Unit 6 Flashcards
plasmids
the DNA of the prokaryote cell
How are Prokaryotes different from Eukaryotes?
- No nucleus, it has a plasmid
- No membrane bound organelles
- They are REALLY small
capsule
And its roles (2)
A sticky outermost layer made up of polysacchrides that
1. keeps it from drying out
2. helps stick to other organisms
what is the cell wall (prokaryotes) made of and used for?
- peptidoglycan
- protection
what type of lipid layer does some archaea have?
Lipid MONOlayer
what type of appendages are there for a prokaryote? (3)
Fimbriae
flagellum
sex pilus
fimbriae
an appendage used for adhesion
flagellum
an appendage used to help movement
sex pilus
an appendage used for DNA sharing
what are the components of a Prokaryote? (7)
- Plasmids
- Capsule
- Cell wall
- Plasma Membrane
- Fimbriae
- flagellum
- sex pilus
topoisomerase
enzyme which unwinds the double helix of the DNA
Helicase
brakes the hydrogen bonds between the nitrogenous bases
Polymerase III
enzyme responsible for transcribing for small RNAs like tRNA
DNA Primase
Enzyme that synthesizes RNA primer - starting the translation
DNA ligase
an enzyme that joins Okazaki Fragments
RNA primase
an enzyme that synthesizes RNA primers to initiate DNA replication
primer is EXTENSIVELY used in lagging,
but only one is needed for leading
Lagging strand
The strand during transcription that is binding toward the five strand
Leading strand
The strand during transcription that is binding toward the three strand
Okazaki Fragment
short DNA sequences that are created during DNA replication when the lagging strand is synthesized discontinuously
How fast does transcription go?
About 1,000 nucleotides/sec
Which type of DNA replication is accurate?
Semi-conservative
Replication fork
a Y-shaped structure formed during DNA replication where the double helix of DNA is split into two single strands
Replication bubble
the bubble like shape caused by replication of DNA
single strand binding protein
keeps the base from coming back together
Sliding clamp
keeps the polymerase III in place during replication
DNA polymerase I
RNA primer is replaced by DNA during DNA replication
What are the steps to create a protein from DNA?
- Transcription
- mRNA is PROCESSED
- Translation happens with tRNA
- Protein!
Transcription
DNA - pre mRNA - mRNA
where does Transcription happen?
the Nucleus
promoter
a specific DNA sequence located at the beginning of a gene that acts as a binding site for RNA polymerase
template
the NON-CODING strand that the RNA binds to during transcription
terminatior
the DNA sequence which stops the RNA replication
Introns
Nonsense parts in the pre-mRNA
Exons
the important parts of the pre-mRNA
Spliceosome
eliminates introns during pre-mRNA processing
What are the two parts of proccessing?
a. protection
b. splicing
What is the protection part of pre-mRNA processing?
5’ cap is added
3’ polymerase A cap is added
RNA interference
a cellular mechanism that uses the gene’s own DNA sequence to turn it off - also known as silencing
What is alternative splicing? (!)
mix and match of exons to make different kinds of proteins
What are the steps of Transcription?
- Initiation
- Elongation
- Termination
What are the three steps to Translation?
- Initiation
- Elongation
- Termination
tRNA
the protein sites
What are the three sites on the tRNA?
A site
P site
E site
Anticodon
the code against the mRNA which codes for the protein
rRNA
the ribosome in the cytoplasm that has the tRNA which synthesizes proteins
start codon
AUG
end codon
UAA, UAG, UGA
Where does Transcription, Translation, and processing happen for Prokaryotes?
All in the Cytoplasm
Where does Transcription, Translation, and processing happen for Eukaryotes?
Transcription and processing - nucleus
Translation - Cytoplasm
What is in between each Coding region and the 3’ cap and 5’ cap in a eukaryotic?
NCR - Non coding region
What does the Prokaryotes have instead of a 3’ cap or a 5’ cap?
a Shine dalgarno sequence, that acts as a “ribosome binding site”
What is Central Dogma?
The process from
DNA - RNA - Protein
Gene Expression
the process by which a cell uses the information in a gene to create a functional product, such as a protein or non-coding RNA
Primary strand
the single-stranded RNA strand that is produced when a gene is transcribed from DNA
Is Adeinine a purine or pyramidine?
purine
Is Thymine a purine or pyramidine?
pyrmadine
Is Cytosine a purine or pyramidine?
pyramadine
Is guanine a purine or pyrimidine?
purine
Is uracil a purine or pyrimidine?
pyrimidine
Heterochromatin
condensed DNA
euchromatin
loose, non-condensed DNA
RNAi
an RNA which marks either protein or mRNA for destruction
examples - siRNA miRNA
Post-Transcriptional Regulation
RNAi tags RNA so protein not is created
Post-Translation Regulation
RNAi tags Protein so it’s either destructed or not used
Morphogenesis
Not all cells are the same, meaning some must be muscle cells, heart cells, etc.
Therefore, some traits are turned off in its early stages by homeotic genes, known as HOX genes
histone
protein in eukaryotic cells that the chromosomes of DNA wraps around for structure
Histone Acetletransfuse
an enzyme that uncoils the DNA so transcription takes place
Histone Deacetylase
an enzyme that could the DNA so it cannot go through transcription
Methylation
Completely inactivines the DNA by
1. physically imedeing
2. MBD - turns gene off
What is the result of Methylation?
Gene silencing
Why do we want to silence genes?
Because we want some cells to be nose cells, others to be blood, etc. etc.
What does an activator do?
enhance interaction between RNA polymerase and the promoter
enhancer
enhances transcription
General Transcription factors
Activates Transcription
Repressors and co-repressers
binds to operator and impedes RNA polymerase from binding
Inducer
causes Repressor to detach
Scilencers
RNA polymerase is not bound to promoter if SILENCER and REPRESSOR bind
What is Cellular Specialization?
Specializing a Cell for its own job
What are the two types of cues for turning on genes vs. turning them off
- Internal
- External
What are Non-Coding RNA?
RNA that does not partake in making protein directly.
MicroRNA (miRNA)
It is used in Gene Silencing
Ribosomal RNA (rRNA)
the part where tRNA is found do translation
tRNA
- it is electronically charged
- it snags the amino acids from the cytoplasm
- shuttles to the ribosome
- peptide bonds!
needs ATP
snoRNA
It is responsible for methylation, which alters DNA expression
snRNA
processes pre-RNA and are the splicesomes
Inducers
activates the activator
Activator
make more transcription
mutation
the effect of an incorrectly produced protein
Why do mutations occur? (3)
- Translation - wrong protein is made
- Transcription - wrong base pair in RNA
- DNA - wrong base on a DNA
Where do mutations come from?
- Inheritance
- Spontaneous - environment, random, etc.
Mutagens
chemical or physical substances or events that causes genetic mutation
endogenous mutagens
mutagens from inside the cell
exogenous mutagens
mutagens from outside the cell
Carcinogens
Exogenous mutagens that causes cancer - increases harmful cell division
Can mutations be good and/or bad?
YES!
They can be “good” or “bad” or both for the bacteria
What are the two main groups of mutations called?
- Base substitutions
- Gene rearrangements
What are the three types of base substitutions and what do they do?
- Nonsense Mutations - a wrong nucleotide, causing the a premature stop codon
- Missense Mutations - where ONE nucleotide is off, messing up the entire mRNA
- Silent Mutations - a mutation that does not cause any change in the protein
What are the six types of Gene Rearrangement mutations?
- Insertion - Frame shift
- Deletion - Frame shift
- Duplication
- Inversions
- Translocations - one chromosome breaks off and attaches to a different chromosome
- Transposons - literally some DNA that jumps around
What are the four ways Genetic Variation occurs in Prokaryotes
- Transformation
- Transduction
- Conjugation
- Transposal Elements
How does transformation cause Genetic Variation?
Floating DNA in Prokaryotes is caught in with the rest of the DNA - its like adoption
How does transduction cause Genetic Variation?
Virus moves from one Bacterium to another bacterium - its like accidently kidnapping
How does conjugation cause Genetic Variation?
Donated DNA is accepted by the Prokaryotes
How does Transposal Elements cause Genetic Variation?
jumping DNA is accepted by the Prokaryotes
Biotechnology
Taking DNA from one genome to give to another genome
How do we do Biotechnology?
DNA sequencing, which is the cutting and pasting of DNA
nucleosome
bunched up histones
Does RNA polymerase need a primer?
Nuhuh
What is the start point of transcription called?
Start Site
telomeres
the are of unimportant DNA sequence that does NOT get coded - it is just there so there’s room for the polymerase to bind
therfore it gets shorter and shorter
polycistronic transcipt
one gene codes ALL proteins
monocistronic transcript
one gene codes one protein
wobble pairing
in mRNA, base pairing is SET in stone
in tRNA, (generally the 3rd base), some non-complementary bases do bind
epigenetic changes
modification of histone protein - which control the winding of the DNA
operon
cluster of genes controlled by one promoter
what are the four parts of an operon
- structural gene
- promoter gene
- operator
- regulatory gene
structural gene in an operon
the part where the info that we WANT is
promoter gene in an operon
RNA polymerase binds here
operator in an operon
the place where repressor/activator binds
regulatory gene
the place where the repressor protein information for itself is
inducer for an operon
trigger that turns the operon on or off
repressible operon
an operon which is usually on, but turns off due to inducer
inducible operon
an operon which is usually off, but turn on due to inducer
Viruses
nonliving agents - needs host cell - that seek to replicate and spread
What are the two stages that viruses CAN have?
- lyctic cycle
- lysogenetic cycle
lyctic cycle
uses the host cell to replicate
eventually the host cell ruptures
lysogenetic cycle
virus inserts itself into host’s genome
this can lead to transduction
envelope virus
has a lipid membrane
retrovirus
a specific type of virus that uses reverse transcriptase
Transduction vs. Transformation vs. Transfection
Transduction - accidently picking up of bacterial DNA to a cell’s DNA
ACCIDENTLY PICKING UP SOMEONES CHILD
Transformation - A cell deliberately taking in floating DNA to its genome
KIDDNAPPING
Transfection - purposefully trying to add DNA to a eukaryotic cell’s genome
FORCED ADOPTION
antisense strand is…
non-coding
