joined by covalent peptide bonds

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16
Q

what is the secondary protein structure

A

local interactions between nearby amino acids with non-covalent hydrogen bonds

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17
Q

what is the tertiary protein structure

A

the entire 3D structure of a protein, generally mediated by non-covalent bonds

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18
Q

what is quaternary protein structure

A

interaction of multiple smaller proteins, to form one large protein

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19
Q

how are covalent peptides formed

A

energy-requiring condensation (aka dehydration reaction), that produces water

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20
Q

what characterizes the alpha-helix

A

rod like structure. looks like a spring, right handed.

stiff due to hydrogen bonds of the carboxyl and amino groups

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21
Q

what characterizes the beta-strand

A

segment of 5-20 amino acids that make up the peptide background

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22
Q

what characterizes the beta-sheet

A

segment of 2-6 beta strands running parallel to one another. held together by hydrogen bonds

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23
Q

what are the amino acids that have high helix-forming potential

A

(MALEK) Methionine, alanine, leucine, glutamic acid, lysine

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24
Q

what amino acids disrupt helices

A

proline (bc easily breaks) and glycine (bc energy costly)

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25
Q

what is the coiled coil

A

structure formed by the interaction of 2+ a-helices, found in proteins

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26
Q

coiled coil characteristics

A

very strong

found in proteins that need the strength, such as muscles, hair, and blood clot fibrin

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27
Q

beta sheet parallel vs antiparallel

A

parallel– sequence matches from left to right

anti-parallel– sequence turns in opposite direction every other strand

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28
Q

the parallel beta sheet is often finds what amino acids

A

proline

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29
Q

what are the super-secondary structures

A

hairpin turn
helix-loop-helix
beta-alpha-beta unit
greek key

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30
Q

whats the hydrophobic collapse

A

pulls a string of hydrophobic molecules together when in water. hydrophilic molecules shift the strand to surround the hydrophobic molecules on the inside

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31
Q

purpose of myoglobin

A

carries oxygen to the muscles

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32
Q

how does a protein embed itself into a lipid bilayer, with regards to water sustainability

A

the potions of hydrophilic and hydrophobic amino strands correspond to their most comfortable locations in the bilayer

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33
Q

what are van der waals forces and their characteristics

A

weak interactions, created from slight fluctuations on electron densities around atoms, that are effective in large groups. The bonds are used to hold small short distance proteins together

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34
Q

what bonds are the strongest and can hold over a long distance range

A

covalent

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35
Q

the oxidation of 2 cysteines creates what?

A

a cystine

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36
Q

what are discrete protein domains

A

part of a given protein sequence that exist and function independently from the rest of the protein strand.

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37
Q

how are protein domains created

A

they are added, restricted, or part of it is duplicated

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38
Q

domains are a part of what part of the protein structure?

A

tertiary

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39
Q

what is the x-ray crystallography used for

A

to determine protein identity

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40
Q

what is the quaternary protein structure

A

arrangement of multiple subunits into a larger protein complex

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41
Q

how is the quaternary protein structure stabilized

A 
hydrogen bonds
ionic bonds 
van der waals forces
hydrophobic interactions 
(sometimes by covalent disulfide bonds
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42
Q

what form of protein structure does hemoglobin example?

A

quaternary bc it is composed of proteins

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43
Q

electrophoresis purpose/ procedure

A

determines protein size

  • proteins are run through gel
  • electrical field migrates charged proteins
  • smaller they are, the further they fall into the gel
  • separated by size bc of molecular weight
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44
Q

what is the solution used in electrophoresis and it’s properties?

A

sodium dodecyl sulfate. negatively charged

has hydrophobic side and hydrophilic side

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45
Q

what is western blotting

A

technique to identify and locate specific individual proteins in a sample of membrane

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46
Q

what is the central dogma of molecular biology

A 
DNA 
copies itself through replication 
transcription
translation
polypeptide is formed\

DNA-> RNA -> protein

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47
Q

what are the purines

A

adenine and guanine

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48
Q

what are the pyrimidine

A

thymine and cytosine

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49
Q

what is a deoxyribonucleoside

A

base plus a sugar molecule

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50
Q

what is a deoxyribonucleotide

A

deoxyribonucleoside plus 1-3 phosphate groups

called mono, di, or triphosphate

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51
Q

what direction does DNA go?

A

5’ to 3’ direction

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52
Q

what is a phosphodiester bond

A

nucleosides joined together by a common phosphate group

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53
Q

what is a prerequisite to adding onto the DNA strand

A

3’ end has to be free to add anything on to the strand

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54
Q

What is the tetranucleotide hypothesis

A

levene discovering the 4 bases, deoxyribose, and phosphate. Believed DNA was composed of equal amounts of A, C, G, T in repetition

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55
Q

explain the transforming principle experiment

A
  • living s cells are injected and mouse dies of pneumonia
  • living r cells are injected and mouse is healthy
  • heat killed s cells are injected and mouse is healthy
  • living r cells and heat killed s cells are injected and mouse dies of pneumonia
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56
Q

what was the outcome of the transforming principle? what did it tell us?

A

the live r strain converted into the s strain. Something must allow the transfer of material to occur, causing sickness. The transforming principle is the DNA

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57
Q

what supports DNA as the transforming principle

A

treatment of s cells with deoxyribonuclease eliminated transforming activity

58
Q

whats the purpose of bacteriophage infection

A

it’s on form of replication

59
Q

explain the process of lytic bacteriophage infection

A

1) attachment of phage to cell
2) entry of phage and degradation of host DNA
3) synthesis of viral genome
4) assembly of phage replication
5) release of phages

60
Q

what did the hershey-chase experiment study?

A

studied if proteins or DNA were the genetic material

61
Q

method of hershey-chase experiment

A

injected sulfur labeled proteins vs injected phosphorus labeled DNA

62
Q

what was the outcome of the hershey-chase experiment

A

experiment supported DNA as the hereditary genetic material

63
Q

what did chargaff discover while studying DNA

A

DNA has varying molar amounts, countering tetranucleotide hypothesis of all 4 bases being equal

64
Q

what is chargaffs rule

A

double stranded DNA must have equal A-T concentrations and G-C concentrations

65
Q

in what direction does the two strands of DNA twist?

A

right handed twist, antiparallel

one goes 3’-5’ and other goes 5’-3’

66
Q

how many hydrogen bonds do the bases have

A

A and T have 2 H bonds

G and C have 3 H bonds

67
Q

what make up the backbone of the helix?

A

phosphate and deoxyribose

68
Q

what is the helix diameter

A

2.0 nanometers

69
Q

the structure repeats itself after how many base pairs

A

about 10.5

70
Q

which ends of the DNA strands have a phosphate group and an OH

A

5’ has phosphate

3’ has OH

71
Q

the watson crick form of DNA is referred to as what?

A

B-DNA

72
Q

what is the most compact form of DNA

A

A-DNA

73
Q

what is the dominant form of DNA

A

B-DNA

74
Q

what is the major difference between B-DNA and A-DNA

A

A-DNA is NOT perpendicular to the helix axis while B-DNA IS

75
Q

which form of DNA is left handed

A

Z-DNA

76
Q

which has the least and most base pairs per helical turn

A

least- B-DNA

most Z-DNA

77
Q

which is more functional, DNA or RNA

A

RNA

78
Q

what does mRNA do?

A

product of transcription, encodes proteins

79
Q

what does rRNA do?

A

structural and enzymatic component, translation machine

80
Q

what does tRNA do?

A

loads amino acids into the ribosome

81
Q

how is the second DNA sequence strand written

A

it is complementary to the original, the 5’ and 3’ are written in the opposite direction

82
Q

What is the most common form of RNA structure

A

stem loop

83
Q

what forms of RNA are involved in protein synthesis

A

tRNA and rRNA

84
Q

what causes nucleic acid strands to separate (denature)

A

heat and alkani

85
Q

what are helicases

A

use energy to pry apart DNA strands to access the genetic info

86
Q

what is hybridization of nucleic acids

A

complementary single-strand can reform double stranded molecules

87
Q

what is the job of DNA polymerase

A

makes new strands by adding free nucleotides to the 3’ daughter strand (dsDNA, not ssDNA)

88
Q

molecular cloning

A

isolation of a DNA sequence and its insertion into a vector for propagation

89
Q

what are plasmid vectors

A

small DNA circles that are physically separated from chromosomal DNA and can replicate independently

90
Q

how does temperature fluctuate based on percentage of G-C

A

the temp rises as percentage of C-G increased

91
Q

what are restriction enzymes

A

bacterial enzymes found in bacteria, that protect from bacterial viruses called phages

92
Q

how do restriction enzymes work

A

recognize, blind to, and cut short specific sequences, that are palindromic (can be read the same forward or backward)

93
Q

what is an isoschizomer

A

new restriction enzyme that that cuts the same sequence as a known restriction enzyme

94
Q

why doesn’t bacterial DNA get degraded by restriction enzymes

A

bacteria produced and add methyl groups to the sequence, preventing digestion by the restriction enzyme

95
Q

by what are digested restriction enzymes catalyzed

A

DNA ligase

96
Q

how do sticky ends play a role in the RE catalyzation

A

overhang of complementary single stranded sticky ends

97
Q

explain plasmids transformation and selection processes

A
  • ligation products are placed into bacteria
  • heat shock
  • some bacteria then takes up the plasmid (some don’t)
  • place bacteria on antibiotic plate
  • bacteria with a plasmid are capable of making a colony
98
Q

explain blue-white screening

A

blue color can be detected of the colonies with a x-gal chemical

99
Q

what is a genome

A

genetic material of an organism (DNA in all organisms)

100
Q

which chromosomes are linear and which are circular

A 
prokaryotic = similar 
eukaryotic = linear
101
Q

explain genome coding

A

regions that encode m/t/rRNA

102
Q

explain genome functional non-coding

A

regions that regulate gene expression, do not encode protein sequences

103
Q

explain nonfunctional genome coding

A

transposable elements–DNA sequence that can change its position in the genome

104
Q

describe the relationship between genome size/ gene number and organism complexity and EXPLAIN

A

there is no relationship between the two. A majority of DNA in large eukaryotic genomes is not protein coding

105
Q

non-protein coding DNA encodes

A

tRNA, rRNA, and regulatory RNA

106
Q

whats a promoter

A

binding sites for general transcription factors

107
Q

whats an enhancer

A

binding site for sequence-specific transcription factors

108
Q

how does the enhancer find the promoter

A

DNA looping

109
Q

whats an insulator

A

site that forms a boundary between different chromatic structures or enhancers

110
Q

whats a silencer

A

denies gene expression

111
Q

what are centromeres

A

part of chromosome thats responsible for cells ability to properly segregate sister chromatids during cell division

112
Q

what are telomeres

A

the ends of eukaryotic linear chromosomes that contain repeated DNA sequences

113
Q

ribosome function

A

synthesize proteins in the cell

114
Q

what percent of RNA is rRNA

A

80-90 percent in a cell

115
Q

a single copy of a human genome has about how many rDNA genes

A

200 ish

116
Q

what are nucleolar organizer regions

A

genome regions that contain clusters of rDNA genes

117
Q

what is a transposable element

A

“jumping gene” that can change its genomic location

118
Q

what are the 2 classes of TEs

A 
class 1: copy and paste
class 2: cut and paste
119
Q

TEs make up about what percentage of the human genome

A

44 percent

120
Q

how were TEs discovered

A

found insertions that could change the color of maize kernels, but “crossing” genetics

121
Q

what happens to the kernel color gene when Ds is involved

A

it becomes inactivated

122
Q

what connection did McClintock find between kernel color and element movement

A

kernel color correlated with Ds element movement by specific breaks in chromosomes

123
Q

what comprises the majority of non-protein coding DNA in most eukaryotes

A

transposable elements

124
Q

what 2 chromosomal sites were required to observe jumping behavior of TEs

A

dissociation element Ds

Activator element Ac

125
Q

what energizes the Ds to make it move

A

The Ac element supplies transposase

126
Q

describe class 1 TE

A

DNA is copied into a RNA intermediate and placed back into genome at a new site

127
Q

describe class 2 TE

A

DNA is cut out, with NO intermediate and placed back into the genome at a new site

128
Q

what is the human genome project

A

sequenced the entire human genome within 15 yrs with billions of dollars

129
Q

what is the most abundant TE in the human genome

A

Alu, about 10.7 percent

130
Q

most bacteria TEs use what class mechanism

A

cut and paste (class 2)

131
Q

what is a mutagen

A

something that causes mutations

132
Q

TEs can cause mutations by

A

jumping into a gene, causing the it to become nonfunctional

improper repair of DNA gaps, cause by its leaving

133
Q

what are real life example of diseases that TEs can cause

A

cystic fibrosis, cancer, hemophilia etc

134
Q

pseudogenes

A

relatives of functional genes that lost expression/ ability to encode proteins

135
Q

what are the 3 types of pseudogenes

A

processed
unprocessed
unitary

136
Q

what was the first significant part of the human genome to be sequences

A

mitochondria DNA

137
Q

why are organelle genomes circular

A

endsymbiotic theory, resembling bacterial genomes

138
Q

explain processed pseudogenes

A

created by reverse transcription, which integrated back into genome without mutation sequences, therefore are dead on arrival

139
Q

how are non-processed pseudogenes created

A

gene duplication

140
Q

how were unitary pseudogenes created

A

bu disabling mutations in a gene, not involving reverse transcription or duplication

141
Q

what shape does mitochondria and plastids take on

A

circular

142
Q

human mtDNA encodes how many genes

A

37

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