exam 1 info Flashcards
(142 cards)
1
Q
what functions do proteins carry out
A
catalyze reactions form cellular structures transmit signals carry oxygen repair damaged DNA
2
Q
why are enzymes used
A
to speed up reactions
3
Q
“ase” means what
A
enzyme
4
Q
what is the the cytoskeleton and its purpose
A
network of filaments and helps regulate a cell’s shape
5
Q
what is the primary level of structure
A
linear sequence of amino acids joined covalent peptide bonds. Disordered and folded string
6
Q
what is the second level of structure
A
hydrogen bonds of nearby amino acids
7
Q
what is the tertiary level of structure
A
entire 3D structure of a protein. non-covalent bonds
8
Q
what is the quaternary level of structure
A
multiple smaller proteins interacting to form one large protein
9
Q
how does the identity change by the varying structure levels
A
- straight chain
- beta sheet
- jumbled protein
- several proteins jumbled
10
Q
what are the components of an amino acid structure
A
amino group
alpha carbon
carboxyl group
r group/ side chain
11
Q
why does the acidity of proteins matter?
A
many proteins act as enzymes
12
Q
what is pepsin
A
stomach enzyme that is very acidic
13
Q
what is salivary amylase
A
saliva, neutral, slightly acidic
14
Q
what is alkaline phosphatase
A
bones, very basic
15
Q
what is the primary protein structure
A
linear sequence of amino acids, joined by covalent peptide bonds
16
Q
what is the secondary protein structure
A
local interactions between nearby amino acids with non-covalent hydrogen bonds
17
Q
what is the tertiary protein structure
A
the entire 3D structure of a protein, generally mediated by non-covalent bonds
18
Q
what is quaternary protein structure
A
interaction of multiple smaller proteins, to form one large protein
19
Q
how are covalent peptides formed
A
energy-requiring condensation (aka dehydration reaction), that produces water
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
21
Q
what characterizes the beta-strand
A
segment of 5-20 amino acids that make up the peptide background
22
Q
what characterizes the beta-sheet
A
segment of 2-6 beta strands running parallel to one another. held together by hydrogen bonds
23
Q
what are the amino acids that have high helix-forming potential
A
(MALEK) Methionine, alanine, leucine, glutamic acid, lysine
24
Q
what amino acids disrupt helices
A
proline (bc easily breaks) and glycine (bc energy costly)
25
what is the coiled coil
structure formed by the interaction of 2+ a-helices, found in proteins
26
coiled coil characteristics
very strong
| found in proteins that need the strength, such as muscles, hair, and blood clot fibrin
27
beta sheet parallel vs antiparallel
parallel-- sequence matches from left to right
| anti-parallel-- sequence turns in opposite direction every other strand
28
the parallel beta sheet is often finds what amino acids
proline
29
what are the super-secondary structures
hairpin turn
helix-loop-helix
beta-alpha-beta unit
greek key
30
whats the hydrophobic collapse
pulls a string of hydrophobic molecules together when in water. hydrophilic molecules shift the strand to surround the hydrophobic molecules on the inside
31
purpose of myoglobin
carries oxygen to the muscles
32
how does a protein embed itself into a lipid bilayer, with regards to water sustainability
the potions of hydrophilic and hydrophobic amino strands correspond to their most comfortable locations in the bilayer
33
what are van der waals forces and their characteristics
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
34
what bonds are the strongest and can hold over a long distance range
covalent
35
the oxidation of 2 cysteines creates what?
a cystine
36
what are discrete protein domains
part of a given protein sequence that exist and function independently from the rest of the protein strand.
37
how are protein domains created
they are added, restricted, or part of it is duplicated
38
domains are a part of what part of the protein structure?
tertiary
39
what is the x-ray crystallography used for
to determine protein identity
40
what is the quaternary protein structure
arrangement of multiple subunits into a larger protein complex
41
how is the quaternary protein structure stabilized
```
hydrogen bonds
ionic bonds
van der waals forces
hydrophobic interactions
(sometimes by covalent disulfide bonds
```
42
what form of protein structure does hemoglobin example?
quaternary bc it is composed of proteins
43
electrophoresis purpose/ procedure
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
44
what is the solution used in electrophoresis and it's properties?
sodium dodecyl sulfate. negatively charged
| has hydrophobic side and hydrophilic side
45
what is western blotting
technique to identify and locate specific individual proteins in a sample of membrane
46
what is the central dogma of molecular biology
```
DNA
copies itself through replication
transcription
translation
polypeptide is formed\
```
DNA-> RNA -> protein
47
what are the purines
adenine and guanine
48
what are the pyrimidine
thymine and cytosine
49
what is a deoxyribonucleoside
base plus a sugar molecule
50
what is a deoxyribonucleotide
deoxyribonucleoside plus 1-3 phosphate groups
| called mono, di, or triphosphate
51
what direction does DNA go?
5' to 3' direction
52
what is a phosphodiester bond
nucleosides joined together by a common phosphate group
53
what is a prerequisite to adding onto the DNA strand
3' end has to be free to add anything on to the strand
54
What is the tetranucleotide hypothesis
levene discovering the 4 bases, deoxyribose, and phosphate. Believed DNA was composed of equal amounts of A, C, G, T in repetition
55
explain the transforming principle experiment
- 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
56
what was the outcome of the transforming principle? what did it tell us?
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
57
what supports DNA as the transforming principle
treatment of s cells with deoxyribonuclease eliminated transforming activity
58
whats the purpose of bacteriophage infection
it's on form of replication
59
explain the process of lytic bacteriophage infection
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
what did the hershey-chase experiment study?
studied if proteins or DNA were the genetic material
61
method of hershey-chase experiment
injected sulfur labeled proteins vs injected phosphorus labeled DNA
62
what was the outcome of the hershey-chase experiment
experiment supported DNA as the hereditary genetic material
63
what did chargaff discover while studying DNA
DNA has varying molar amounts, countering tetranucleotide hypothesis of all 4 bases being equal
64
what is chargaffs rule
double stranded DNA must have equal A-T concentrations and G-C concentrations
65
in what direction does the two strands of DNA twist?
right handed twist, antiparallel
| one goes 3'-5' and other goes 5'-3'
66
how many hydrogen bonds do the bases have
A and T have 2 H bonds
| G and C have 3 H bonds
67
what make up the backbone of the helix?
phosphate and deoxyribose
68
what is the helix diameter
2.0 nanometers
69
the structure repeats itself after how many base pairs
about 10.5
70
which ends of the DNA strands have a phosphate group and an OH
5' has phosphate
| 3' has OH
71
the watson crick form of DNA is referred to as what?
B-DNA
72
what is the most compact form of DNA
A-DNA
73
what is the dominant form of DNA
B-DNA
74
what is the major difference between B-DNA and A-DNA
A-DNA is NOT perpendicular to the helix axis while B-DNA IS
75
which form of DNA is left handed
Z-DNA
76
which has the least and most base pairs per helical turn
least- B-DNA
| most Z-DNA
77
which is more functional, DNA or RNA
RNA
78
what does mRNA do?
product of transcription, encodes proteins
79
what does rRNA do?
structural and enzymatic component, translation machine
80
what does tRNA do?
loads amino acids into the ribosome
81
how is the second DNA sequence strand written
it is complementary to the original, the 5' and 3' are written in the opposite direction
82
What is the most common form of RNA structure
stem loop
83
what forms of RNA are involved in protein synthesis
tRNA and rRNA
84
what causes nucleic acid strands to separate (denature)
heat and alkani
85
what are helicases
use energy to pry apart DNA strands to access the genetic info
86
what is hybridization of nucleic acids
complementary single-strand can reform double stranded molecules
87
what is the job of DNA polymerase
makes new strands by adding free nucleotides to the 3' daughter strand (dsDNA, not ssDNA)
88
molecular cloning
isolation of a DNA sequence and its insertion into a vector for propagation
89
what are plasmid vectors
small DNA circles that are physically separated from chromosomal DNA and can replicate independently
90
how does temperature fluctuate based on percentage of G-C
the temp rises as percentage of C-G increased
91
what are restriction enzymes
bacterial enzymes found in bacteria, that protect from bacterial viruses called phages
92
how do restriction enzymes work
recognize, blind to, and cut short specific sequences, that are palindromic (can be read the same forward or backward)
93
what is an isoschizomer
new restriction enzyme that that cuts the same sequence as a known restriction enzyme
94
why doesn't bacterial DNA get degraded by restriction enzymes
bacteria produced and add methyl groups to the sequence, preventing digestion by the restriction enzyme
95
by what are digested restriction enzymes catalyzed
DNA ligase
96
how do sticky ends play a role in the RE catalyzation
overhang of complementary single stranded sticky ends
97
explain plasmids transformation and selection processes
- 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
explain blue-white screening
blue color can be detected of the colonies with a x-gal chemical
99
what is a genome
genetic material of an organism (DNA in all organisms)
100
which chromosomes are linear and which are circular
```
prokaryotic = similar
eukaryotic = linear
```
101
explain genome coding
regions that encode m/t/rRNA
102
explain genome functional non-coding
regions that regulate gene expression, do not encode protein sequences
103
explain nonfunctional genome coding
transposable elements--DNA sequence that can change its position in the genome
104
describe the relationship between genome size/ gene number and organism complexity and EXPLAIN
there is no relationship between the two. A majority of DNA in large eukaryotic genomes is not protein coding
105
non-protein coding DNA encodes
tRNA, rRNA, and regulatory RNA
106
whats a promoter
binding sites for general transcription factors
107
whats an enhancer
binding site for sequence-specific transcription factors
108
how does the enhancer find the promoter
DNA looping
109
whats an insulator
site that forms a boundary between different chromatic structures or enhancers
110
whats a silencer
denies gene expression
111
what are centromeres
part of chromosome thats responsible for cells ability to properly segregate sister chromatids during cell division
112
what are telomeres
the ends of eukaryotic linear chromosomes that contain repeated DNA sequences
113
ribosome function
synthesize proteins in the cell
114
what percent of RNA is rRNA
80-90 percent in a cell
115
a single copy of a human genome has about how many rDNA genes
200 ish
116
what are nucleolar organizer regions
genome regions that contain clusters of rDNA genes
117
what is a transposable element
"jumping gene" that can change its genomic location
118
what are the 2 classes of TEs
```
class 1: copy and paste
class 2: cut and paste
```
119
TEs make up about what percentage of the human genome
44 percent
120
how were TEs discovered
found insertions that could change the color of maize kernels, but "crossing" genetics
121
what happens to the kernel color gene when Ds is involved
it becomes inactivated
122
what connection did McClintock find between kernel color and element movement
kernel color correlated with Ds element movement by specific breaks in chromosomes
123
what comprises the majority of non-protein coding DNA in most eukaryotes
transposable elements
124
what 2 chromosomal sites were required to observe jumping behavior of TEs
dissociation element Ds
| Activator element Ac
125
what energizes the Ds to make it move
The Ac element supplies transposase
126
describe class 1 TE
DNA is copied into a RNA intermediate and placed back into genome at a new site
127
describe class 2 TE
DNA is cut out, with NO intermediate and placed back into the genome at a new site
128
what is the human genome project
sequenced the entire human genome within 15 yrs with billions of dollars
129
what is the most abundant TE in the human genome
Alu, about 10.7 percent
130
most bacteria TEs use what class mechanism
cut and paste (class 2)
131
what is a mutagen
something that causes mutations
132
TEs can cause mutations by
jumping into a gene, causing the it to become nonfunctional
| improper repair of DNA gaps, cause by its leaving
133
what are real life example of diseases that TEs can cause
cystic fibrosis, cancer, hemophilia etc
134
pseudogenes
relatives of functional genes that lost expression/ ability to encode proteins
135
what are the 3 types of pseudogenes
processed
unprocessed
unitary
136
what was the first significant part of the human genome to be sequences
mitochondria DNA
137
why are organelle genomes circular
endsymbiotic theory, resembling bacterial genomes
138
explain processed pseudogenes
created by reverse transcription, which integrated back into genome without mutation sequences, therefore are dead on arrival
139
how are non-processed pseudogenes created
gene duplication
140
how were unitary pseudogenes created
bu disabling mutations in a gene, not involving reverse transcription or duplication
141
what shape does mitochondria and plastids take on
circular
142
human mtDNA encodes how many genes
37
