AP Bio Unit 6: Gene Expression and Regulation Cheat Sheet (2024)

DNA:

RNA:

double stranded

single stranded

deoxyr­ibose

ribose

A-T

A-U

G-C

G-C

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

Eukaryotic modifi­cations to primary transcript (pre mRNA)

~ before it leaves the nucleus

~ bond altera­tions to the ends

~ removal in interv­ening sequences

regulate gene activity

single gene may be able to synthesize more than one protein

RNA -> protein

inform­ation in RNA is passed to proteins

1) codon recogn­ition

2) peptide bond formation

3) transl­ocation

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

chromatin: a complex of DNA and protein

histones: proteins associated with DNA packing

"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

"on switch­"

loosely wrapped around histones

genes can be transc­ribed

acetul groups are added to amino acids of histone proteins

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

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

phosphate group

sugar

nitrog­enous base

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:

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

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

made in nucleotide

P site: holds the polype­ptide

A site: holds amino acids

E site: exit site

some are free and some are fixed

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: 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"

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

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

double helix

~ "­bac­kbo­ne": sugar + phosphate

~ "­run­gs": nitrog­enous bases

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

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

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

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:

~ 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:

Eukary­otic:

takes place in cytoplasm

takes place in cytoplasm

ribosomes begin transl­ating while mRNA is still transc­ribing

transc­ription and transl­ation separate

redund­ancy: more than one codon for an amino acid

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

early evolution since shared among living species

genes can be transf­erred within species and among others as well

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