5 Flashcards
(94 cards)
1
Q
nutrients
A
the chemicals
necessary as building blocks and energy for metabolism
2
Q
catabolism
A
breakdown
- catabolic pathways are exergonic; Cells store some of this released energy in
the bonds of ATP, though much of the energy is lost as heat.
3
Q
precursor metabolites
A
Using enzymes, cells catabolize nutrient molecules to form
elementary building blocks called precursor metabolites.
4
Q
anabolism
A
Because building anything requires energy,
anabolic pathways are endergonic 1en@der@gon´ik2; that is, they
require more energy than they release. The energy required for
anabolic pathways usually comes from ATP molecules produced
during catabolism.
5
Q
a chemical may be reduced by
A
gaining either a simple electron or an electron that is part of
a hydrogen atom—which is composed of one proton and one
electron.
6
Q
a moelcule may be oxidized
A
by losing a simple electron, by losing a hydrogen atom, or
by gaining an oxygen atom.
7
Q
dehydrogenation rxns
A
biological oxidations often involve the loss of H atoms
8
Q
e- carrier molecules
A
carry e- as H atoms
- nicotinamide adenine dinucleotide (NAD+) NADH - nicotinamide adenine dinucleotide phosphate (NADP+) NADPH - flavin adenine dinucleotide (FAD) FADH2
9
Q
phosphorylation
A
inorganic phosphate (PO4 3-) is added to a substrate
10
Q
substrate-level phosphorylation
A
involves
the transfer of phosphate to ADP from another phosphorylated
organic compound
11
Q
oxidative phsophrylation
A
energy from
redox reactions of respiration (described shortly) is used to
attach inorganic phosphate to ADP
12
Q
photophospyrlation
A
light
energy is used to phosphorylate ADP with inorganic
phosphate
13
Q
enzymes
A
organic catalysts
14
Q
human genome bp
A
6 bill
15
Q
nucleoid
A
A typical prokaryotic chromosome (Figure 7.2a) consists of
a circular molecule of DNA localized in a region of the cytoplasm
called the nucleoid.
16
Q
histones
A
Archaeal DNA
is wrapped around globular proteins called histones.
17
Q
plasmids
A
1% to 5% of the size of a prokaryotic chromosome
(see Figure 7.2b), ranging in size from a few thousand base pairs
to a few million base pairs. Each plasmid carries information required
for its own replication and often for one or more cellular
traits. Typically, genes carried on plasmids are not essential for
normal metabolism, for growth, or for cellular reproduction but
can confer advantages to the cells that carry them
18
Q
F plasmids
A
Fertility (F) plasmids carry instructions for conjugation, a
process by which some bacterial cells transfer DNA to
other bacterial cells.
19
Q
R plasmids
A
carry genes for resistance to one or
more antimicrobial drugs or heavy metals. By processes
we will discuss shortly, certain cells can transfer resistance
plasmids to other cells, which then acquire resistance to the
same antimicrobial chemicals.
20
Q
bacteriocin plasmids
A
carry genes for proteinaceous
toxins called bacteriocins, which kill bacterial
cells of the same or similar species that lack the plasmid.
In this way a bacterium containing this plasmid can kill its
competitors
21
Q
virulence plasmids
A
carry instructions for structures, enzymes,
or toxins that enable a bacterium to become pathogenic.
22
Q
helicawes
A
An enzyme called DNA helicase locally untwists n separates
the DNA molecule by breaking the hydrogen bonds between
complementary nucleotide bases, which exposes the bases in a
replication fork
23
Q
polymerase
A
All DNA polymerases replicate DNA by adding nucleotides
in only one direction—5′ to 3′ (only to a hydroxyl group at 3’ end). DNA polymerase
III is the usual enzyme of DNA replication in bacteria.
24
Q
leading strand
A
synthesized continuously
25
lagging strand
also synthesizd 5′ to 3′ but in short
| segments that are later joined.
26
primase
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.
27
synthesis of leading strand
1. primer
2. Triphosphate deoxyribonucleotides form hydrogen bonds
with their complements in the parental strand.
3. DNA pol III joins the deoxyribonucleotides covalently one at a time to leading strand
4. proofread by pol III
5. pol I replaces RNA primer w/ DNA
28
ligase
in lagging strand synthesis, DNA ligase seals the gaps between adjacent Okazaki fragments
to form a continuous DNA strand.
29
lagging vs leading rep fork
synthesis of the leading strand proceeds continuously
toward the replication fork from a single RNA primer
at the origin, following helicase and the replication fork down
the DNA. The lagging strand is synthesized away from the replication
fork discontinuously as a series of Okazaki fragments,
each of which begins with its own RNA primer.
30
DNA replication is bidirectional; that is, 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
31
supercoils
The unzipping and unwinding action of helicase introduces
supercoils into the DNA molecule ahead of the replication forks.
Excessive supercoiling creates tension on the DNA molecule—like
your grandmother’s overwound phone cord—and would stop
DNA replication. 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.
32
methylation
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.
33
roles methylation
Control of genetic expression
Initiation of DNA replication
Protection against viral infection
Repair of DNA
34
replicatio pro vs eu
- euk: 4 diff DNA pols
- thousands of origins per molecule
- euk Ok fragments shorter
- plant and animal cells methylate cytosine bases only
35
genotype vs genome
a genome also includes nucleotides that are not part of genes,
such as the nucleotide sequences that link genes together.
36
nucleoside
pentose + N base
37
rRNA
combine with
| ribosomal polypeptides to form ribosomes
38
regulatory RNA
interact with DNA to
control gene expression
- microRNA, small interfering RNA,
and riboswitches
39
initiation
```
RNA polymerase attaches
nonspecifically to DNA and
travels down its length until
it recognizes a promoter
sequence. Upon recognition of the
promoter, RNA polymerase
unzips the DNA molecule
beginning at the promoter
```
40
sigma factor
enhances promoter
| recognition in bacteria.
41
elongation
```
Triphosphate ribonucleotides
align with their DNA
complements and RNA
polymerase links them
together, synthesizing RNA.
No primer is needed. The
triphosphate ribonucleotides
also provide the energy
required for RNA synthesis
```
42
rna pol vs dna pol
RNA polymerase does not require helicase
RNA polymerase slower than DNA polymerase
Uracil incorporated instead of thymine
RNA polymerase proofreading function is less efficient than DNA polymerase (more errors)
43
terminator
Self-termination occurs when RNA polymerase
transcribes a terminator sequence of DNA composed of
two symmetrical series: one that is very rich in guanine and cytosine
bases, followed by a region rich in adenine bases
44
2 types of termination
- Self-termination: transcription of GC-rich terminator
region produces a hairpin loop, which creates tension,
loosening the grip of the polymerase
on the DNA.
- Rho pushes between polymerase
and DNA. This causes release of polymerase, RNA transcript,
and Rho
45
transcription eu vs pro
RNA transcription occurs in the nucleus
Transcription also occurs in mitochondria and chloroplasts
Three types of RNA polymerases
Numerous transcription factors
mRNA processed before translation
46
capping
cap 5' end w/ modified guanine nucleotide
47
polyadenylation
add hundreds of adenine nucleotides to the 3′ end
48
splicing
Ribozymes further process pre-mRNA by removing
introns and splicing together exons to form a molecule that codes
for a single polypeptide.
49
codons
triplets of mRNA nucleotides
50
tRNA structure
tRNA has an
anticodon (an@te@ko´don) triplet in its bottom loop and an acceptor
stem for a specific amino acid at its 3′ end.
51
smaller unit of ribosome
shaped to accommodate
three codons at one time—that is, nine nucleotide bases of
a molecule of mRNA.
• The A site accommodates a tRNA delivering an amino acid.
• The P site holds a tRNA and the growing polypeptide.
• Discharged tRNAs exit from the E site.
52
translation initiation
the two ribosomal subunits,
mRNA, several protein factors, and tRNAfMet form an initiation
complex.
53
trnaslation elongation
Transfer RNAs
sequentially deliver amino acids as directed by the codons of the mRNA.
Ribosomal RNA in the large ribosomal subunit catalyzes a peptide bond
between the amino acid at the A site and the growing polypeptide at the
P site.
54
polyribosome
one mRNA and many ribosomes and
polypeptides. one ribosome after another attaches at the start
codon and begins to translate identical polypeptide molecules
from the same message.
55
termination trnaslation
Release factors somehow recognize stop codons and modify ribosome to activate ribozymes which sever polypeptide from final tRNA
Ribosome dissociates into subunits
Polypeptides released at termination may function alone or together
56
euk vs prok 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.
57
quorum sensing
a process whereby cells secrete quorumsensing
molecules into their environment and other cells detect
these signals so as to measure their density. The result is that
Pseudomonas cells synthesize harmful proteins only after there
are numerous bacterial cells, overwhelming the body’s defenses.
58
inducible operons
Inducible operons are not usually transcribed and must
| be activated by inducers, such as some quorum-sensing polypeptides.
59
represible opersons
they are transcribed continually until deactivated by repressors,
which bind to the operator and inhibit transcription.
60
operon
promoter + genes + adjacent ergulatory element called an operator
61
lac operon
The repressor,
a protein encoded by a regulatory gene, is constantly synthesized.
(a) When lactose is absent from the cell’s environment, the repressor
binds to the operator, blocking the movement of RNA polymerase and
halting transcription. (b) When lactose is present in the cell’s environment,
its derivative, allolactose, acts as an inducer by inactivating the repressor
so that the repressor cannot bind to the operator, allowing transcription
to proceed.
62
trp operon
(a) When
tryptophan is absent from the cell’s environment, the repressor is inactive,
so the structural genes are transcribed and translated, and the five
enzymes needed in the synthesis of tryptophan are produced. (b) When
tryptophan is present in the cell’s environment, it acts as a corepressor,
activating the repressor and inhibiting its own synthesis.
63
miRNAs
Ribosomes
do not translate microRNA molecules; rather, miRNA
joins with regulatory proteins to form a miRNA-induced silencing
complex (miRISC).
miRISC binds to messenger RNA that is complementary to
the microRNA within the miRISC. Once bound, miRISC performs
one of two functions:
1. cut mRNA
2. bind to mRNA, hiding it from ribosome
64
siRNA
Another method of regulation involving RNA uses small
interfering RNA (siRNA). siRNAs are about the same length
as miRNAs but differ from miRNAs in that siRNAs are double
stranded. Further, siRNAs may be complementary to mRNA,
tRNA, or DNA. siRNAs unwind and join RISC proteins to form
siRISC. siRISC appears to always bind to and cut the target nucleic
acid.
65
riboswitch
A riboswitch is another RNA molecule that helps regulate
translation. Riboswitches change shape in response to environmental
conditions such as changes in temperature or shifts
in the concentration of specific nutrients, including vitamins,
nucleotide bases, or amino acids. Some mRNA molecules themselves
act as riboswitches. When conditions warrant, riboswitch
mRNA folds to either favor or block translation.
66
point mutations
in which just a single nucleotide base pair is affected.
Point mutations include substitutions and frameshift mutations
(insertions and deletions).
67
missense
A
| change that specifies a different amino acid
68
nonsense
A third type of mutation occurs when a base-pair substitution
changes an amino acid codon into a stop codon. This is
called a nonsense mutation (Figure 7.24d). Nearly all nonsense
mutations result in nonfunctional proteins.
69
nonionizing radiation
Nonionizing radiation in the form of ultraviolet (UV) light is
also mutagenic because it causes adjacent pyrimidine bases to
covalently bond to one another, forming pyrimidine dimers
(Figure 7.25). The presence of dimers prevents hydrogen bonding
with nucleotides in the complementary strand, distorts the
sugar-phosphate backbone, and prevents proper replication
and transcription.
70
ionizing radiaiton
X rays and gamma
rays are ionizing radiation; that is, they energize electrons in
atoms, causing some of the electrons to escape from their atoms
(see Chapter 9). These free electrons strike other atoms, producing
ions that can react with the structure of DNA, creating mutations.
More seriously, electrons and ions can break the covalent bonds between the sugars and phosphates of a DNA backbone,
causing physical breaks in chromosomes and complete loss of
cellular control.
71
nucleotide analogs
Compounds that are structurally similar to
normal nucleotides are called nucleotide analogs (Figure 7.26a).
When nucleotide analogs are available to replicating cells, they
may be incorporated into DNA in place of normal nucleotides,
where their structural differences either inhibit nucleic acid
polymerases or result in mismatched base pairing.
- disrupt DNA and RNA replication and cause point mutations
72
nucleotide altering chemicals
- result in base-pair substitution mutations and missense mutations
- alter STRUCTURE of nucleotides
73
frameshift mutagens
Still other mutagenic chemical agents
insert or delete nucleotide base pairs, resulting in frameshift
mutations. -- nonsense
74
mutation frequency
As we have seen,
about one of every 10 million (107
) genes contains an error.
75
light repair
The most common type of mutation is a pyrimidine dimer
caused by ultraviolet light. Many cells contain DNA photolyase,
an enzyme that is activated by visible light to break pyrimidine
dimers, reversing the mutation and restoring the original DNA
sequence
76
dark repair
Dark repair enzymes cut the damaged
section of DNA from the molecule, creating a gap that is
repaired by DNA polymerase I and DNA ligase
77
base excision repair
excises the erroneous base, and then DNA polymerase
| I fills in the gap
78
mismatch repair
Mismatch
repair enzymes scan newly synthesized DNA looking for mismatched
bases, which they remove and replace. They distinguish
a new DNA strand from an old strand because old strands are
methylated.
79
SOS response
Sometimes damage to DNA is so extreme that regular repair
mechanisms cannot cope with the damage. In such cases, bacteria
resort to what geneticists call an SOS response involving a
variety of processes, such as the production of novel DNA polymerases
(IV and V) capable of copying less-than-perfect DNA.
These polymerases replicate DNA with little regard to the base
sequence of the template strand. Of course, this introduces
many new and potentially fatal mutations, but presumably SOS
repair allows a few offspring of these bacteria to survive.
80
+ selection
Positive selection involves selecting a mutant by eliminating
wild-type phenotypes.
81
- selection
aka indirect. involves replica plating
82
auxotroph
An organism with nutritional requirements that differ from
those of its wild-type phenotype is known as an auxotroph. Obviously,
if a researcher attempts to grow tryptophan auxotrophs
on media lacking tryptophan, the bacteria will be unable to synthesize
all its proteins and will die. Therefore, to isolate such
auxotrophs, we must use a technique called negative (indirect) selection.
83
his-
bacteria
possessing a point mutation that prevents the synthesis of the
amino acid histidine; in other words, they are histidine auxotrophs
84
ames test
A mixture containing his− Salmonella
mutants, rat liver extract, and the suspected mutagen is inoculated onto
a plate lacking histidine. Colonies will form only if a mutagen reverses the
his− mutation, producing revertant his+ organisms with the ability to
synthesize histidine. A control tube that lacks the suspected mutagen
demonstrates that reversion did not occur in the absence of the mutagen.
85
griffith
It was one of the first experiments showing that bacteria can get DNA through a process called transformation.
86
transformatio
a recipient cell takes up DNA from the environment,
| such as DNA that might be released by dead organisms.
87
vertical gene trasnfer
—the passing of genes to the
| next generation.
88
horizontal gene trasnfer
In horizontal 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.
89
transduction
involves the transfer of DNA from one cell to another via
a replicating virus.
- After a virus called a bacteriophage
(phage) attaches to a host bacterial cell, it injects its genome into the
cell and directs the cell to synthesize new phages. During assembly of
new phages, some host DNA may be incorporated, forming transducing
phages, which subsequently carry donor DNA to a recipient host cell.
90
pili
thin, proteinaceous
tubes extending from the surface of a cell. The gene
coding for conjugation pili is located on a plasmid called an
F (fertility) plasmid.
91
conjugaton w/ pili
2. cells attach
3. 1 strand of F plasmid DNA transfers to reciient
4. each synthesizes complementary strand
92
Hfr cells
In some bacterial cells, an F plasmid does not remain independent
in the cytosol but instead integrates at a specific
DNA sequence in the cellular chromosome. Such cells, which
are called Hfr (high frequency of recombination) cells
93
Hfr recombo
An Hfr cell is formed when an F+ cell integrates
its F plasmid into its chromosome. Hfr cells donate a partial copy of their DNA and a portion of the F
plasmid to a recipient, which is rendered a recombinant cell but remains F−.
94
inverted repeat
palindromic sequence
