Chapter 7 Flashcards
1
Q
Entire genetic complement which includes genes and nucleotide sequences that connect genes to one another
A
Genome
2
Q
Specific sequences of nucleotides that code for RNA or polypeptide molecules
A
Genes
3
Q
Basic building block of DNA
A
Nucleotides
- made up of phosphate attached to nucleoside (pentose sugar + a nitrogenous base)
Nitrogenous bases - G,C,T,A,U
4
Q
Bases of nucleotides are held together by…
A
Hydrogen bond in a specific way called complementary base pair
For DNA: A-T by 2H bonds
For RNA: A-U by 2H bonds
C-G by 3H bonds
5
Q
Arrangement of DNA
A
5’ carbon
3’ hydroxyl group
Antiparallel
6
Q
Carries instructions for the synthesis of polypeptides and RNA molecules in much the way a sequence of letters carries info used to form words and sentences
A
Linear sequence of nucleotides
7
Q
Allows cell to make exact copies to pass to its progeny
A
Complementary structure of the two strands
8
Q
DNA of prokaryotic genomes are found in…
A
Chromosomes and plasmids
9
Q
Consists of circular molecule of DNA localized in a region of the cytoplasm
A
Nucleotides
- is typically in prokaryotic chromosome
10
Q
Is a globular protein that has archaea DNA wrapped around them
A
Histones
11
Q
Further folds and supercoils the entire prokaryotic chromosome like a skein of yarn into a compact mass
A
Gyrase
12
Q
Small molecules of DNA that replicate independently of the chromosome
A
Plasmids
- usually circular
- found in prokaryotic cells
- carries info required for its own replication
- carries gene that give advantages to the cell that is carrying them
13
Q
Have two copies of each chromosome
A
Eukaryotic cells
- are diploids
- are linear
- located in a nucleus
- has globular histones
14
Q
Charge of DNA
A
Negative charged
- has positively charged histones wrapped around it
15
Q
Histones + DNA
A
Nucleosomes
- found in eukaryotic cells
Nucleosomes + proteins = chromatin fibers (important during mitosis)
16
Q
When are chromatin fibers loosely packed?
A
In regions with chromosomes where genes are active
When chromatin are in this way they form euchromatin
17
Q
When inactive DNA is more tightly packed it is called…
A
Heterochromatin
18
Q
Type of DNA in mitochondria
A
Circular DNA
- similar to prokaryotic DNA
- contains 5% of DNA
19
Q
Has a haploid genome
A
Prokaryotic cells
- also has chromosomal DNA in the form of single circular chromosome
- also has plasmids
20
Q
Has a diploid genome
A
Eukaryotic cells
- nuclear chromosomal DNA in linear chromosomes
- also has extra nuclear DNA in mitochondria, chloroplasts, and any plasmids present
21
Q
Has a haploid copy of one or rarely two chromosomes
A
Bacteria
22
Q
Plasmids are present in some cells
A
Bacteria
- usually more than one per cell
Archaea
- in some cells
Eukaryotic
- fungi
- algae
- Protozoa
23
Q
Has circular or linear dsDNA
A
Bacteria
24
Q
Has circular dsDNA
A
Archaea
25
Has linear dsDNA in nucleus
Circular dsDNA in mitochondria, chloroplasts, and plasmids
Eukaryotic
26
DNA is located in cytoplasm and plasmids
Bacteria and archaea
27
Does not have histones
Bacteria
| - chromosome are associated with a small amount of no histones protein instead
28
Process of DNA replication is described as...
semiconservative process
| - each daughter DNA molecule is composed of one original strand and one new strand
29
DNA replication starts at....
origin
30
enzyme that unzips the DNA to do replication
helicase
- breaks the hydrogen bond between nitrogenous bases
- exposes the bases in a replication fork
- proteins will attach to the separated single strands so they do not rejoin when replication is occurring
31
of bacterial DNA polymerase
5
32
catalyze synthesis of DNA by the addition of new nucleotides
polymerase
| - adds nucleotide only to hydroxyl group at 3' end so adds in 5' to 3' direction
33
usual enzyme used in DNA replication for bacteria
DNA polymerase III
34
Leading strand is made continuously in what direction?
5' to 3' end
35
Lagging strands are made in what direction
5' to 3' end in sections
36
Synthesis of Leading strand
1 An enzyme called primase synthesizes a short RNA molecule that is complementary to the template DNA strand.
This RNA primer provides the 3’ hydroxyl group required by DNA polymerase III.
2 Triphosphate deoxyribonucleotides form hydrogen bonds with their complements in the parental strand. Adenine
nucleotides bind to thymine nucleotides, and guanine nucleotides bind to cytosine nucleotides.
3 Using the energy in the high-energy bonds of the triphosphate deoxyribonucleotides, DNA polymerase III covalently joins them one at a time to the leading strand. DNA polymerase III can add about 500 to 1000 nucleotides per
second to a new strand.
4 DNA polymerase III also performs a proofreading function
(not shown). About one out of every 100,000 nucleotides is mismatched with its template; for instance, a guanine might become incorrectly paired with a thymine. DNA
polymerase III recognizes most of these errors and removes the incorrect nucleotides before proceeding with synthesis.
This role, known as the proofreading exonuclease function, acts like the backspace key on a keyboard, removing the most recent error. Because of this proofreading exonuclease
function and other repair strategies beyond the scope of this discussion, only about one error remains for every
10 billion (1010) bp replicated.
5 Another DNA polymerase—DNA polymerase I—replaces the RNA primer with DNA (not shown). Note that researchers
named DNA polymerase enzymes in the order of their discovery, not the order of their actions.
37
formed away from replication fork
lagging strands
| - begins with its own RNA primer
38
direction of DNA replication
bidirectional
DNA synthesis proceeds
in both directions from the origin. In bacteria, the process of
replication proceeds from a single origin, so it involves two sets
of enzymes, two replication forks, two leading strands, and two
lagging strands
39
Removes supercoil after DNA is unwind
The enzymes gyrase and topoisomerase
remove such supercoils by cutting the DNA, rotating
the cut ends in the direction opposite the supercoiling, and then
rejoining the cut ends
40
joining the cut ends.
Bacterial DNA replication is further complicated by
methylation of the daughter strands, in which a cell adds a
methyl group (¬CH3) to one or two bases that are part of specific
nucleotide sequences. Bacteria typically methylate adenine
bases and only rarely a cytosine base
Methylation plays a role in a variety of cellular processes,
including the following:
■ Control of genetic expression. In some cases, genes that
are methylated are “turned off” and are not transcribed,
whereas in other cases methylated genes are “turned on”
and are transcribed.
■ Initiation of DNA replication. In many bacteria, methylated
nucleotide sequences play a role in initiating DNA
replication.
■ Protection against viral infection. Methylation at specific sites
in a nucleotide sequence enables cells to distinguish their
DNA from viral DNA, which lacks methylation. The cells
can then selectively degrade viral DNA.
■ Repair of DNA. The role of methylation in some DNA repair
mechanisms is discussed later in the chapter (pp. 223–224).
41
How is eukaryotic DNA replication different?
■ Eukaryotic cells use four different DNA polymerases to
replicate DNA. DNA polymerase α initiates replication,
including synthesis of a primer—the function performed
by primase in bacteria. DNA polymerase δ elongates
the leading strand, and DNA polymerase ε appears to
be responsible for replicating the lagging strand. DNA
polymerase γ replicates mitochondrial DNA.3
■ The large size of eukaryotic chromosomes necessitates
thousands of origins per molecule, each generating two
replication forks; otherwise, the replication of eukaryotic
genomes would take days instead of hours.
■ Eukaryotic Okazaki fragments are shorter than those
of bacteria—100 to 400 nucleotides long.
■ Plant and animal cells methylate cytosine bases
exclusively
42
m is the actual set of
| genes in its genome
genotype
-e. A genotype differs from a genome in that
a genome also includes nucleotides that are not part of genes,
such as the nucleotide sequences that link genes together. At
the molecular level, the genotype consists of all the series of
DNA nucleotides that carry instructions for an organism’s
life
43
) refers to the physical features and
functional traits of an organism, including characteristics such
as structures, morphology, and metabolism
phenotype
44
How does genotype lead to phenotype?
phenotypic traits result from
the actions of RNA and protein molecules that are themselves
coded by DNA
45
Are genes always active?
no
46
Making a RNA copy of the DNA
Transcription
47
RNA is then used to make protein
Translation
48
Central dogma is...
DNA transcribed to RNA which is then translated to form polypeptides
49
Carry genetic info from chromosomes to ribosomes
.mRNA
50
Combines with ribosomal polypeptides to form ribosomes
.rRNA
51
Deliver the correct amino acids to ribosomes based on the sequence of nucleotides in mRNA
.tRNA
52
Steps in initiation of transcription
Attaches to DNA and goes down its sequence until it reaches the promoter
- sigma factor is needed to recognize promoter in bacteria
After recognition, RNA polymerase will unzip the DNA at the promoter and form a bubble
53
Steps in elongation of transcription
Triphosphate ribonucleotides align with their DNA complements
- triphosphate ribonucleotides also give the energy needed for RNA synthesis
RNA polymerase links them together and make RNA
No primer needed
54
Steps in termination of transcription
For self-termination, transcription of GC rich terminator region produces a hairpin loop to create tension and loosen the grip of the polymerase on the DNA
For rho-dependent termination, tho pushes between polymerase and DNA to cause release of polymerase, RNA transcript, and Rho
55
Can multiple copies of RNA be transcribed simultaneously?
Yes for bacteria
56
Differences in transcription for eukaryotes
Transcription occurs in nucleus, mitochondria, and chloroplast
Has 3 types of nuclear RNA polymerase
- transcribe mRNA
- transcribe major rRNA
- transcribe tRNA and small rRNA
Has many transcription factors to help RNA polymerase bind to promoter while bacteria only has sigma factor
Has elongation factors
Process mRNA before doing translation
- capping by adding guanine to 5’ end of mRNA
- polyadenylation by adding adenine nucleotide to 3’ end *does not need DNA template to occur*
- splicing by removing introns to only have exons in the functional mRNA
57
Define genetic code
Triplets of mRNA nucleotides called codon which code for specific amino acids
58
Start codon AUG is for
Methionine
For bacteria
-fMet
59
With most redundant codons, the... determine the amino acid
First 2 nucleotides
60
Eukaryotic mRNA is different from prokaryotic mRNA due to....
Processing of pre-mRNA
Eukaryotic mRNA contains instructions for only one polypeptide
Eukaryotic mRNA is not translated until it is fully transcribed and processed and has left the nucleus
- so transcription and translation of mRNA does not occur simultaneously
61
Has the anticodon
.tRNA
| - has 3 hairpin loops held by hydrogen bonds
62
Ribosomes of bacteria are
70S
| - 50S and 30S
63
Ribosomes for eukaryotes are
80S
| -60S and 40S
64
The tRNA binding site of ribosomes
A site
- accepts the tRNA varying the next amino acid to be added to the growing polypeptide
P site
- holds the tRNA carrying the polypeptide
E site
- is where the empty tRNA molecules exit
65
Initiation of translation
The smaller ribosomal subunit attaches to mRNA at a ribosome-binding site (known as shine-dalgarno sequence) so as to position a start codon (AUG) at ribosomal subunit P site
.tRNA whose anticodon is UAC to complement the start codon, attaches at the ribosome’s P site
The larger ribosomal subunit then attaches to form a complete initiation complex
66
Elongation of the translation
The transfer RNA whose anticodon is complementary to the next codon-delivers its amino acid- to the A site
Proteins called elongation factor escort the tRNA along with a molecule of GTP
- energy from GTP is used to stabilize each tRNA as it binds at the A site
An enzymatic RNA molecule called ribozymes- is the larger ribosomal subunit - forms a peptide bond between the terminal amino acid of the growing polypeptide chain and the newly introduced amino acid so that the polypeptide is now attached to the tRNA occupying the A site
6 Using energy supplied by more GTP, the ribosome moves
one codon down the mRNA. This transfers each tRNA
to the adjacent binding site; that is, the first tRNA moves
from the P site to the E site, and the second tRNA (with
the attached polypeptide) moves to the vacated P site.
7 The ribosome releases the “empty” tRNA from the E site.
In the cytosol, the appropriate enzyme recharges the empty
tRNA with another molecule of the type of amino acid
carried by that tRNA.
8 The cycle repeats, each time adding another amino acid,
at a rate of about 15 amino acids per second
67
Termination of translation
uses release factors to stop elongation
ribosome seperates
68
Differences in eukaryotic translation
■ Initiation of translation in eukaryotes occurs when the
small ribosomal subunit binds to the 5’ guanine cap rather
than a specific nucleotide sequence.
■ The first amino acid in eukaryotic polypeptides is methionine
rather than formylmethionine.
■ Ribosomes attached to membranes of endoplasmic reticulum
(ER), forming rough ER (RER), can synthesize polypeptides
into the cavity of the RER.
69
Prokaryotic operon consists of...
promoter
series of genes that code for enzymes and structures
adjacent regulatory element called an operator which controls movt of RNA polymerase
70
Inducible operons
not usually transcribed
| must be activated by inducers
71
Repressible operons
are transcribed continually until deactivated by repressors which bind to the operator and inhibit transcription
72
lactose operon is example of...
inducible operon
lac operon controlled by regulatory gene located outside operon
- produces a repressor protein that attaches to DNA at lac operator
= repressor prevents RNA polymerase from binding to the promoter to stop mRNA synthesis
- allolactose is an inducer that inactivates the repressor by changing the repressor's quaternary structure so that it can no longer attach to DNA so that transcription of the three structural genes can proceed--> operon is induced and can become active
- ribosomes then translate the newly synthesized mRNA to produce enzymes that catabolize lactose
- once lactose supply has been depleted, there is no more inducer and the repressor becomes active again to suppress the transcription of the lac operon
73
condition that needs to be met before transcribing lac operon
glucose is absent
- see increase in cAMP and binds to CAP--> together binds to the lac promoter and begin transcription of lac
if glucose present, cell does not synthesize cAMP so low lvl cAMP
74
tryptophan operon is...
repressible operon
- repressor of repressible operon is usually inactive
if no tryptophan present, tryptophan operon is active---> leads to tryptophan synthesis
if tryptophan is available, repressor is activated and binds to operator and leads to stopping tryptophan synthesis
75
point mutation is...
when a single nucleotide base pair is affected
| - includes substitution and frameshift mutations (insertions and deletions)
76
mutation causes a different amino acid to form
missense mutation
77
mutation causes a stop codon to form
nonsense mutation
78
radiation can lead to...
pyrimidine dimers
- prevents hydrogen bonds
- distorts sugar backbone
- prevent proper replication and transcription
79
Types of chemical mutagens
nucleotide analogs
- used in antiviral and anticancer drugs
Nucleotide-altering chemicals
- change structure of nucleotides
frameshift mutagen
- insert or delete a nucleotide base pair
80
exchange nucleotide sequences between two DNA molecules and often involves segments that are composed of identical or nearly identical nucleotide sequences called homologous sequences
genetic recombination
81
define genetic recombination
Simplified depiction of
one type of recombination between two DNA molecules. After an enzyme
nicks one strand (here, strand A), a recombination enzyme rearranges the
strands, and ligase seals the gaps to for m recombinant molecules.
82
example of ancestors passing on their gene to their descendants
vertical gene transfer
83
many prokaryotes acquire genes
| from other microbes of the same generation
horizontal (lateral) gene transfer
- a donor cell contributes part of its genome to a recipient cell,
which may be of a different species from the donor. Typically,
the recipient cell inserts part of the donor’s DNA into its own
chromosome, becoming a recombinant cell. Cellular enzymes
then usually degrade remaining unincorporated DNA. Horizontal
gene transfer is a rare event, typically occurring in less
than 1% of a population of prokaryotes.
84
types of horizontal gene transfer
transformation, transduction, and bacterial conjugation.
85
cell takes up DNA from the environment
transformation
- Cells that have the ability to take up DNA from their environment
are said to be competent.
86
cells get DNA from a virus that took the DNA from another cell
transduction
| - a virus that infects bacteria is called a bacteriophage or a phage
87
uses a pilus to transfer DNA
conjugation
- the gene coding for the pili is located in the F plasmid
- cells that have F plasmid are F+ cells
88
HFr cells are...
cells that have the F plasmid integrated at a specific DNA sequence in their chromosome
