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AP Biology: Unit 6 Cheat Sheet (DRAFT) by

Gene Expression and Regulation

This is a draft cheat sheet. It is a work in progress and is not finished yet.

Early Genetics

- bioche­mical group first thought to contain genetic inform­ation =
proteins
Griffith bacterium experi­ment~
  
smooth strain (S)
outer capsule; pathogenic
rough strain (R)
NO capsule; NOT pathogenic
Conclu­sion~
  
R cells combined w/ killed S cells transf­ormed into living S cells
  
Avery bacterium experi­ment~
  
- deacti­vated parts of dead S cells to find what transf­ormed the cells
  
Conclu­sion~
  
DNA transforms the bacteria
  
Hershey & Chase DNA experi­ment~
  
phages reproduced in presence of DNA (not proteins)
  
Conclu­sion~
  
DNA is the genetic material
  
Chargaff nucleotide experi­ment~
  
Conclu­sions~
  
base compos­ition varies between each species (diff. % nucleo­tides)
  
# of nitrog­enous bases equaled (A=T G=C)
  

DNA Structure

- x-ray crysta­llo­graphy images of DNA by:
Rosalind Franklin
↳ DNA is a helical shape
- constr­uction of the double helix model by:
Watson & Crick
- purines (2 rings)
A & G
- pyrimi­dines (1 ring)
T & C
- A pairs with T by...
2 H bonds
- C pairs with G by...
3 H bonds
- base pairs present in 1 helix turn =
10
antipa­rallel:
subunits run in opposite directions

DNA Replic­ation Experiment

- experiment done by:
Meselson & Stahl
Prediction
replic­ation style
# bands 1st rep.
# bands 2nd rep.
conser­vative
2
2
semico­nse­rvative
1
2
dispersive
1
1
Results
# bands 1st rep.
1
# bands 2nd rep.
2
conclusion =
semico­nse­rvative

Replic­ation Process

origin of replic­ation:
site where the replic­ation of DNA molecules begins
replic­ation fork:
Y-shaped region on the replic­ating DNA molecule
- E. coli
↳ 1 replic­ation origin
↳ 500 nucleo­tid­es/sec
- human
↳ 100s-1000s of replic­ation origins
↳ 50 nucleo­tid­es/sec
- 2 items required to start replic­ation:
1. primer
2. DNA template strand
- how added nucleo­tides bring energy:
↳ nucleo­tides carried by tripho­sphate
↳ DNA polymerase catalyzes tripho­sphate
↳ 2 phosphates are released
- DNA polymerase adds to the...
3' end
 
(elongates from 5' to 3')
- lagging strand created from series of...
Okazaki fragments

Replic­ation

helicase: enzyme that unwinds & separates the DNA strands
topois­ome­rase: enzyme that breaks, swivels, & rejoins the DNA
primase: enzyme that synthe­sizes RNA primers
primer: a short sequence of RNA that starts Okazaki fragments
polymerase III: enzyme that adds nucleo­tides
polymerase I: enzyme that removes the primer and replaces the nucleo­tides
ligase: enzyme that forms the final bonds between the fragments and nucleo­tides

Errors in DNA

- as replic­ation occurs, DNA polymerase finds & corrects any mistakes ---- reducing the error rate
- change in the DNA nucleotide is perman­ent­/mu­tation when ---- the pair is replicated
- changes in DNA nucleo­tides due to...
↳ 1. replic­ation errors 2. chemicals 3. x-rays 4. sponta­neously
telomeres: multiple repeti­tions of a short nucleotide sequence at the end of a chromosome
↳ buffer zone to delay erosion of the genes as they get replicated
telome­rase: enzyme that catalyzes the length­ening of telomeres (restore original length)
histone: protein respon­sible for the first level of packing of chromo­somes
nucleo­some: segment of DNA wound around a protein unit
 

Gene Expression Background

gene:
region of DNA expressed to produce a functional product (polyp­ept­ide/RNA molecule)
transc­rip­tion:
synthesis of RNA from DNA template
transl­ation:
synthesis of proteins from encoded mRNA
primary transc­ript:
initial RNA transcript from any gene (pre-mRNA)
codon:
3 nucleotide sequence that specifies a particular amino acid
- eukary­otes~
transcribe DNA to pre-mRNA
 
from nucleus to ribosome
- prokar­yotes~
transcribe DNA to mRNA
 
from cytoplasm to ribosome

Transc­ription

RNA polyme­rase:
enzyme that controls the transc­ription of DNA to RNA
↳ pries DNA strands apart & joins the RNA nucleo­tides
↳ moves 3' to 5'
(strand formed 5' to 3')
↳ attaches at the promoter
3 STAGES OF TRANSC­RIPTION
1. Initiation
- transc­ription factors:
protein that allows for polymerase to attach to DNA and transcribe
- 3 items to make up transc­ription initiation complex =
transc­ription factors, RNA polyme­rase, & promoter
- TATA box:
promoter that is 20-25 nucleotide from the starting point
* prokar­yotes have NO transc­ription factors
2. Elongation
a. 10-20 nucleo­tides exposed at a time
b. nucleo­tides added to the 3' end of the RNA molecule
- difference between RNA & DNA nucleo­tides =
different sugars
- nucleotide RNA that DNA doesn't have...
uracil
- RNA & DNA nucleo­tides held together by...
hydrogen bonds
3. Termin­ation
a. transc­ription of the polyad­eny­lation signal adds nucleo­tides of AAUAAA to RNA
b. protein cuts the pre-mRNA from polymerase = end of process!

Transc­ription Diagram

Pre-mRNA Modifi­cation

- 5' end receives 5' cap
- 3' end receives poly-A tail (enzyme adds 50-250 more A nucleo­tides)
↳ facilitate export from nucleus
↳ protect mRNA from hydrolytic enzymes
↳ help ribosomes attach to end of mRNA
RNA splicing:
process of removing RNA sections from pre-mRNA
- introns:
noncoding sequences of pre-mRNA
- exons:
sequences of pre-mRNA used for transl­ation
- 3 benefits of introns:
↳ make many differnet polype­ptides
↳ discrete struct­ura­l/f­unc­tional regions
↳ increase exon shuffling (new protein function)
ribozymes:
RNA molecule that functions as an enzyme
 
(create 3D structure; contain functional groups; H bond w/ DNA or RNA)

Ribosome Structure

tRNA: transfers amino acids from cytoplasm to ribosomes (& contain anticodon)
↳ anticodon: nucleotide triplet on tRNA molecule
↳'wobble': flexible base pairing at the 3rd codon position
- # of amino acids used= 20
-makeup of a ribosome:
- large & small subunit~ made of proteins and rRNAs
(eukar­yotes in nucleolus & prokar­­yotes in cytoplasm)

Transl­ation

3 STAGES OF TRANSL­ATION
1. Initiation
a. small subunit binds to mRNA & initiator tRNA
b. transl­ation initiator complex=
attachment of large subunit (& initiation factors)
2. Elongation
a. codon recogn­ition-
anticodon of tRNA pairs w. mRNA codon
b. peptide bond formation-
removes polype­ptide from tRNA by forming peptide bond
c. transl­oca­tion-
empty tRNA released
* ribosome moves 5' to 3'
3. Termin­ation
a. stop codon-
"­rel­eas­e" factor accepted
b. hydrolysis of bond-
freeing polype­ptide
c. subunits dissoc­iate-
mRNA can be used again

Transl­ation Diagram

polyri­­bo­s­omes: series of ribosomes moving over an mRNA at the same time
chaperone protein: proteins that assist polype­­ptides in forming 3D structures
signal peptides: sequence of amino acids at beginning of polype­­ptide tagging it to where it will go

Nucleotide Mutations

point mutation: change in a single nucleotide
frameshift mutation: change in nucleotide # to not be a multiple of 3
↳ may still code for same amino acid
↳ may code for stop codon early
↳ may result in protein not functi­oning properly

Regulation of Gene Expression

- responds to changes in enviro­nmental conditions
- either adjusts activity of enzymes present or production of enzymes
- 3 things to make up an operon:
operator; promoter; genes
operator:
segment of DNA within promoter that controls the access of RNA polymerase to the genes
repressor:
protein that binds to operator to block attachment of RNA polymerase
↳ made by activity of regulatory gene
repres­sible operon:
transc­ription is inhibited by small molecule binding to regulatory protein
inducible operon:
stimulated when small molecule binds to regulatory protein

Lac Operon

- high lactose = allola­ctose bind to repressor to change shape & no longer attach
- low glucose = high levels of cAMP combine with CAP

Differ­ential Gene Expression

- differ­ential gene expression = different cell types
- 3 processes of develo­pment:
1. cell division 2. cell differ­ent­iation 3. morpho­genesis
cytopl­asmic determ­inants: substances in the egg that influence the course of early develo­pment
induction: embryonic cells influence the develo­pment of another (change in gene expres­sion)
homeotic genes: genes that control pattern formation as an organism develops

Biotec­hnology

Gel electr­oph­oresis
- separates DNA by size and charge
- DNA negatively charges
↳ smaller segments = farther to bottom
Polymerase Chain Reaction (PCR)
- create many copies of DNA segment
↳ DNA denatured → primers added → DNA replicated
Recomb­inant DNA
- DNA segment put into plasmid to be reproduced
DNA Sequencing
- establish the order of nucleo­tides
↳ labeled with dye