Unit 6: Gene Expression and Regulation Flashcards
Griffith Experiment
experiment: injected mice with strains of pneumonia, some died some didn’t
Conclusion: something survives heat treatment and becomes a “Transformation Factor”
Avery, McCarthy, Macleod
built off of Griffith (wanted to figure out what the transformation factor was)
Conclusion: DNA is the transformation factor
Hershey and Chase
sole purpose was to back up results from Avery, McCarthy, and Mcleod
used bacteriophage virus + radiation
Conclusions: exact same as Avery, just proved it in a different way (DNA not proteins are the source of genetic information)
Franklin, Watson, and Crick
used x-ray to determine structure of DNA (Photo 51)
Conclusion: DNA is a three-dimensional double helix structure
Eukaryotic vs Prokaryotic DNA
Eukaryotes have multiple LINEAR chromosomes and cannot have plasmids
Prokaryotes have a SINGLE CIRCULAR chromosome and can have plasmids
Plasmid
small, circular piece of DNA that can be transferred between bacteria
Recombination
the mixing of DNA from two different sources (aka sex)
Bateriophaege
virus that specializes in infecting and killing bacteria in order to reproduce
Bacterial Reproduction
when conditions are good, they prefer ASEXUAL reproduction through binary fission (this is the most efficient option)
- problem: NO GENETIC DIVERSITY (any change could kill whole population)
when the environment is less ideal and tough, bacteria must have sex (mix DNA) and use either Transformation, Conjugation, or Transduction
Transformation (bacterial sex)
- when prokaryotes acquire new genetic information from the environment (pick it up from dead bacteria/find it lying around)
BENEFITS: free genes, could provide new traits to overcome evolutionary and environmental challenges
COSTS: not all genes are useful to species. Also, it could waste energy and possibly harm the bacteria itself or it’s host (it might need the host to live to survive)
Conjugation (bacterial sex)
- requires TWO LIVING CELLS
- the transfer of DNA between 2 living cells
HOW: a plasmid containing genes is copied and transferred to a new cell that didn’t have the plasmid (cells connect using a pilus b/c they need to be in direct contact)
BENEFITS: creates a new donor cell that can give the genes to more cells, these genes could help the bacteria survive
CONS: it takes a lot more work and energy to find other bacteria and do this process - only worth it when conditions aren’t as favorable
Transduction (bacterial sex)
- transfer of DNA by viruses (viruses accidentally transfer bacterial DNA instead of the virus and don’t kill the cell)
Viruses (purpose, shape, and cycles)
viruses aren’t dead or alive, they’re somewhere in between (virus = more virus + super organized, but they can’t reproduce themselves and don’t respond to the environment)
PURPOSE: Spread disease (infect cell, make more, kill cell, continue cycle)
SHAPE: protein shell/coat = CAPSID (genetic information is stored in the capsid, viruses can have DNA or RNA and both can be single and doubled stranded)
LYTIC CYCLE: virus hacks cellular machinery to rapidly make more viruses that will explode/ lyse out of the host cell
- basically, turns cell into a virus factory making thousands - millions of new viruses
LYSCOGENIC CYCLE: the viral genome is incorporated to the host DNA through recombination. So, when the host replicates its DNA, the viral DNA is also copied and passed to the daughter cell
- these viruses take a long time to detect
- these cells eventually enter the lytic cycle and spread rapidly
Topoisomerase
enzyme that uncoils DNA
Helicase
enzyme that unzips DNA
DNA Polymerase
enzyme that builds new strands of DNA (only can build new strand in the 5’ to 3’ direction - moves 3’ to 5’ direction on the old strand)
NEEDS RNA primer as a landing pad on DNA strand to start synthesis. once it gets started it keeps going until something stops it.
Primase
enzyme that builds RNA primers
Ligase
enzyme that covalently bonds the backbone together
Exonuclease
enzyme that removes RNA primers
DNA Polymerase III
enzyme that “proofreads” DNA strand and fixes mistakes by replacing the mistake with a new base
DNA Replication Process
Semi Conservitive (half-keeping) and results in two identical strands of DNA that have one strand from the old DNA and one newly synthesize strand.
STEP 1: Topoisomerase uncoils the DNA to form a ladder like structure
STEP 2: Helicase unzips the DNA by breaking hydrogen bonds (single strand binding proteins - SSBs - prevent the strand from rebinding with itself) - creates a REPLICATION FORK
STEP 3: Leading strand and lagging strand synthesis happen at the SAME TIME
STEP 4: Exonuclease goes back and removes RNA primers, creating gaps in strands
STEP 5: DNA poly comes back and fills in the gaps left by Exonuclease (DNA poly can land on the newly synthesized DNA instead of an RNA primer now)
STEP 6: DNA Ligase comes through and creates covalent bonds to glue strands together
THERE ISN’T JUST ONE REPLICATION FORK, THIS PROCESS HAPPENS AT MULTIPLE SPOTS AT ONCE - ALL STEPS ARE OCCURING BASICALLY SIMULTANEOUSLY
Leading Strand Synthesis
When DNA polymerase attaches to an RNA primer (on the 3’ of old strand) on and builds one continuous strand of DNA in the 5’ to 3’ direction (this follows closely behind the helicase as it unzips the DNA)
Lagging Strand Synthesis
When helicase is unzipping DNA in the opposite direction of synthesis. Requires DNA poly to build DNA backwards
- RNA primers land on DNA as helicase unzips DNA, DNA poly lands on primers and creates a short section of DNA called an Okazaki Fragment
- DNA poly waits for helicase to unzip another section then RNA primer lands and DNA poly can fill in that next section until it hits the other RNA primer
- the lagging strand has a lot more gaps in the new DNA than the leading strand once exonuclease goes through and removes RNA primers
Telomeres
Regions at the end of chromosomes with non-coding sequences of DNA (allows cells to replicate and then destroys the single strand parts leftover without destroying important codes)
Necessary because DNA Poly can fill in backwards so the areas with the first RNA primers are left as gaps and our bodies are programmed to destroy any single strand DNA so those ends are destroyed.
Sense vs Antisense Strand
SENSE: the unused strand in RNA replication
ANTISENSE: the strand used as a template for replication (also known as the minus strand or non-coding strand)
Central Dogma of Biology
TRUE FOR EVERYTHING
DNA is the code for life and it is TRANSCRIBED into mRNA which then is TRANSLATED into proteins
ALL living things follow the flow: DNA –> mRNA –> proteins
Viruses are the only exception to this pattern
Transcription
The process of turning DNA into mRNA (using DNA as a template to create strands of RNA)
STEP 1: same as DNA replication (topoisomerase uncoils and helicase unzips)
STEP 2: RNA polymerase binds to a promoter (landing strip on DNA for RNA poly to land in correct position)
- starts synthesizing at INITIATION SITE and stops at the TERMINATION SEQUENCE
- once complete RNA poly falls off and the newly formed RNA falls off/disassociates from DNA
At the end of transcription, RNA is produced as an intermediate molecule that will be used for proteins (Prokaryotes can use mRNA to make proteins immediately after transcription, Eukaryotes have to modify it to be used)
Codon
the groups of three base pairs in DNA/RNA ( GCA CTA TCA AAG)
Each triplet (codon) codes for 1 specific amino acid (3 nucleotides = 1 amino acid)
mRNA processing
WHY: transcription created pre- mRNA that isn’t ready to be used b/c cells destroy random DNA + RNA outside of the nucleus so pre-mRNA can’t leave nucleus yet
The mRNA undergoes modifications to protect it from viral defenses outside the nucleus. It also is spliced to keep the important codes and then can be alternatively spliced to code for different proteins from the same RNA
RESULTS: mature mRNA has been created and will leave nucleus to code for proteins
RNA modifications
RNA MODIFICATIONS: chemical alteration to protect the mRNA
- A methylated guanine (methyl-guanine cap) is added to the 5’ end of pre- mRNA
- A poly- adenine is added to 3’ end (AAAAAAAA…….)
These modifications help avoid viral defenses the destroy RNA and DNA in the cytoplasm
The length of the poly adenine tail can range greatly and is dependent on the environment
mRNA splicing
mRNA SPLICING: only 2% of you DNA codes for proteins, splicing keep the coding parts and gets rid of the non-coding parts
EXONS: the coding sequences
INTRONS: non-coding sequences
All DNA is coded into RNA during transcription, introns were removed by a spliceosome (protein complex) leaving the coding exons to build proteins
Alternative Splicing
Last step in mRNA processing, it allows multiple uses for the same sequence of DNA
- one gene spliced differently = multiple different proteins
Alternative splicing is just different combinations of the exons on a gene which lead to a different protein being created from that sequence
- example of gene regulation b/c it can do multiple things with one gene
- the spliceosome takes out introns and changes exons to make new combinations
Translation
the process of using mRNA to make a protein
Step one: ribosome binds to mRNA (ribosome has three active sites, each holds one tRNA)
- tRNA is transfer RNA and it carries amino acids to the mRNA strand, knows where to go b/c anticodons find their complementary codon and are specific to one amino acid
First codon is always AUG
Step two: the ribosome shifts a whole codon towards the 3’ end (allows a new tRNA to come in with a new amino acid). Amino acids bond together and build a chain of amino acids/polypeptide (tRNA can be reused and bring more amino acids in)
Step 3: ribosome encounters a stop codon (UUA, UAG, UGA) triggering the termination factor and removing the ribosome from the mRNA
Prokaryotic Translation
- don’t have a nucleus
- no separation between creation of mRNA and creating the protein (as soon as it comes off DNA it is translated into proteins
- EXACT SAME SYSTEMS BUT TIMING IS DIFFERENT
Redundancy of DNA
64 possible codons but only 20 amino acids can be made
- multiple codons code for the same acid
* means that not every mutation causes a change = protections from mutations *
- normally the third letter doesn’t matter/ least important in determining the amino acid
Mutation
change in the DNA SEQUENCE of an organism (critical for evolution b/c it creates variation that leads to natural selection/ individuals harmed but species helped by mutations)
Mutagen
anu outside force or chemical that can case mutations to happen at a rate higher than the normal rate (ex. radiation, x-rays, smoking, alcohol, and processed meats)
Point Mutations
a substitute or mismatch in the mRNA (a single nucleotide is replaced = one codon changes = one amino acid changes)
Sense: mutation codes for the same amino acid & does not alter protein function (harmless)
Missense: mutation codes for a different amino acid (can harm or help function, mostly harmful)
Nonsense: mutation codes for a premature stop codon. An incomplete protein will NEVER be close to correct conformation (always HARMFUL and likely deterimental)
Frameshift mutations
Change the reading frame of the ribosome (reads incorrect frame of codons)
- indels = insertion + deletion, they add or remove 1 or multiple nucleotides
- often end up altering MANY amino acids in a sequence + have major impacts on conformation
ALWAYS BAD
Duplication, Inversion, and Translocation mutations
Duplication: sequence of dna is copied and repeated in DNA
Inversion: sequence of DNA (small or large) is reversed
Translocation: a piece of a chromosome breaks off and reattaches to a completely different chromosome
- reciprocal translocation: chromosomes switch with each other
* Different from crossing over b/c it’s not homologous chromosomes
Differentiation
how our cells now what cells should develop into which tissues (example of gene regulation)
in multicellular organisms, ALL CELLS CONTAIN THE SAME GENOME, all cells contain the genetic info for every single gene + protein that organism can product
different cell types express different types and amounts of proteins
Gene regulation
turning on or off the transcription and or translation of genes (some genes always expressed, some never expressed, some sometimes expresses)
Advantages:
1. cells can conserve resources by only producing proteins when they need them
2. cells can respond to changes in their environment
3. cells can specialize to do a certain job or fill a role in the organism
Operon
cluster of genes that is controlled buy a single on/off switch (light a light switch) - respond based on different things (improves fitness by being able to respond to the environment and conserve energy and reasources)
Parts:
- promoter: DNA sequences were RNA polymerase will bind to DNA to initiate transcription
- operator: on/off switch (DNA sequence)
- repressor: protein that binds to the operator preventing RNA poly from binding to promotor
- structural/functional genes: the genes that lead to a cellular response (coding genes that are being controlled by the operator)
Inducible Operon
An operon that is normally turned off but can be turned on when conditions are meet
- ex. lac operon, prescence of lactose induces operon
Repressible Operon
An operon that is normally turned on but can be turned off when conditions are meet
Transcription Factors
- proteins that increase or decrease a certain gene (do this by recruiting or repressing RNA polymerase)
- frequently involved in the end of signal transduction pathways
- a single transcription factor can regulate many genes
Regulatory DNA sequences
- sequences of non-coding DNA (not gene or promotor) that control regulation
- these “enhancer regions” often use activator proteins to forces conformation change (bend or fold) in DNA/ triggers activation
- enhancer regions allow transcription factors to bind more easily and effectivly to attract RNA polymerase to begin transcription
Looks like a SNOWMAN
Epigenetic modifications
MULTIPLE FORMS OF MODS
- changes to the DNA or associate proteins that alter expression ( not all made to increase expression)
ex. histone acetylation results in conformation changes that loosen DNA and make it more accessible by RNA (promotes transcription)
- DNA is really really condensed so it can be hard to transcribe in that state
Post translation modifications
- changes made to the amino acids after translation 9changes to the protein itself)
- acids can be added, removed, or chemical groups are changed
