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AP Bio Unit 6: Gene Expression and Regulation Cheat Sheet by

AP Bio Unit 6: Gene Expression and Regulation

DNA vs. RNA

DNA:
RNA:
double stranded
single stranded
deoxyr­ibose
ribose
A-T
A-U
G-C
G-C

DNA Replic­ation Steps Image

DNA Comparison

Prokar­yotic DNA:
Eukaryotic DNA:
double stranded
double stranded
circular
linear
one chromosome
usually more than one chromosome
in cytoplasm
in nucleus
no histones
DNA wrapped around histones (proteins)
superc­oiled DNA
forms chromatin

RNA Processing

Eukaryotic modifi­cations to primary transcript (pre mRNA)
~ before it leaves the nucleus
~ bond altera­tions to the ends
~ removal in interv­ening sequences

Role of Introns

regulate gene activity
single gene may be able to synthesize more than one protein

Transc­ription and Transl­ation Image

Transl­ation

RNA -> protein
inform­ation in RNA is passed to proteins
1) codon recogn­ition
2) peptide bond formation
3) transl­ocation

Transl­ation Image

Regulation of Gene Expression

what makes cells different:
~ cells have different shapes and proteins
~ cells use the DNA in the nucleus differ­ently
~~ some gene are turned on/off
differ­ent­ation:
~ when a cell changes from one form to another
~ cells become specia­lized in structure and function
differ­ential gene expres­sion:
~ the expression of different genes by cells with the same genome

DNA Packing

chromatin: a complex of DNA and protein
histones: proteins associated with DNA packing

DNA methyl­ation

"off switch­"
tightly wrapped around histones
genes can not be transc­ribed
methyl groups are added to the DNA
gene expression is reduced
less transc­ription
barr bodies: one X chromosome condenses because of DNA methyl­ation

Histone Acetyl­ation

"on switch­"
loosely wrapped around histones
genes can be transc­ribed
acetul groups are added to amino acids of histone proteins

Gene Regulation

DNA is made up of DNA
DNA is used to give instru­ctions for the production of proteins in the process of protein synthesis
gene regulation determines which genes are turned on/off
proteins can increase or decrease transc­ription

Types of Mutations

point mutations:
~ caused by just one nucleotide base pair substi­tution of a gene
~ ex:
~~ missense mutation
~~~ still codes, but not properly (sickle cell anemia)
~~ nonsense mutation
~~~ altera­tions codes for a stop codon
~~ silent mutation
~~~ a change in DNA but not a change in the amino acid sequence
frameshift mutations:
~ caused by insertions and deletions of base pairs
~ alters the three letter reading frame
 

Parts of a Nucleotide

phosphate group
sugar
nitrog­enous base

Transc­ription Image

DNA Replic­ation

in S phase of Mitosis
making DNA from DNA
nucleo­tides can only be added to the 3' end of a nucleotide
5' to 3' direction
enzymes mediate the process of DNA replic­ation
1) helicase unwinds DNA at origin of replic­ation and creates replic­ation forks
2) topois­omerase prevents overwi­nding and single­-strand binding proteins support the replic­ation bubble
3) primase adds RNA primer
4) DNA polymerase III adds nucleo­tides in 5' to 3' direction on leading strand
5) lagging strand grows in 3' to 5' direction away from the replic­ation fork by the addition of okazaki fragments
6) DNA ligase seals together okazaki fragments (short segments of DNA that grow 5' to 3' that are added onto the lagging strand)
7) DNA polymerase replaces RNA primers with DNA

Prokar­yotic vs. Eukaryotic Transc­ription

Prokar­yotic:
Eukary­otic:
takes place in cytoplasm
takes place in nucleus
several gene transc­ribed at one time
single gene transc­ribed at one time
no modifi­cations before transl­ation
primary transcript modified before transl­ation

Main Types of RNA

mRNA:
~ "­mes­sen­ger­"
~ carries genetic code to the ribosome
~ codon
tRNA:
~ "­tra­nsf­er"
~ transfers amino acids to the ribosome
~ anticodon
rRNA:
~ "­rib­oso­mal­"
~ makes up ribosomes
~ ribosomes build proteins

Ribosomes

made in nucleotide
P site: holds the polype­ptide
A site: holds amino acids
E site: exit site
some are free and some are fixed

Leading Strand

need RNA primer from DNA primase
RNA primer allows DNA polymerase to add nucleo­tides at the 3' end
can not add nucleo­tides at 5' end

Operon

operon: way of regulating genes and is usually made up of a few genes that involve enzymes
RNA polyme­rase: builder enzyme, needed in order to start transc­rip­tion, needs a promoter to bind to DNA
operator: a part of the DNA where a repressor can bind, if repressor is bound to operator it blocks RNA polymerase which means mRNA can not be made so neither can proteins
lac operon: operator and promoter region of DNA and three genes that code for enzymes that help in breaking down lactose
~ there is a gene that codes for the repressor production and this gene has its own promoter
~ if lactose is not present, then the repressor binds to the operator and blocks RNA polymerase which means mRNA and proteins can not be produced
~ if lactose is present, the lactose (sugar) binds to the repressor (repressor can not bind to operator) and RNA polymerase finds its promoter, binds, and transc­ribes to make mRNA from the genes on operon, the mRNA will be used to make enzymes to break down the lactose sugar
~ no lactose: "­off­"
trp operon:
~ evolved in bacteria to deal with absence of tryptophan
~ tryptophan is on amino acid which moves proteins
~ designed to make tryptophan if it is not present
~ if bacteria does not have trypto­phan, there is a number of genes that are required to make it
~ tryptophan fits inside the repressor and the repressor will change it's shape to fit in the receptor
~ if a lot of tryptophan is present, then we do not want to make more so the repressor is going to set operator in "­off­"

Chromo­somal Mutations

involves a change in the structure or number of chromo­somes
deletion: loss of all or part of a chromosome
duplic­ation: reverses the direction of parts of a chromosome
inversion: reverses the direction of parts of a chromosome
transl­oca­tion: part of one chromosome break off and attaches to another chromosome

Differ­ent­iation

when a cell changes from one type to another
all specia­lized cells come from stem cells (unspe­cia­lized)
DNA contains genes and genes contain proteins that change the way cells look and act
every somatic cell in your body contain the same DNA
using genes -> expressing -> turned "­on"
the specia­lized cells can not specialize again and can not go backwards to the stem cells
cells decide what they will be based on internal or external enviro­nmental cues
internal: transc­ription factors will activate certain genes and turn them on (factors are bunched up because of when the zygote will divide)
external: (induc­tion) (like peer pressure) a group of cells can induce another group to differ­entiate by using signals (like diffusion, direct contace, gap junctions)
goal: to change gene expression (turn on/off genes
 

Structure of DNA

double helix
~ "­bac­kbo­ne": sugar + phosphate
~ "­run­gs": nitrog­enous bases

DNA Replic­ation Image

DNA Replic­ation Key Factors

Eukary­otic: replic­ation before mitosis or meiosis (inter­phase)
helicase: unzipping enzyme
~ breaks the hydrogen bonds holding bases together
DNA polyme­rase: builder
~ replicates DNA molecules to build new strand of DNA
primase: initia­lizer
~ makes the primer so that DNA polymerase can figure out where to go to start to work
ligase: gluer (binder)
~ helps glue/bind DNA fragments together

DNA Replic­ation Process (2nd example)

starts at the origin (ident­ified by DNA sequence)
1) helicase unwinds DNA
~ single stranded binding protein bind to DNA strands to prevent the strands from going back together
~ topois­omerase keeps DNA from superc­oiling
2) primase makes RNA primers on both strands
3) DNA polymerase builds new strand in 5' to 3' direction
~ this means it moves along old template strand in 3' to 5' direction
~ adds new bases to 3' end on new strand
4) ligase takes care of gaps between Okazaki fragments
at the end of replic­ation there is two identical DNA molecules
~ semi-c­ons­erv­ative: each copy contain a new and original strand

Transc­ription

DNA -> RNA
1) Initiation
~ promoter sites: region of the DNA where the RNA polymerase binds
~~ 100 nucleo­tides long
~~ transc­ription factors: binding protein
~~ TATA box: promoter sequence
2) Elongation
~ RNA polymerase in action
~~ separates and untwists helix
~~ links nucleo­tides in a 5' to 3' direction
3) Termin­ation
~ termin­ation sequence: AAUAAA

Transcript Modifi­cations

5' cap: GTP is added
two functions:
1) protects transcript from hydrolytic enzymes
2) tags the end as "­leader segmen­t" for the ribosome
s' end: last to be translated
poly(A­)tail: 30 to 200 nucleo­tides added to end
~ inhibits degrad­ation
~ facili­tates ribosomal attachment
~ attached to stop codon
RNA splicing
~ removal of introns (noncoding sequences) (inter­vening sequences)
~ pasting of exons (coded sequences) (exit the nucleus)
small nuclear ribonu­cle­opr­oteins found in nucleus (snRNP; snurps): complexes of small RNA units and proteins found in nucleus
splice­osome: complex of snurps involved in the locating and cutting out of introns

Codons

codons:
~ mRNA triplet that codes for an amino acid
~ start codon: AUG
~ stop codon: UAA, UAG, UGA
reading frame:
~ start to stop sequence of nitrogen bases
antico­dons:
~ complement of the codon found on tRNA

Prokar­yotic vs. Eukaryotic Transl­ation

Prokar­yotic:
Eukary­otic:
takes place in cytoplasm
takes place in cytoplasm
ribosomes begin transl­ating while mRNA is still transc­ribing
transc­ription and transl­ation separate

Redundancy and Ambiguity of the Code

redund­ancy: more than one codon for an amino acid
ambiguity: codon do not code for more than one amino acid

Evolution of the Codes

early evolution since shared among living species
genes can be transf­erred within species and among others as well

Lagging Strand

primer is several nucleo­tides
DNA primase goes along the lagging strand and adds RNA primer
once you have primer, polymerase can add on DNA at 3' end (5' to 3')
end up with Okazaki fragments
slower process
DNA ligase puts all fragments together as one strand
~ RNA is replaced with DNA

Mutations Image

 

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