Biology DAT Ch. 6-10 Flashcards
Nucleosomes
are complexes of DNA wrapped around histone proteins.
Each nucleosome has
9 histones total. The central core contains 2 of each histone H2A, H2B, H3 and H4. On the outside, a single histone H1 holds the DNA in place.
Chromatin
refers to the overall packaging of DNA and histones.
Two types of chromatin
Euchromatin and heterochromatin
Euchromatin
nucleosomes are “loosely packed”, so DNA is readily accessible for transcription.
Heterochromatin
nucleosomes are “tightly packed”, so DNA is mostly inactive.
Histones
are positively charged while DNA is negatively charged, allowing proper binding.
Deacetylation
of histones increases positive charges, tightening DNA histone attractions and decreasing transcription.
Methylation
of histones adds methyl groups, either increasing or decreasing transcription.
Origin of replication
replication is required to initiate DNA replication, where the DNA strands first separate. Organisms w circular DNA (bacteria) have a single origin of replication while organisms with linear DNA such (humans) have multiple origins of replication.
Semiconservative replication
where each new double helix produced by replication has one “new” strand and one “old” strand.
DNA
DNA is antiparallel, the 5’ end (terminal phosphate group) of one strand is always next to the 3’ end (terminal hydroxyl group) of the other strand and vice versa.
Initiation replication
creating origins of replication at
A-T rich segments of DNA because they only have 2 Hydrogen bonds.
Elongation
producing new DNA strands using different types of enzymes.
Elongation enzymes
helicase, single-stranded binding proteins, topoisomerase, DNA polymerase, primase, sliding clamp proteins, RNA primers, DNA ligase
Helicase
unzips DNA by breaking hydrogen bonds between strands, creating the replication fork
Single-stranded binding proteins
bind to uncoiled DNA strands, preventing reattachment.
Topoisomerase
nicks the DNA double helix ahead of helicase to relieve built-up tension.
DNA polymerase
adds free nucleoside triphosphates to 3’ ends.
Primase
places RNA primers at the origin of replication to create 3’ ends for nucleotide addition.
Sliding clamp proteins
hold DNA polymerase onto the template strand.
Leading strand
is produced continuously because it has a 3’ end that
faces the replication fork.
Lagging strand
is produced discontinuously because its 3’ end is facing
away from the replication fork. Thus, RNA primers are needed to produce Okazaki fragments.
Okazaki fragments
short DNA fragments
DNA ligase
glues separated fragments of DNA together.
Termination
replication fork cannot continue, ending DNA replication.
Telemores
are noncoding, repeated nucleotide sequences at the ends of linear chromosomes.
Telomerase
is an enzyme that extends telomeres to prevent DNA loss, prevents critical information from being lost.
Genes
are instructions within DNA that code for proteins. Must first be transcribed into RNA before being translated into proteins.
messenger RNA
DNA undergoes transcription to produce single-stranded messenger RNA (mRNA).
Transcription
initiation (promoter sequence attracts RNA polymerase to trasncribe the gene), elongation, termination (signals RNA polymerase to stop transcribing)
Transcription bubble
forms during elongation and RNA polymerase travels in the 3’–>5’ direction on the template strand, it extends RNA in the 5’–>3’ direction
Prokaryotes: Before transcription occurs, a sigma factor combines with…
prokaryotic core RNA polymerase to form RNA polymerase holoenzyme, giving it the ability to target specific DNA promoter regions.
Prokaryotes: Operon
is a group of genes that is controlled by one promoter, functioning as a single unit.
Prokaryotes: Operator region
is present near the operon’s promoter and binds activator/repressor proteins to regulate the promoter.
Prokaryotes: lac operon
is an inducible operon (must be
induced to become active). LacZ, lacY, and lacA are the 3 genes contained within the lac
operon that encode proteins required for lactose metabolism. The lac operon will only be induced when glucose is not available as an energy source, so lactose must be used.
Prokaryotes: lac repressor protein
is the first way that the lac operon is controlled. This protein is encoded by an entirely separate gene called lacI, which is constitutively expressed (always on). Thus, the lac repressor protein is always bound to the operator, blocking transcription.
Prokaryotes: Constitutively expressed
always on
Prokaryotes: Lactose is present
it is converted to allolactose.
Prokaryotes: Allolactose
binds directly to the repressor and removes it from the operator, allowing transcription to occur.
Prokaryotes: cAMP levels and catabolite activator protein (CAP)
are the 2nd level of lac operon regulation. cAMP levels are inversely related to glucose levels, so when glucose is low, cAMP is high. cAMP binds
to catabolite activator protein (CAP), which then attaches near the lac operon promoter to help attract RNA polymerase, promoting transcription.
Prokaryotes: Glucose & lactose present
moderate transcription. Repressor not bound and CAP not bound
Prokaryotes: Glucose present & lactose absent
no transcription.
repressor is bound and CAP not bound
Prokaryotes: Glucose absent & lactose present
high transcription.
repressor not bound and CAP bound
Prokaryotes: Glucose absent & lactose absent
no transcription.
repressor is bound and CAP is bound
Prokaryotes: trp operon
is responsible for producing the amino acid tryptophan. It is a repressible operon, it codes for tryptophan synthetase and is always active unless the presence of tryptophan in the environment represses the operon.
Prokaryotes: trp repressor protein
Tryptophan binds to the trp repressor protein, which then attaches to the operator on the trp operon to prevent tryptophan production. When
tryptophan is not present in the environment, the trp operon will undergo transcription because the trp repressor protein will be inactive.
RNA polymerase
eukaryotic transcription occurs in the nucleus and uses RNA polymerase II to transcribe most genes
Transcription factors
are needed in eukaryotes
to help RNA polymerase bind to promoters.
TATA box
The TATA box is a sequence in many promoters that transcription factors can recognize and bind to.
Enhancers
are DNA sites that activator proteins can bind to and help increase transcription of a gene.
Silencers
are DNA sites that repressor
proteins can bind to and decrease transcription
of a gene.
Enhancers and silencers
can be far upstream or downstream from the gene, so DNA from these sites are thought to loop around to colocalize with RNA polymerase.
poly A signal
is located within the terminator sequence and stimulates polyadenylation (addition of adenine nucleotides to the 3’ end of the mRNA).
Post-transcriptional modification
describes the conversion of pre-mRNA into processed mRNA which leaves the nucleus.
3 main types of post-transcriptional modification
5’capping, polyadenylation of the 3’ end, and splicing out introns
5’capping
7-methylguanosine cap is added to the 5’ end of the mRNA during elongation, protecting the mRNA from degradation.
Polyadenylation of the 3’end
addition of the poly A tail to prevent degradation.
Splicing out introns
introns are interruptions in DNA between protein coding DNA called exons. Splicing refers to removing introns from pre mRNA using spliceosomes. “Splice signals” are present within introns, signaling to the spliceosome where to cut.
snRNAs
(small nuclear RNA) and proteins make up the functional part of a spliceosome and are collectively referred to snRNPs (small nuclear RiboNucleic Protein).
Alternative splicing
describes a single pre-mRNA
having various possible spliced mRNA products. Thus, the same pre-mRNA can produce many different proteins.
Ribosomes & tRNA
are important players in translation, the process of converting mRNA into protein products.
Ribosomes are made up of
of one small and one large subunit
Codon
is a group of three mRNA bases (A, U, G, or C) that code for an amino acid or terminate translation. There are 64 codon combinations total but only 20 amino acids.
Degeneracy
is present (multiple codons code for the same amino acid).
Start codon
AUG (methionine)
Stop codon
UAA, UAG, UGA (end translation, do not code for any amino acid)
Anticodon
is a group of three tRNA bases (A, U, G, or C) that base pairs with a codon. Each tRNA carries an amino acid to be added to the growing protein.
Aminoacyl-tRNA
refers to a tRNA bound to an amino acid.
Aminoacyl-tTRNA synthetase
is the enzyme that attaches an amino acid to a specific tRNA using the energy from ATP.
Ribosomal binding sites for tRNA
- A site - A for aminoacyl-tRNA, which first enters at this site.
- P site - P for peptidyl-tRNA, which carries the growing polypeptide.
- E site - E for exit site. The tRNA from the P site is sent here and released from the ribosome.
DNA mutation
is a heritable change in the DNA nucleotide sequence that can be passed down to daughter cells.
3 main types of DNA mutatoins
substitutions, insertions, and deletions
Base substitutions (point mutations)
one nucleotide is replaced by another.
Silent mutations
no change in aa sequence. Due to “third base wobble”, mutations in the DNA sequence that affect the 3rd base of
a codon can still result in the same amino acid being added to the protein. Relies on the degeneracy (redundancy) of translation.
Missense mutations
single change in aa sequence. Can be conservative (mutated amino acid similar to unmutated) or non-conservative (mutated amino acid different from unmutated).
Nonsense mutations
single change in aa sequence that results in a stop codon. Results in early termination of protein.
Insertions
adding nucleotides into the DNA sequence - can shift reading frame.
Deletions
removing nucleotides from the DNA sequence - can shift reading frame.
Factors that contribute to DNA mutations
●DNA polymerase errors during DNA replication.
● Loss of DNA during meiosis crossing over.
● Chemical damage from drugs.
● Radiation.
Factors that prevent DNA mutations
● DNA polymerase proofreading by DNA polymerase.
● Mismatch repair machinery that checks uncaught errors.
● Nucleotide excision repair that cuts out damaged DNA and replaces it with correct DNA using complementary base pairing.
Viruses
are not living because they must infect living cells to multiply.
Capsid
is a viral protein coat that is made of subunits called capsomeres. Some viruses also
have a phospholipid envelope that they pick up from the host cell membrane.
2 viral life cycle types
lysogenic and lytic cycle
Lysogenic cycle
virus is considered dormant
because it inserts its own genome into the host’s genome and does not harm the host.
Each time the host genome undergoes replication, so does the viral genome.
Lytic cycle
virus takes over host to replicate and does harm the host. The viral particles produced can lyse the host cell to find other hosts to infect.
Switch between lysogenic and lytic cycles
favorable conditions can stimulate a virus in the lysogenic cycle to replicate and enter to lytic cycle.
Retroviruses
(eg. HIV) have an RNA genome that infects host cells. They contain an enzyme called
reverse transcriptase.
Reverse transcriptase
which converts their RNA into cDNA (complementary DNA). The cDNA can integrate into the host genome and enter the lysogenic cycle.
Molecular genetics of bacteria
asexual and divide by binary fission, so they only receive genes from one parent cell
and do not increase genetic diversity through reproduction.
Horizontal gene transfer
bacteria increase genetic diversity through horizontal gene transfer which describes the transfer of genes between individual organisms, through; conjugation, transformation, transduction
conjugation
bacteria use a cytoplasmic
bridge called a pili to copy and transfer a special plasmid known as the F plasmid
(fertility factor). If a bacteria contains an F plasmid, it is referred to as F+. If not, it is
referred to as F-.
transformation
bacteria take up extracellular
DNA. Bacteria are referred to as competent if they can perform transformation.
electroporation
is the process of using electrical impulses to force bacteria to become competent.
transduction
viruses transfer bacterial DNA
between different bacterial hosts. This occurs when a bacteriophage enters the lysogenic cycle in its host and carries bacterial DNA along with its own genome upon re entering the lytic cycle.
Acetylation
of histones removes positive charges, relaxing DNA-histone attractions and allowing for more transcription to happen.
