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Amino Acid
building blocks of proteins

organic cmpd with amino group, carboxyl group, and various R side groups
poly-A tail
polyadenylation
addn of 20-200 adenines to the 3' end of processed mRNA
r-groups
side chains of amino acids

hydrophobic
hydrophilic
basic
acidic
5'cap
7-methylguanosine added to the 5' end of processed mRNA
intron
intervening sequences of eukaryotic mRNA that are spliced out of a mature mRNA
exon
expressed sequences
codon
set of 3 adjacent nucleotides in an mRNA molecule that specifies the incorporation of an aa to a polypeptide
anti-codon
3 bases in a tRNA molecule that are complementary to the 3 bases of a specific codon in mRNA
tRNA
transfer RNA
acts as adapter molecule
transfers amino acid to ribosome in accordance to codon sequence
ribosome
made of proteins and RNA

structure in which proteins are synthesized
E site
exit site

-where the tRNA exits the ribosome
P site
peptidyl site

location where peptide bonds are created. amino acid from A site is added to the growing polypeptide chain

ribosome binding site that contains the tRNA to which the growing polypeptide chain is attached
A site
aminoacyl site

aminoacyl tRNA enters the ribosome in this location

ribosome binding site that contains the incoming aminoacyl tRNA
shine-dalgarno sequence
conserved sequence of prokaryotic mRNA that is complementary  to a sequence near the 5' terminus of the 16s ribosomal DNA

initiation factor
point mutation
changes that occur at specific sites in genes
incluedes nucleotide pair substitutions and insertion or deletion of one or few NT pairs
frame shift mutation
mutation that changes the reading frame of an mRNA either by inserting or deleting nucleotides
transition mutation
between pyridine and pyridine or purine and purine
transversion mutation
mutation caused by substitution of a purine for a pyrimidine and vice versa
conditional lethal mutation
mutations that are lethal in some environmental conditions, but viable in others
chromosomal translocation
segment of a chromosome is moved to another place (of another chromosome or the same)
chromosomal inversion
chromosome rearrangement that reverses the order of a liner array of genes in a chromosome
tautomeric shift
the transfer of hydrogen atom from one position in an organic molecule to another position
palindromic site
segments of DNA that read the same on the 5' and 3' direction and has a point of symmetry
restriction enzyme
an endonuclease that recognizes specific short sequences of DNA and cleaves DNA at or near that site
methylase
an enzyme that adds methyl groups
Concepts of protein translation
mRNA is translated to a polypeptide

initiation- initiation factors/subunits bind to shine dalgarno or kozak sequencies. Start at first aug 5'-3' tRNA relase of factors

elongation- aminoacyltRNA binds to A via codon. aa transferred from tRNA in P, to tRN in A via peptide bond. ribosome translocates. new tRNA enters A, P gives aa to trna in A. trna in T is uncharged and exits. repeat

termination- when reaches stop codon UAA/UAG/UGA polypeptide release factor. ribosome dissociates
DNA sequence to amino acid
5'-TCAGAGGTG-3'
3'-AGTCTCCAC-5'

5'-UCAGAGGUG-3'

N-ser-glut-etc-C
6 characteristics of genetic code
  1. nucleotide triplets- 3NT=1 codon=1aa
  2. genetic code is nonoverlapping
  3. comma free- read consecutively
  4. degerate- >1 codon specifies for aa
  5. ordered- multiple codons for an amino acid- related
  6. start/stop codons- initiate and terminate
  7. nearly universal- except in mitochondria
What is a reading frame?
sequence of NT, read as triplets in translation

6 ways in transcription (DNA)
DNA sequence ATG read in triplets until stop codon.
possibility of overlapping genes
longest one with uninterrupted code is correct.
Why are there six possible reading frames on any piece of dsDNA?
3 on each strand
each stand has 3 positions
Wobble hypothesis
explains how one tRNA may recognize >1 codon. first two bases pair properly, 3rd in anticodon has some wobble that premits it to pair with more than one base
mutation
a change in DNA at a particular locus in an organism
types of mutation
spontaneous
induced
somatic
germinal
chromosomal
forward
reverse
neutral
null
lethal
conditional lethal
How different types of mutation affect gene expression?
Change in amino acid
frame shift changes or can terminate polypeptide
affect how polypeptide assembles
mutation & evolution
mutations create new alleles which create new genotypes and phenotypes. This genetic variation creates new variation taht may lead an organism to be better fit than other. evolution will select for the individuatls with the mutations.
Ames test
simple and inexpensive method for detecting mutagenicity    

  1. place auxotrophic strand of bacteria (salmonella) that has several mutations (point, frameshift, etc)
  2. make sure that bacteria cannot codes for histinine aa
  3. place his- bacteria in a medium with no his (control)
  4. separately place his- bacteria into medium with trace histidine
  5. let bacteria proliferate
  6. count numbe rof reverse mutations (phototrophic) in both control and experiment
  7. in the control, the mutations are sponataneous
  8. in the experimental variable, the mutations are induced
mutagen dose & mutation rate
directly proportional
x rays- roentgen # ionizations/unit volume
DNA electrophoresis
involves the suspension of DNA segments in a gel meium. an electric current is introduced and allows the segments to segregate by size and charge, creating bands

Whwere did restriction enzymes evolve?
DNA cutting enzymes evolved as a defense mechanism against invading viruses

host DNA methlated and virus is cut up

recodnition sites, 2 cuts in backbone
RFLP uses
restriction fragment length polymorphism

genetic maps/testing
maping chromosomes
DNA cut into small fragments via restriction enzymes
electrophoresis
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