Unit 5 Exam Flashcards
nutritional mutants
unable to synthesize arginine
central dogma of biology
DNA to RNA to protein
enzyme to convert RNA to DNA
reverse transcriptase
one gene/ one polypeptide hypothesis
genes specify the structure of enzymes and each gene encodes the the structure of one enzyme
transcription
converting DNA to RNA, produces an exact copy of DNA on RNA, directly transfers info
translation
RNA to protein, requires translating from the nucleic acid to the protein “languages”
retroviruses
class of viruses that can convert their RNA genome into a DNA copy
template strand (antisense)
one of the 2 DNA strands that is used to be copied, complementary to RNA’s transcript’s sequence, 3’ to 5’
coding strand (sense)
the non copied strand of DNA, same sequence as RNA transcript, 5’ to 3’
mRNA
messenger RNA, used to direct the synthesis of polypeptides, carries DNA message to ribosome for processing
rRNA
ribosomal RNA, multiple sub types used by ribosomes
tRNA
transfer RNA, interpret mRNA and escort amino acids
small RNAs (miRNA, siRNA)
regulate gene expression
snRNA
small nuclear RNA, part of the machinery involved in nuclear processing of eukaryotic pre mRNA
SRP
signal recognition particle, contains both RNA and proteins, mediates protein synthesis by ribosomes in rough ER
codons
basic unit of genetic code, sequence of 3 adjacent nucleotides in DNA/mRNA that codes for one amino acid
RNA polymerase
synthesizes RNA from DNA template, in prokaryotes it is divided into core and holoenzyme
core polymerase
synthesizes RNA using a DNA template, made of 2 alpha subunits, beta subunit, and beta’ subunit
2 alpha subunits in core polymerase
help to hold the compex together and bind to regulatory molecules
beta and beta’ subunits in core polymerase
the active site, bind to DNA template
holoenzyme
initiates synthesis, sigma added to core polymerase
promoter
start site for RNA transcription, forms a recognition and binding site for the RNA polymerase
terminator
site on DNA that sends a signal to RNA polymerase to end transcription
transcription unit
from promoter to terminator
transcription bubble
region containing the RNA polymerase, the DNA template, and the growing RNA transcript
difference between transcription in eukaryotes vs prokaryotes
- in prokaryotes, transcription is occuring at the same time as translation (coupling)
in eukaryotes, transcription is in nucleus and translation is in cytoplasm - prokaryotes organize multiple genes on the same mRNA with operons
- eukaryotes have 3 RNA polymerases while prokaryotes have 1
operons
single transcription unit that encodes multiple enzymes
RNA polymerase 1
transcribes rRNA
RNA polymerase 2
transcribes mRNA, TATA box promoter
RNA polymerase 3
transcribes tRNA and small RNAs
transcription factors
interact with RNA polymerase 2 to form an initiation complex at the promoter that is necessary for transcription to occur
initiation complex
in eukaryotes, transcription requires binding of transcription factors to promoter before RNA polymerase 2 binds to DNA
primary transcript
RNA synthesized by RNA polymerase 2, which is processed to produce the mature mRNA
5’ cap
methylated GTP added to protect 5’ end while transcription is still in process, protecting the end from degradation
3’ poly A tail
polyadenylation signal sequence, series of 100-200 adenine residues is added after the cleavage by enzyme poly A polymerase
introns
non coding DNA, that interrupts the sequence of the gene, intervening sequences
exons
coding sequences that are expressed
spliceosome
organelle that removes noncoding sequences (introns) from mRNA
structure of tRNA
has to be able to interact with mRNA and amino acids, made of acceptor stem and anticodon loop
acceptor stem
3’ end of the molecule, binds to amino acid
anticodon loop
bottom loop of clover leaf, can base pair with codons in mRNA
tRNA charging reaction
reaction catalyzed by activating enzymes to bind an amino acid to a tRNA, making it a charged tRNA
A site on ribosome
aminoacyl, binds to tRNA carrying next amino acid in sequence (docking)
P site on ribosome
peptidyl, binds to tRNA attached to peptide chain (attaching)
E site on ribosome
binds to tRNA that carried previous amino acids (exiting)
initiation of translation
AUG start codon on mRNA codes for methionine, tRNAmet is positioned over the first chain AUG codon of mRNA, forms EPA sites where successive tRNA molecules bind to the ribosomes
elongation of translation
tRNA go through elongation cycle, moving their bound amino acid to mRNA by forming peptide bonds, tRNA anticodon must match mRNA codon, translates in 5’ to 3’ direction
termination of translation
requires a stop codon on the mRNA, stop codons don’t bind tRNA but bind to release factors, release of a polypeptide from the final tRNA and dissociation of ribosome, concludes the process of gene expression
mutation
heritable change in genetic material
base substitution
changing 1 nitrogenous base on DNA, may not lead to change in expression
polymorphisms
genetic differences between individuals in a population, different blood types
point mutation
mutation that alters a single base
missense mutation
“sense” of the codon involved has not been changed, changes an amino acid
conservative missense mutation
occur when substituted amino acid is chemically similar (nonpolar for nonpolar)
nonconservative missense mutation
occur when substitute is chemically different (polar for nonpolar), ex. sickle cell
nonsense mutation
mutation leads to formation of stop codon, codon no longer makes “sense”
copy number variation
(CNV) genomic rearrangements result in differences in the number of copies of a particular genomic region
4 types of copy number variation
- deletion (loss of DNA)
- insertion
- duplication (gain of DNA)
- reciprocal translocation (one chromosome is broken and becomes part of another chromosome)
direction of transcription and translation of RNA
reads DNA 3’ to 5’, but builds mRNA strand 5’ to 3’
epigenetics
altering gene expression based on environment
forms of epigenetics
adding methyl/acetyl groups and altering access to DNA
ex. women in great depression has extra methyl groups inherited
cell determination
when a cell’s fate is decided (going to bone, brain, stomach, etc.)
cell differentiation
develop unique cellular properties
recombinant DNA
one DNA from different sources (difference organisms)
anneal
joining 2 DNA strands at complementary sequence
genomics
study of whole genomes, complete makeup of organisms
genetic markers
any detectable genetic difference among individuals
genetic map
shows relative positions on gene on chromosomes
physical map
shows precise location/sizes for genes
gene expression
conversion of genotype to phenotype
regulatory proteins
modulating the ability of RNA polymerase to bind to the promoter
positive control
increases the frequency of initiation
negative control
decreases the frequency of initiation
repressors
proteins that bind to regulatory sites on DNA called operators to decrease initiation of transcription, mediates negative control, prevents polymerase from binding
activators
mediates positive control, allosteric proteins that bind to DNA and enhance the binding of RNA polymerase to promoter
induction
occurs when enzymes for a certain pathway are produced in response to a substrate
repression
occurs when bacteria capable of making biosynthetic enzymes do not produce them
glucose repression
preferential use of glucose when other sugars are present
increase in glucose levels, ___ in cAMP
decrease in cAMP, CAP is unable to activate promoter, blocking lactose
cAMP
allosteric modulator
operon
multiple genes with a single promoter that make 1 transcription unit
general transcription factors
necessary for transcription to occur at all
protein - primary structure
amino acid sequence
protein - secondary structure
initial folding and twisting (motifs)
protein - tertiary structure
combinations of secondary structures (domains)
DNA binding motifs
directly involved in protein binding specificity
most common DNA binding motif
helix-turn-helix, recognition helix fits into major groove
specific transcription factors
alter transcription in certain cell types or in response to specific stimuli
promoters
binding sites for general transcription factors
enhancers
DNA sequences necessary for high levels of transcription that can act independently of position or orientation
chromatin remodeling complexes
use factors to modify histones and DNA, and alter chromatin structure directly
ATP dependent remodeling factor
molecular motors that use energy from ATP hydrolysis to alter the relationship between histone and DNA
DNA methylation
doesn’t interfere with H-bonds but can interact with proteins
histone methylation
methyl groups inhibit transcription
histone acetylation
acetyl groups promote transcription
4 major structural changes from histone remodeling
nucleosome sliding, remodeled nucleosome, nucleosome displacement, histone replacement
cytoplasmic determinants
inherited maternally and deposited in oocyte
recombinant DNA
building a single DNA molecule from different sources
restriction endonucleases
enzymes that cleave DNA at specific locations, free ends can be joined to other strands of DNA
EcoRI
typically cleave at GAATTC
gel electrophoresis
technique using the negative charge on DNA to separate DNA molecules based on size
molecular cloning
producing recombinant DNA molecules
cDNA
complimentary DNA, the DNA sequence created from mRNA by reverse transcriptase, used in quantitative PCR
polymerase chain reaction (PCR)
mimics the process of DNA replication to produce millions of copies of a DNA sequence by amplification without the need for molecular cloning
PCR: denaturation
heat is used to separate strands of double stranded DNA
PCR: annealing of primers
primers provide the 3’ OH required for elongation by DNA polymerase
PCR: synthesis
DNA polymerase makes new DNA
transgenic organisms
contains a gene from a different species (transgene) which has been incorporated into genome through genetic engineering
genetically modified organisms
organisms that have been genetically altered by techniques other than conventional breeding
knockout animal
one that has had a gene inactivated so that the function of the gene is lost, using embryonic stem cells
FISH
fluorescent in situ hybridization, technique to allow for detection of gross chromosomal abnormalities (large deletions, inversion, duplications, and translocations)
quantitative PCR
isolate mRNA, use reverse transcriptase to generate cDNA, use PCR to amplify cDNAs
pros to GMOs
potential to reduce world hunger, reduced use of fossil fuels, reduced use of pesticides, reduced conversion of land
cons to GMOs
potential to transfer allergens, unintended effects on non target organisms, genes escaping through hybridization
genetic markers
any detectable differences in individuals
genetic maps (linkage maps)
abstract maps that place the relative location of genetic markers on chromosomes based on recombination frequency between markers
physical maps
precisely position genetic markers in the genome, with the ultimate physical map being the complete DNA sequence of a genome
restriction maps
not suitable for large DNA molecules, used for organelle and viral genomes, uses restriction enzymes to cut DNA for mapping
chromosome maps
use of different stains allows for the construction of a cytological map of the entire genome based on banding patterns on chromosomes
sequence tagged site mapping
combines the best of restriction mapping with the best mapping via FISH
2 types of genome fragment assembly for whole genome sequencing
clone-contig assembly and shotgun assembly
clone-contig assembly
assemble portions of a chromosome first and then figure out how the bigger pieces fit together
shotgun assembly
try to assemble all the pieces at once, instead of in a stepwise fashion, no prior information about the sequenced genome is required
how many genes in all mammals
20k-25k
