Unit 6 Flashcards
1
Q
purines
A
two-ring structures
- adenine and guanine
2
Q
pyrimidines
A
single-ring structures
- thymine, cytosine, uracil
3
Q
nucleic acid strands are always _____, no matter the interaction
A
antiparallel
4
Q
nucleic acids
A
- encode exactly what is passed on from parent to offspring cell
- phosphate group, ribose sugar, nitrogenous base
- phosphate + sugar = backbone
5
Q
DNA REPLICATION
A
- can only add to 3’ end
- begins at site called the origins of replication
6
Q
helicase
A
- enzyme that unwinds DNA
- causes tighter twisting ahead of the replication fork
7
Q
topoisomerase
A
enzyme that helps relieve tension created from untwisting
- breaks and reforms the DNA strands
8
Q
RNA primase
A
puts RNA primer onto one of the split ends
- starts replication
- more primer added as fork (section of RNA) gets bigger
9
Q
DNA polymerase
A
- catalyzes the elongation of new DNA at the replication fork
- adds new nucleotides one by one to their 3’ ends
10
Q
leading strand
A
replication occurs continuously along the 5’ - 3’ strand
11
Q
lagging strand
A
the other strand (3’ - 5’)
- copied in a series of segments in a process called discontinuous replication
- fragments called okazaki fragments
12
Q
DNA ligase
A
seals the okazaki fragments to make the new DNA
13
Q
because DNA polymerase can add nucleotides only to the 3’ end of a molecule,
A
it cannot complete the 5’ end of the DNA molecule at the end of the chromosome
- to avoid losing terminal genes due to degradation over time, the linear ends of eukaryotic chromosomes are capped with telomeres
14
Q
telomeres
A
have repetitive nucleotide sequences but do not have genes
15
Q
in tumor cells, a mutation activates telomerase, which prevents ______ of telomeres and renders the cancer cells ______
A
degradation ; immortal
16
Q
semi conservative replications
A
keeps some of the original DNA
17
Q
conservative replication
A
keeps all of the original DNA
18
Q
dispersive replication
A
keeps none of the original DNA
19
Q
bacterial chromosome
A
a double-stranded, circular DNA molecule associated with a small amount of protein
20
Q
eukaryotic chromosomes
A
linear DNA molecules associated with large amounts of protein
21
Q
TRANSCRIPTION
A
the process of copying a segment of DNA into RNA for the purpose of gene expression
22
Q
as DNA becomes more highly packed, it becomes ______ accesible to transcription enzymes, which reduces gene expression
A
less
23
Q
when chromatin condenses to chromosomes during mitotic division, the more condensed chromatin is ________ available for transcription
A
no longer
24
Q
TRANSLATION
A
of an mRNA transcript to produce a polypeptide chain (in ribosomes)
25
mRNA
- produced during transcription to send messages to ribosomes to make proteins
- results in pre-mRNA which undergoes mRNA processing to produce mRNA (prokaryotes produce non-processed DNA
- has introns and extrons
26
translation and transcription can occur at the same times (T/F)
true
27
gene expression:
process by which DNA directs the synthesis of proteins (or sometimes RNA)
- transcription then translation
28
alternative RNA splicing
introns are not useful and therefore are cut out
29
one gene-one polypeptide hypothesis
states that each gene codes for a polypeptide, which can be, or constitute of, a protein
30
central dogma of biology
DNA -> RNA -> protein
31
triplet code
the instructions of building a polypeptide chain are written as a series of three-nucleotide groups called codons for each amino acid
- contribute to the reading frame
32
after transcription, the mRNA that is produced is _______ to the original DNA’s template strand
complementary
- ribosome sees this code and translates it into a protein (translation)
33
coding strand
exact same as mRNA strand
- also called sense or non-template strand
34
35
one of the mRNA triplets serves as the ____ codon and four serve as the ____ codon, while the rest of the combinations all code for specific amino acids
START ; STOP
36
the genetic code is redundant, because:
there are only 20 amino acids, so some of them are coded for by more than one codon
- also nearly universal, being powerful evidence for the common ancestry of all living organisms
37
prokaryotes have no nucleus or compartmentalization, so RNA can go straight into _______ to make protein
ribosomes
38
transcription factors
assist the binding of RNA polymerase to the promoter so transcription may begin
39
transcription unit
entire stretch of DNA that is transcribed into an RNA molecule
- may code for a type of RNA, or a protein
40
after transcription:
addition of 5’ cap and poly-A tail
- both facilitate exportation, and protect from degradation by enzymes, and facilitate the attachment of the mRNA to the ribosome
41
5’ cap
modified guanine nucleotide (GTP) that is added to the 5’ end of the mRNA
42
poly-A tail
group of 50 to 250 adenine nucleotides added to the 3’ end
43
spliceosome
composed of small RNAs and proteins
- leftover exons after RNA splicing are spliced together by ____
44
an intron removed in the production of one polypeptide (can/cannot) be an exon in a second polypeptide
can
45
alternative RNA splicing
allows for different combos of exons, resulting in more than one polypeptide per gene
46
ribozyme
a small RNA molecule that serves a catalytic role
47
tRNA
transfers amino acids from cytoplasm to the mRNA at the ribosome during translation
- amino acid on top, anticodon on bottom to code with complementary codon on mRNA
48
ribosome
- composed of rRNA and protein
- P site of large subunit holds the tRNA that carries the growing polypeptide chain
- binds to mRNA to build protein based on amino acid code
49
translation steps
1. initiation: small ribosomal subunit binds to mRNA, tRNA hydrogen bonds to AUG (START), large subunit attaches
2. elongation: codon recognition, peptide bond formation, translocation
3. termination: STOP codon is reached, translation stops, release factor protein binds to STOP, polypeptide is freed
50
polypeptides are _______ modified further to render them functional
almost always
51
signal polypeptide
sequence of about 20 amino acid at the leading end of a polypeptide chain that directs proteins to their final destination
52
MUTATIONS
- result in the process of natural selection
- caused by mutagens and carcinogens
53
point mutation
alteration of just one nucleotide base pair of a gene
- base pair = group of three nucleotides
54
frame shift mutation
causes the mRNA to be read incorrectly on each remaining codon
55
aneuploidy mutation
wrong # of chromosomes
56
REGULATION OF GENE EXPRESSION
57
every cell in an organism has the same genome, yet
not all genes are expressed in each cell type
58
patterns of gene expression are altered in response to:
internal signals as well as changes in environmental conditions
59
operon
- regulates how much protein is created
60
promoter region
DNA sequence at which RNA polymerase attaches
- followed by operator, which prevents further binding, where the repressor binds to
61
terminator
DNA sequence that signals the end of transcription
62
repressor protein
- produced by regulatory genes
- may bind to the operator site, blocking RNA polymerase from the genes on the operon
63
operon can activate transcription by:
adding activator before promoter and not repressor
- also enhancer section after operator where transcription factors can bind and regulate gene expression
64
if RNA polymerase cannot get to the genes, they (will/will not) be expressed
will not
65
lac operon
- an inducible operon
- codes for proteins that metabolize lactose
- bacteria produce only the enzymes needed to break down lactose when it is present, so lactose induces the expression of those enzymes
66
when lactose is in the body, it produces aloe lactose
- binds to that repressor, which causes it to dissociate from the operator so ENA polymerase can transcribe genes
67
allolactose
inducer (something that binds to a repressor/activator to cause gene to express)
- opposite called coverpress
68
inducible operon
- normally off
- usually catabolic, breaking down food molecules for energy
- to turn on, small molecule called induced must inactivate the repressor protein, taking it out of the operator site
69
repressive operon
- normally on
- normally anabolic, building an essential organic molecule
- produces enzymes that produce products the cell normally needs all the time
- environment can provide amino acid to turn off
70
EUKARYOTIC GENE EXPRESSION
71
differential gene expression
the expression of different genes by cells with the same genome
72
nucleosome
packaging unit of DNA, consists of histones
73
histones
- are what keep the DNA really coiled
- the more tightly bound DNA is to its _______, the less accessible it is for transcription
- more coiled = less activated
74
DNA methylation
addition of methyl group (CH3) to DNA -> more tightly packed -> less gene expression
75
histone acetylation
addition of acetyl groups to amino acids of histone proteins -> less tightly packed -> more gene expression
76
epigenetic inheritance
inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
- DNA sequence not changed, expression changed
- caused by methylation
77
transcription initiation process
- enhances gene expression
- enhancer regions bound to the promoter region by proteins called activators
78
eukaryotes do not have operon, instead they do thinks like control the rate of gene expression
79
RNA interference
small molecules of RNA can complex with protein and influence gene expression
80
zygote
a diploid cell resulting from the fusion of two haploid gametes
81
zygote undergoes these processes:
1. cell division
2. cell differentiation
3. morphogenesis
82
cell differentiation
the process by which cells become specialized in structure and function resulting from different activators and repressors in the cells
83
morphogenesis
gives and organism its shape
84
cytoplasmic determinants
- what controls cell differentiation and morphogenesis
- maternal substances in the egg that influence the course of early development
- distributed unevenly in early cells of embryo and result in different cells
- controls cell differentiation and morphogenesis
85
embryonic cells
cells found in embryos during their earliest stages of development
86
surrounding environment
- controls cell differentiation and morphogenesis
- as # cells increases, cell-cell signals result from molecules (such as growth factors) causing cells to differentiate
87
determination
the series of events that leads to observable differentiation of a cell
88
differentiation
when immature cells develop into mature cells with specific functions
- caused by cell-cell signals
- irreversible
- some programmed to die during process
89
pattern formation
sets up the body plan and is a result of cytoplasmic determinants and inductive signals
- uneven distribution of substances called morphogens plays into what looks like what
90
homeotic genes
master control genes that control several other genes at one time
91
proto-oncogenes
- code for normal cell growth
- become oncogenes when a mutation occurs that causes an increase in the product of the proto-oncogene or an increase in the activity of each protein molecule produced by the gene
92
p53 protein
a tumor-repressor gene (usually inhibits) that activated a group of miRNAs that inhibits the cell cycle
- activates apoptosis, etc.
93
VIRUSES
- smaller than ribosomes
- limited host range
94
essential components of a virus
**capsid**, which is a protein shell that surrounds the **genetic material**
95
many viruses found in animals have:
membraneous viral envelopes that surround the capsid and help infect hosts
96
two major types of viral reproduction:
lyric cycle and lysogenic cycle
97
lytic cycle
bacteriophage injects its DNA into host bacteria cell and takes over the cell’s machinery to synthesize new copies of it as well as protein coats, then bacterial cell is lysed, or ruptured
98
lysogenic cycle
bacteriophages DNA becomes incorporated into host cell's DNA and is replicated along with host cell's genome
- viral DNA hnown as prophage, and under certain conditions can become active and initiate the lytic cycle
99
100
bacterial defense against viral invasion
- natural selection favors bacterial mutants with surface proteins
that are no longer recognized as receptors by a particular type of
phage
- restriction enzymes destroy the foreian DNA of the phage by cutting
it up
- methylated in a way that prevents attack by its own restriction enzymes
101
CRISPR-Cas9 system
repetitive DNA sequences (CRISPRs) correspond to DNA from a phage that had infected the call, then interacts with nucleases called Cas9 proteins to identify and cut viral DNA to be digested and rendered harmless
102
retroviruses
- RNA viruses that use the enzyme reverse transcriptase to transcribe DNA from an RNA template
- new DNA then permanently integrates into a chromosome
in the nucleus of an animal cell
- the host then transcribes the viral DNA into RNA to be used to synthesize viral proteins or to be released to infect more calls
103
transduction
moving foom one nost to another, viruses may pick up pieces of the first host's DNA and carry it to the next cell to be infected
104
RNA viruses lack replication _______ mechanisms and thus have higher rates of mutation
error-checking
- may result in diverse clone of virus and new genetic strains that could cause disease
105
vaccines
- stimulate the immune system to defend the host against specific viruses, however RNA viruses muster frequently as RNA polymerase does not have a proofreading function before replication takes place
106
prions
misfolded, infectious proteins that cause the misfolding of normal proteins in the brains of various animal species
- damage accumulates over time and eventually leads to death
107
DNA sequencing
used to determine the complete nucleotide sequence of a DNA molecule and uses complementary base pairing
108
genetic engineering
process of manipulating genes and genomes for practical purposes
109
biotechnology
process of manipulating organisms or their components for the purpose of making useful products
110
recombinant DNA
DNA that has been artificially made, using DNA from different sources- and often different species
111
plasmid
a small, circular extrachromosomal loop of DNA
- many bacteria have DNA outside the main circular chromosome in plasmids
112
restriction enzymes
- used to cut strands of DNA at specific locations (restriction sites)
- mostly derived from bacteria where they protect from invading viruses
- result is restriction fragments, which may have at least one single-stranded end (“sticky end”), which can form hydrogen bonds with complementary single-stranded pieces of DNA, to be sealed by DNA ligase
113
gene cloning steps:
1. identify and isolate the gene of interest and a cloning vector: the vector will carry the DNA sequence to be cloned and is often a bacterial plasmid
2. cut both the gene of interest and the vector with the same restriction enzymes
3. join the two pieces of DNA
4. get the vector carrying the gene of interest into a host cell: the plasmids are taken up by the bacterium by transformation
5. select for cells that have been transformed: the bacteria cells carrying the clones must be identified or selected
114
polymerase chains reaction (PCR)
a method used to amplify a particular piece of DNA without the use of cells
- target segments of DNA are produced quickly by using heat to denature and separate the strands, then cooling to allow primers to attach to the single strands and DNA polymerase to synthesize new strand of target DNA by adding nucleotides to the 3’ end of each primer on the two strands
115
restriction fragment length polymorphism (RFLPs)
result from differences in DNA sequences and can be detected by electrophoresis
116
bioinformatics
the use of computers, software, and mathematical models to process and integrate the volume of data from sequencing projects
117
in general, bacteria and archaea have _____ genes than eukaryotes
fewer
118
transposable elements
stretches of DNA that can move from one location to another in the genome with the aid of transpotase
- can interrupt normal gene function, if inserted in the middle of a functional gene, or alter gene expression, if inserted into a regulatory element
119
multigene family
collection of two or more identical or very similar genes
120
polyploidy
having an extra set of chromosomes
- occurs much more in plants than in animals and contributes to speciation
121
gel electrophoresis
molecules of different lengths travel at different speeds across a electric charge gradient
- shorter fragments travel faster
122
selection pressure
an agent of differential mortality or fertility that tends to make a population change genetically
123
morphological
relating to the form or structure of things
124
a synthesis inhibitor will stop a process for a time until removed
/
______ /
/
/
125
viruses can incorporate their DNA into a host’s genome to be:
transcribed and translated
126
DNA is always synthesized in the _____ direction
5’ to 3’
127
Bacterial Defenses Against Viral Invasion
- natural selection favors bacterial mutants with surface proteins that are no longer recognized as receptors by a particular type of phage
- restriction enzymes destroy the foreign DNA of the phage by cutting it up
- methylated in a way that prevents attack by its own restriction enzymes
128
CRISPR-Cas9 system
repetitive DNA sequences (CRISPRs) correspond to DNA from a phage that had infected the cell, then interacts with nucleases called Cas9 proteins to identify and cut viral DNA to be digested and rendered harmless
129
What are retroviruses?
RNA viruses that use the enzyme reverse transcriptase to transcribe DNA from an RNA template.
130
What happens to new DNA from retroviruses?
It permanently integrates into a chromosome in the nucleus of an animal cell.
131
How do retroviruses replicate?
The host then transcribes the viral DNA into RNA to be used to synthesize viral proteins or to be released to infect more cells.
132
What is transduction in the context of viruses?
The process by which viruses may pick up pieces of the first host's DNA and carry it to the next cell to be infected.
133
Why do RNA viruses have higher rates of mutation?
RNA viruses lack replication error-checking mechanisms.
134
What can rapid accumulation of mutations in RNA viruses lead to?
The rise of diverse strains of the virus within one organism.
135
What is a consequence of new genetic strains of RNA viruses?
They could cause disease.
136
What role do vaccines play against viruses?
Vaccines simulate the immune system to defend the host against specific viruses.
137
Why do RNA viruses mutate frequently?
RNA polymerase does not have a proofreading function before replication takes place.
138
What are prions?
Misfolded, infectious proteins that cause the misfolding of normal proteins in the brains of various animal species.
139
What is the result of prion accumulation?
Damage accumulates over time and eventually leads to death.
140
What are DNA sequencing and DNA cloning used for?
They are valuable tools for genetic technology, engineering, and biological inquiry.
141
What does DNA sequencing determine?
The complete nucleotide sequence of a DNA molecule and uses complementary base pairing.
142
What is genetic engineering?
The process of manipulating genes and genomes for practical purposes.
143
What is biotechnology?
The process of manipulating organisms or their components for the purpose of making useful products.
144
What is recombinant DNA?
DNA that has been artificially made, using DNA from different sources and often different species.
145
What is gene cloning?
The process by which scientists can produce multiple copies of specific segments of DNA.
146
What is a plasmid?
A small, circular extrachromosomal loop of DNA. Many bacteria have DNA outside the main chromosome in plasmids.
147
What are restriction enzymes?
Enzymes used to cut strands of DNA at specific locations (restriction sites). They are mostly derived from bacteria where they protect from invading viruses.
148
What are restriction fragments?
The result when DNA is cut by restriction enzymes, which may have at least one single-stranded end ('sticky end') that can form hydrogen bonds with complementary single-stranded pieces of DNA.
149
What are the steps to clone a gene?
1. Identify and isolate the gene of interest and a cloning vector.
2. Cut both the gene of interest and the vector with the same restriction enzymes.
3. Join the two pieces of DNA.
4. get the vector carrying the gene of interest into a host cell: the plasmids are taken up by the bacterium by transformation
5. select for cells that have been transformed: the bacteria cells carrying the clones must be identified or selected
150
What is polymerase chain reaction (PCR)?
A method used to amplify a particular piece of DNA without the use of cells.
## Footnote
PCR involves heating to denature DNA strands and cooling to allow primers to attach, followed by DNA polymerase synthesizing new strands.
151
What are restriction fragment length polymorphisms (RFLPs)?
Results from differences in DNA sequences and can be detected by electrophoresis.
## Footnote
RFLPs are used in various genetic analyses.
152
What is bioinformatics?
The use of computers, software, and mathematical models to process and integrate data from sequencing projects.
## Footnote
Bioinformatics is crucial for analyzing genomes and their functions.
153
How do genomes vary among different organisms?
They vary in size, number of genes, and gene density.
## Footnote
In general, bacteria and archaea have fewer genes than eukaryotes.
154
What is a characteristic of multicellular eukaryotes regarding their genome?
They have much noncoding DNA and many multigene families.
## Footnote
This noncoding DNA does not code for proteins.
155
What percentage of the human genome codes for proteins or is transcribed into RNA?
Only 15%.
## Footnote
The majority of the human genome consists of repetitive DNA.
156
What are transposable elements?
Stretches of DNA that can move from one location to another in the genome with the aid of transposase.
## Footnote
Transposable elements play a role in genetic variation.
157
Fill in the blank: The rest of the human genome is mostly _______.
repetitive DNA.
158
What can transposons do when inserted into a functional gene?
Interrupt normal gene function
## Footnote
Transposons can also alter gene expression when inserted into regulatory elements.
159
What is a multigene family?
A collection of two or more identical or very similar genes
## Footnote
Example: human globin genes.
160
Where are the genes for different human globins located?
On different chromosomes.
161
What processes contribute to genome evolution?
Duplication, rearrangement, and mutation as PNA.
162
What is polyploidy?
Having an extra set of chromosomes.
163
In which organisms does polyploidy occur more frequently?
Plants.
164
How does polyploidy contribute to speciation?
It leads to the formation of new species.
165
What is selection pressure?
An agent of differential mortality or fertility that tends to make a population change agretically.
## Footnote
Selection pressure can lead to evolutionary changes within a population over time.
166
What does morphological refer to?
Relating to the form or structure of things.
## Footnote
Morphology is a key concept in biology and other fields, focusing on the shape and structure of organisms.
167
What happens to short fragments of DNA in terms of travel speed?
Short fragments of DNA travel faster.
## Footnote
This is relevant in techniques like gel electrophoresis, where DNA fragments are separated based on size.
168
What is the function of a synthesis inhibitor?
It will stop a process for a time until removed.
## Footnote
Synthesis inhibitors are often used in research and medicine to halt specific biochemical processes.
169
How can viruses interact with a host's genome?
Viruses can incorporate their DNA into a host's genome to be transcribed and translated.
## Footnote
This process is crucial for viral replication and can affect the host's cellular functions.
170
In which direction is DNA always synthesized?
In the 5' to 3' direction.
## Footnote
This directional synthesis is fundamental to DNA replication and transcription processes.
171
What type of bonds join a double-ringed structure to a single-ringed structure in each pair of DNA?
Hydrogen bonds.
## Footnote
Hydrogen bonds are essential for the stability of the DNA double helix.
