Lecture Final Study Flashcards
1
Q
What are the seven characteristics of living things?
A
Homeostasis Energy usage/metabolism Reproduction Organization Growth and development Adaptation Stimuli response
2
Q
Which four elements compose 95% of living material?
A
carbon, hydrogen, oxygen, nitrogen
3
Q
Who published the cell theory?
A
Matthias Schleiden and Theodor Schwann
4
Q
List hydrogen bonds, ionic bonds, covalent bonds, and van der Waals interactions in order from strongest to weakest bond type
A
covalent > ionic > hydrogen > van der Waals interactions
5
Q
hydrophilic functional groups
A
carboxyl, phosphate, hydroxyl, amino, carbonyl
6
Q
hydrophobic functional groups
A
methyl and thiol (sulfyhydryl)
7
Q
protein monomer
A
amino acid
8
Q
protein bond type
A
peptide bond
9
Q
carbohydrate monomer
A
saccharide
10
Q
carbohydrate bond type
A
glycosidic linkage
11
Q
nucleic acid monomer
A
nucleotide
12
Q
nucleic acid bond type
A
phosphodiester bond
13
Q
when amino acids are polymerized, covalent bonds form between which two functional groups?
A
amino and carboxyl
14
Q
what type of bond forms between the glycerol head and fatty acid tails of a triglyceride?
A
ester linkage
15
Q
primary protein structure
A
bonds between amino acids (peptide bonds), looks like a straight chain
16
Q
secondary protein structure
A
involves hydrogen bonding between the amino acid backbones, looks like alpha helixes or beta-pleated sheets
17
Q
tertiary protein structure
A
folding occurs due to side-chain interactions, looks like a clump or knot
18
Q
quaternary protein structure
A
involves 2+ protein chains bonded to each other
19
Q
Anton Van Leeuwenhoek was the first to observe what?
A
living organisms under a microscope
20
Q
Glycolysis
location
A
cytoplasm
21
Q
Glycolysis
substrates
A
1 glucose
2 ATP
22
Q
Glycolysis
products
A
2 pyruvate
2 NADH
4 ATP
23
Q
Glycolysis
ATP production process
A
substrate-level phosphorylation
24
Q
Pyruvate Oxidation
location
A
intermembrane space of the mitochondria
25
# Pyruvate Oxidation
substrates
2 pyruvate
26
# Pyruvate Oxidation
products
2 Acetyl CoA
2 NADH
2 CO2
27
# Krebs Cycle
location
mitochondrial matrix
28
# Krebs Cycle
substrates
2 Acetlyl CoA
29
# Krebs Cycle
products
6 NADH
2 FADH2
4 CO2
2 ATP
30
# Krebs Cycle
ATP production process
substrate-level phosphorylation
31
# Electron Transport Chain
location
inner mitochondrial membrane space
32
# Electron Transport Chain
substrates
3 O2
10 NADH
2 FADH2
33
# Electron Transport Chain
products
6 H2O
| 28 ATP
34
# Electron Transport Chain
ATP production process
oxidative phosphorylation
35
What molecule transports electrons and hydrogen ions from glycolysis and the Krebs cycle to the ETC?
NAD+
36
helicase function
opens DNA helix by breaking h-bonds between nucleotide pairs to separate the DNA during DNA replication
37
primase function
provides 3' end for adding new nucleotides during DNA replication
38
topoisomerase function
nicks DNA to relieve tension from unwinding during DNA replication
39
DNA polymerase III
adds nucleotides to an RNA primer or existing DNA strand during DNA replication
40
DNA polymerase I function
removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides at the adjacent fragment during DNA replication
41
DNA ligase function
links Okazaki fragments to form a continuous strand
42
indicate the hierarchy of DNA organization in eukaryotic cells
double helix > nucleosomes > chromatin fibers > looped domains > chromosomes
43
splice-o-some complex function
to process pre-mRNA into mRNA by removing introns and adding the Poly A tail and 5' cap
44
what is the start codon's amino acid?
methionine
45
ribosomes use ____ to produce ____________ based on the ____ copy of DNA code
tRNA; polypeptides; mRNA
46
where do most proteins reside in a cell?
cytoplasm
47
three process involved in synthesizing proteins from genes
1. Transcription
2. RNA processing
3. Translation
48
what is the purpose of transcription?
RNA copy of DNA is made
49
what happens during transcription?
- Template Strand: contains gene to be expressed
- RNA Polymerase: creates a complimentary RNA strand of the template strand
- rNTPs: Used as building blocks for the primary transcript
- pre-mRNA/primary transcript: The exact complimentary RNA strand created by
RNA polymerase
50
RNA processing purpose
RNA is added or deleted to make mRNA
51
what happens during RNA Processing?
- splice-o-somes remove introns, adds 5' cap to the 5' end to help ribosomes locate the beginning of the mRNA molecule more quickly, adds 3' Poly Adenine tail to aid in stability
- mRNA: contains sequences necessary for protein synthesis
- preMRNA/primary transcript: the exact complimentary RNA strand created by RNA polymerase
52
translatio purpose
turning RNA into proteins
53
what happens during translation?
- mRNA: contains sequences necessary for protein synthesis, contains codons to be translated at the ribosomes into polypeptides
- ribosomes: protein complexes that mRNA runs through and acts as a vessel for protein synthesis
- tRNA: matches codon sequences to their corresponding amino acids to create polypeptides
- C-terminus and N-terminus: completes and stabilizes the polypeptide chain produces at the ribosomes
54
what does the regulatory gene code for in prokaryotes?
repressor protein
55
what was the first DNA sequencing method?
Sanger sequencing method
56
what are the structures that resemble beads on a string when DNA is in Euchromatin form?
nucleosomes
57
who discovered the operon model?
Francois Jacob and Jacques Monod
58
for gene regulation in eukaryotes, transcription factors bind to
promotor proximal element
59
promotor-proximal element definition
any regulatory sequence in eukaryotic DNA that is located near (within 200 bp) a promoter
60
what form of control is a bacterial inducible operon?
negative control
61
in prokaryotic operons, what does RNA polymerase bind to?
promoter sequence
62
in prokaryotic operons, which molecule binds to the operator sequence?
regulatory molecules (repressor protein)
63
The condensation of DNA into heterochromatin prevents _____________ because genes cannot be accesed
transcription
64
examining the metabolism of tryptophan led to the discovery of:
the repressible operon
65
what binds to the leader segment of an mRNA molecule to regulate protein synthesis by preventing the mRNA from binding to a ribosome?
a regulator protein
66
nucleosomes are formed by winding a DNA strand around:
histones
67
when an _________ _______ binds to the ________ ________ of a eukaryotic gene, the transcription rate increases
activator protein; enhancer sequence
68
what does PCR stand for?
polymerase chain reaction
69
what is the purpose of PCR
to make several copies of one specific sequence of DNA
70
denaturing step
- 95 degrees celsius
| - hydrogen bonds are broken in the DNA molecule
71
annealing step
- temperature is lowered to 60 degrees celsius
| - primers bond to template DNA
72
extension step
- temperature is raised to 73 degrees celsius
| - Taq Polymerase makes new complementary strands
73
what is a genomic library?
A collection of bacteria cells transformed with plasmids composed of recombinant DNA.
74
what is the function of ddNTPs?
dideoxynucleotide triphosphates remove a hydroxyl group from a nitrogenous base, halting DNA synthesis
75
what process are ddNTPs used for?
Sanger method of DNA sequencing
76
what resources do you need for DNA sequencing?
- gel electrophoresis
- PCR
- ddNTP
- restriction enzymes
- DNA polymerase
- genomic library
77
what is the function of reverse transcriptase?
to allow a virus to be in the form of RNA and not DNA; it makes DNA without introns from RNA
-makes cDNA to be amplified by PCR
78
who was the first person to sequence an entire human genome?
John Craig Venter
79
fruit fly scientific name
Drosophila melanogaster
80
zebra fish scientific name
Danio rerio
81
in order for genes from two different organisms to be combines, they must be cut by..
the same restriction enzyme
82
genes are not expressed when a _________ _______ attaches to the control region in the operon
repressor protein
83
proteasome
a protein complex that breaks down proteins that are tagged by ubiquitin
84
the nucleic acid of a viral particle is enclosed in what?
capsid
85
what is the function of telomerase enzymes?
catalyzes the lengthening of the telomeres in eukaryotic germ cells, thus restoring their original length and compensating for the shortening that occurs during DNA replication
86
in order to create a transgenic bacterium through transformation, new genes are inserted into the _______
plasmid
87
pluripotent
capable of differentiating into many different cell types (but can only differentiate once)
88
John Dalton
wrote the atomic theory
89
Robert Hooke
made the first microscope
90
Anton Van Leeuwenhoek
viewed first living organism under microscope
91
Gregor Johann Mendel
studies patterns of inheritance in garden pea plants
92
Matthias Schleiden and Theodor Schwann
published the cell theory
93
Thomas Hunt Morgan
confirmed that genes are the hereditary units
94
Frederick Griffith
discovered DNA is the carrier of genetic information
95
Erwin Chargaff
ratios of adenine to thymine and cytosine to guanine are almost exactly equal
96
dNTPs
inserts nucleotides into the existing chain to generate a completely new DNA strand using the DNA polymerase enzyme
97
origins of replication
places in the DNA molecule where the strands seperate, forming bubbles that can be replicated on the inside
98
replication forks
where the origins of replication meet the regular DNA strand
99
primers
lays down RNA nucleotides to prepare for DNA polymerase, they are replaced with DNA nucleotides
100
primase
synthesizes primers
101
DNA polymerase
accurately and efficiently replicate the genome
102
phosphodiester bonds
bonds linking nucleotides together: joins a phosphate group in the pentose sugar of one nucleotide to the hydroxyl group in the pentose sugar of the next nucleotide
103
leading and lagging strands
leading strand goes from the 3' side to the 5' side
| lagging strand is replicated from the 5' side to the 3' side in chunks using Okazaki fragments
104
Okazaki Fragments
short fragments of DNA that are laid down on the lagging strand of DNA and later joined together by DNA ligase
105
helicase
opens helix
106
single strand binding proteins
wraps single-stranded DNA with high affinity to protect it from degradation and prevent secondary structure formation
107
DNA ligase
joins breaks in the phosphodiester backbone of DNA that occur during replication and recombination
108
DNA proofreading
1. DNA Polymerase (III) corrects as it goes and chops off incorrect piece and replaces with correct piece
2. "other" DNA repair enzymes (100+ known)
109
Methylation: directed mismatched base repair
1. where a mismatch occurs, the correct base is located on the methlyated strand; the incorrect base occurs on the unmethylated strand
2. enzymes detect mismatch and nick unmethylated strand
3. DNA Polymerase I excises nucleotides on unmethylated strand
4. DNA polymerase I fills in gap in 5' -> 3' direction
5. DNA ligase links new and old nucleotides
110
DNA Methylation
- addition of CH3 group to adenine molecules
| - identifies template strand
111
Excision Repair System
1. DNA nuclease: removes damaged nucleotide
2. DNA Polymerase (I): replaces with undamaged nucleotide
3. DNA ligase: joins phosphodiester bonds
112
DNA nuclease
catalyze cleavage of phosphodiester bonds
113
telomeres
a sequence of repetitive base pairs that prevent a DNA molecule from losing its length
114
telomerase enzymes
an enzyme made of protein and RNA subunits that elongates chromosomes by adding TTAGGG sequences to the end of existing chromosomes; found in fetal tissues, adult germ cells, and also tumor cells
115
gene
specific sequences of DNA on a nucleic acid that codes for characteristics in an organism
116
DNA template strand
each original strand of DNA (unreplicated)
117
RNA polymerase
used during transcription:synthesizes RNA by following a strand of DNA
118
problem with linear DNA
5' ends are lost with each replication, so DNA molecules grow shorter and shorter with each replication
119
introns
DNA sequences that do not code for amino acids
120
exons
codons that dictate amino acid production
121
how many introns and exons are in a nucleic acid?
95% introns and 5% exons
122
splice-o-some complexes:
remove introns
123
5' cap
added to 5' end to help ribosomes locate the beginning of the mRNA molecule
124
Poly Adenine tail
aids in stability of the molecule
125
codon
3-nucleotide-long sequence that tells what amino acid to produce
126
anticodon
the RNA counterpart of a DNA molecule that is used to create the amino acid in a ribosome
127
ribosome small subunit
decodes genetic message
128
ribosome large subunit
catalyzes peptide bond formation (think of the video of the chain moving along and forming amino acid chains)
129
ribosomal RNA (rRNA)
non-coding RNA that helps to form ribosomes
130
biotechnology
the use of bacteria and viruses to create biological tools that can contribute to medicine
131
proteomics
the study of the entire complement of proteins that is or can be expressed by a cell, tissue, or organism
132
virus
- phage
- have proteins sticking out of them that only help them gain access to 1 cell
- viruses either have RNA inside or DNA
133
genome
the complete set of genes or genetic material present in a cell or organism
134
capsid
the thing that contains a virus's genetic material
135
retrovirus
any of a group of RNA viruses which insert a DNA copy of their genome into the host cell in order to replicate
136
reverse transcriptase
allows virus to be in the form of RNA, not DNA
137
spike proteins
allow the virus to enter a specific cell
138
viral envelope
outermost layer of many types of viruses
139
lytic cycle
- fast viruses
| - as soon as the virus enters the body, it immediately starts taking over cells
140
lysogenic cycle
- slow viruses
- sits in a cell and injects its DNA into the cell, and inserts itself into your DNA
- viral infection can last for years
141
provirus
the genetic material of a virus as incorporated into, and able to replicate with, the genome of a host cell
142
bacteriophage
viruses that infect bacteria and archaea
143
phytophage
viruses that infect plants
144
zoophage
viruses that infect animals
145
DNA loop
bacteria DNA is organized in a loop
146
plasmids
a genetic structure in a cell that can replicate independently of the chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium or protozoan; used in the laboratory manipulation of genes
147
bacterial transformation
a section of bacterial DNA is removed and replaced with DNA from another organism for storage
148
genomic DNA (gDNA)
original DNA with introns
149
complimentary DNA (cDNA)
a copy made from gDNA using reverse transcriptase that does not contain introns
150
restriction enzymes
cleaves DNA molecules at or near a certain sequence of bases (made by certain bacteria)
-used in Venter DNA sequencing
151
recombinant DNA
the method of joining two or more DNA molecules to create a hybrid
152
DNA sequencing
use of PCR, electrophoresis, ddNTPs to sequence a DNA molecule
153
Frederick Sanger
made it easier to sequence DNA
154
Sanger DNA sequencing improvements
1. use of fluorescently tagged ddNTPs
| 2. DNA fragments are seperated on mass-prouced capillary gels
155
ddNTPs
dideoxynucleoside triphosphates
- chemically similar to dNTPs
- remove a hydroxyl group from a nitrogenous base
156
John Craig Venter
used computer technology and PCR and electrophoresis to make the process of DNA sequencing go faster
157
Whole-Genome Shotgun Sequencing
- created by John Craig Venter, requires restriction enzymes, genomic library, enhanced Sanger method, and computer technology
1. cut DNA into overlapping fragments short enough for sequencing
2. clone the fragments in plasmid or phage vecots
3. sequence each fragment
4. order the sequences into 1 overall sequence with computer software
158
human genome project
multi-million dollar project to sequence the entire human genome
159
RFLP
random fragment length polymorphisms
- variations among people in their DNA sequences at sites recognized by restriction enzymes
- used for crime scene stuff
160
short tandem repeats
- short repeated sequences of DNA (2–6 bp)
- number of repeat units is variable among individuals, which offers a high power of discrimination when analyzed for identification purposes
161
transposable elements
jumping genes
162
Francois Jacob and Jacques Monod
discovered operon gene control in prokaryotic cells
163
inducible operon
- lactose pathway
- as long as the repressor protein is filled by lactose, the gene for digesting lactose is on because lactose removes the repressor protein from the gene
- repressor protein attaches in between the promoter sequence and the structural gene
- inducible operons are off most of the time, unless the repressor protein is removed
164
repressible operon
- tryptophan pathway
- gene needs to be on most of the time
- excess tryptophan binds to repressor protein when it needs to stop being consumed
165
parts of an operon
- regulator gene
- promoter sequence
- operator sequence
- structural gene
166
regulator gene
codes for synthesis of a repressor molecule that binds to the operator and blocks RNA polymerase from transcribing the structural genes
167
repressor protein
inhibits the expression of one or more genes by binding to the promoter sequence
168
promoter sequence
DNA sequences that define where transcription of a gene by RNA polymerase begins
169
terminator sequence
DNA sequences that define where transcription of a gene by RNA polymerase ends
170
structural gene
the gene that codes for the production of an amino acid chain
171
eukaryotic transcription unit
Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of transportable complementary RNA replica
172
positive control
requires transcription factors to turn on a gene
173
promoter proximal element
any regulatory sequence in eukaryotic DNA that is located close to (within 200 base pairs) a promoter and binds a specific protein thereby modulating transcription of the associated protein coding gene
174
transcription factors
proteins that attach RNA polymerase to the promoter sequence
175
activator proteins
consist of two main domains: a DNA-binding domain that binds to a DNA sequence specific to the activator, and an activation domain that functions to increase gene transcription by interacting with other molecules
176
enhancer sequence
a DNA sequcne that enhances the transcription of a gene
| -activator proteins bind to the enhancer sequence
177
transcription level control
-determines whetehr DNA can be reached by transcription factors
178
euchromatin
transcription is possible when DNA is in this form
179
heterochromatin
transcription is prevented when DNA is in this form
180
histones
wind DNA into nucleosomes
181
nucleosomes
a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones
182
DNA methylation
- addition of methyl (-CH3) groups to nitrogenous bases of DNA
- prevents transcription
- long-term inactivation of genes
- methylated genes are passed on to daughter cells
183
histone acetylation
- addition of CH3COO gropus to amino acids of histones
- acetelyated histones hold DNA less tightly
- gives easier access to genes in an acetylated region
- prevents DNA from becoming heterochromatin
184
post-transcription level control
1. RNA processing
| 2. mRNA degradation
185
RNA processing
- alternative splicing of mRNA
| - splice-o-some complex takes out multple introns and and a some exons out, which goes on to form alternative proteins
186
mRNA degradation
- trailer segment of mRNA determines stability
- a poly A tail: a long train of adenines at the end of mRNA that creates a more stable mRNA
- cells can determine how strong a gene expression is
187
translation level control
1. regulatory proteins
188
regulatory proteins
- bind to mRNA leader segments
- prevents ribosomes from binding
- useful if you have 2 cells with similar characteristics, but a gene should only be made in one, so the regulatory proteins should only be found in the other one
189
post-translation level control
1. protein passing and degradation
| 2. affecting concentration of active enzymes
190
protein processing and degradation
1. cleavage activation
2. phosphorylation activation
3. transport to activating environment
4. change concentration of active enzymes
191
cleavage activation
- more effective than cofactors
- if the protein/enzyme is not meant to be used yet, a piece can be added to it in order to prevent the substrate from binding to it
192
phosphorylation activation
activates a protein or turns it off with kinase
193
transport to activating environment
some proteins are denatured the moment they are produced because they were produced in the wrong pH environment, so to save it they are transported to an environment with the right pH
194
ubiquitin
tags a protein for destruction by proteasome
| -needs 3 molecules of ubiquitin to be tagged
195
proteasome
protein shredder
| -degrades proteins
196
affecting concentration of active enzymes
1. create/destroy
2. change reaction environment
3. activate/deactivate existing enzymes
4. localization/containment
197
model organisms
organisms that represent other organisms for genetic purposes
198
Drosophila melanogaster
fruit fly; representative of all flying insects
199
Mus musculus
mouse; representative of vertebrates
200
Caenorhabditis elegans
nematode worm; representative of invertebrates
| -transparent body so good for studying
201
Danio rerio
zebrafish; representative of all fish
| -transparent during enbryonic stage
202
Arabidopsis thaliana
wall cress plant; representative of plants
