Genetics Unit 4

describe the organization of a protein coding gene

shine-dalgarno sequence, start location for the ribosome

codons which code for a specific amino acid

start codon which initiated transcription

stop codon

describe the organization of a gene mRNA' transcript

antiparllell to the coding gene with the complimentary sequence

what are the three stages of transcription?

imitation, elongation and termination

what is the invitation stage of transcription?

the start of transcription

what is the elongation stage of transcription?

the building of mRNA

what is the termination stage?

the end of transcription

what is a transcription unit?

the full sequence of DNA from the binding sequence, all codons and stop codon

what is a promotor sequence

the site including the -35 and -10 sequences that allow transcription to begin

what is a coding sequence

the group of codons producing polypeptides which form the final protein

what are key aspects of the bacterial promoter?

-35 box and -10 box

what is the sequence and function of the -35 box

TTGACA, initial contact of RNA polymerase

what is the sequence of the -10 box?

TATAAT, unwinding of DNA

what are the components of the bacterial transcription apparatus?

a core enzyme and sigma factor

what the term for the core enzyme bound to sigma factor

a holoenzyme

what is the purpose of the core enzyme?

catalyzing RNA synthesis

what is the purpose of sigma factor?

directing the enzyme to the promotor

how is bacterial DNA transcription initiated?

RNA polymerase loosely binds to DNA and scans for the promoter

once its found sigma factor binds the holoenzyme and DNA is unwound at the -10 forming the open complex

sigma factor detaches and elongation occurs

describe the elongation stage of transcription?

RNA polymerase slides along DNA forming a complimentary strand using NTP’s

in what direction is a template strand read?

3’ to 5’

what direction is complimentary RNA synthesized?

5’ to 3’

what are the two types of termination in bacterial cells?

rho-dependent and rho-independent termination

describe the process of rho-dependent termination?

rho prooien binds to the RUT site and travels towards RNA polymerase

once it earaches up, RHO causes the polymerase to dissociate for DNA

describe the process of Rho-independent termination?

RNA strand forms a hairpin loop after a stretch of U, de-stablizing the RNA-DNA hybrid

RNA polymerase detaches from DNA and the RNA is released

what is the function of RNA polymerase I?

to transcribe ribosomal RNA genes

what is the function of RNA polymerase II

to transcribe all portion coding genes

what is the function of RNA Polymerase II

to transcribe all tRNA

describe the two parts of a eukaryotic promoter?

the TATA box, an extended promotion region, and the transcription start point

what is the function a TATA box?

to position RNA polymerase before the exact start site

what is the function of TFIID?

to help the RNA polymerase find the TATA box

what is the function of TFIIF?

find RNA polymerase

what is the function of TFIIH?

open the DNA and create the open complex

what direction does RNA polymerase II read?

3’-5’

what direction does RNA Polymerase II add nucleotides?

5’- 3’w

what is the function of activator proteins?

to bend DNA around transcription factors to increase the rate of transcription

what is the function of the mediator complex?

to keep the general transcription factors attached to DNA and increase the rate of synthesis

what is basal transcription?

transcription without the use of activators or enhancers

what is the open-complex in eukaryote transcription

once all the general transcription factors are found and TFIIH unwind the DNA

how does transcription stop in eukaryotes?

RNA polymerase runs into a long trail of A’s and dissociates

what is post translation modification?

additions or removals from the pre-RNA before it is exported from the nucleus

what are the 4 types of RNA modification in eukaryotes?

5’ capping, RNA splicing, 3’ cleavage and polyadenylation

what is 5’ capping?

a methylguanosine is added to the 5’ end of RNA to help protect from degradation and aid with ribosome binding

what is RNA splicing?

the removal of introns from pre-mRNA and ruling exons together?

what is the role of the spliceosome?

to remove introns and join exons

describe the splicing process?

• protein binds to the 5’ splice side

• cuts are made a the 5’ and 3’ sites

• exons are joined together and introns degrade?

what is polyadenylation?

addition of adenines to. the 3’ end of mRNA to maintain mRNA stability

what is 3’ cleavage?

removal of pre-mRNA downstream of the poly-a tail

what is the difference between an intron and an exon?

introns are cut from pre-mRNA and remain in the nucleus, exons stay in the RNA and leave the nucleus

what is alternative splicing?

when the same sequence of pre-mRNA is spliced in several different ways

what are constitutive exons?

exons that are always in mature mRNA

what are alternative exons?

exons that are sometimes included in mature mRNA and alter the function of proteins

what is DNA redundancy?

what is DNA degradation?

how does the structure of RNA support it’s biological role?

by being single stranded RNA can easily be

what is the function of mRNA?

to cary genetic code from DNA

what is the function of tRNA?

to transfer amino acids into a polypeptide chain

what is the purpose of the Beadle and Tatum experiment?

to discern weather there gene code for one protein or multiple

describe the first step of the Beadle and Tatum experiment?

bread mold was mutated and plated on minimal media, if it couldn’t grow then it was identified as a mutant

describe the second stage of the Beadle and Tatum experiment?

the mutant mold was grown on a minimal media with one amino acid added in, whichever one if grew on is the amino acid that’s process was mutated

describe the their stage of the Beadle and Tatum experiment?

mold was grown on minimal media with the different intermediates of the amino acid pathway added in to identify which step had been mutated

how did the results of the Beadle and Tatum Experiment support the one gene-one protein hypothesis

each mutation disrupted one specific enzyme in the pathway

what is the function of genetic code?

to connect DNA to actual proteins accurately

what is a codon?

a sequence of three bases that code for an amino acids

what is the n-terminus of an amino acid?

a nitrogen containing group, amino group

what is the c-terminus of an amino acid?

a carboxyl group attached to the central carbon?

what part of an amino acid is variable?

the r-group

how many common amino acids are there?

20

how do peptide bonds form?

the negative oxygen of the c-terminu bonds to the positively charged H of the n-terminus

what is primary protein structure?

the sequence of amino acids jointed by peptide bonds

what is secondary protein structure?

coils or folds formed by hydrogen bonds between the polypeptides

what is tertiary structure?

the shape formed by unique interactions between the R-chains

what types of interactions are involved in tertiary structure?

hydrogen bonds, iconic bonds, hydrophobic interactions, disulfide bridges and van Der Waals interactions

what is quaternary protein structure?

option level of structure when multiple formed polypeptide chains join together to form a macromolecule

what is the P-site of a ribosome?

the midpoint of the ribosome where amino acids are attached?

what is the A site of a ribosome?

holds the waiting amino acids that will be added to chain

what is the E-site of the ribosome?

the exit site where translated tRNA’s leave the ribosome

what is the general structure of t-RNA?

a clover-leaf shape with step loops

what is the acceptor stem?

a long end of the tRNA that binds to the amino acid

what are the instances of molecular recognition required for translation?

tRNA and amino acid via aminoacyl-tRNA synthatases and tRNA anti-codon and mRNA codon

what is the wobble rule?

mismatch in the mRNA and tRNA in the third position can be tolerated

what are isoacceptors tRNAs?

tRNA’s that can tolerate wobble?

what are the general steps of translation?

initation, the mRNA and tRNA are joined and the ribosome assembled

elongation, polypeptides are added

termination: ribosome dissambles

what happens during prokaryote translation initiation?

shine-dalgarno sequence binds mRNA to the small subunit

initiator tRNA binds to the start codon

initiation factors bring in the large subunit and form the initiation complex

what is simultaneous translation and transcription?

when a ribosome attached to the 5’ end of mRNA as that strand is actively being transcribed downstream

in what type of cell does simultaneous transcription-translation occur and why?

prokaryotes because there is no nucleus

describe the steps of translation invitation in eukaryotes?

imitation fact beings to the 5’ cap

the small subunit strand for the AUG start codon

the large subunit joins forming the initiation complex

what are the three steps of elongation in eukaryotes?

codon recognition, peptide transfer and translocation

describe the step of codon recognition?

the ribosome identifies the correct amino acids to add and charged tRNA binds

describe the peptide transfer step?

the polypepetide is removed from the tRNA and the ribosome catalyzes the formation of a peptide bonds between this amino acids and the previous amino acid

describe the translocation step?

the next codon is moved up and tRRNA is moved to the e-site

describe translation termination?

a stop codon in the mRNA sequence reaches the A-site and the release factor attaches

a water molecule is attached to the end of the polypeptide chain and the ribosome comes apart

what is a mutation?

a heritable change in genetic material?

what are mutations significant?

because they alter the composition and structure of proteins

describe the experimental design of the experiment supporting random mutation theory?

e.coli were incubated overnight and then replicated onto two plates that contain a T1 bacteriophage the kills wild-type cells

describe the results of the random mutation experiment?

resistant-mutant colonies appeared on both plates on the same location, which meant that the mutations occurred before exposure to a selective pressure

what are germ-line mutations?

mutations in egg/sparm cells that are passed onto offspring?

what are somatic mutations?

mutations in non-reproductive cells

what are spontaneous mutations?

mutations due to biological or chemical processes

what are induced mutations?

mutations due to environmental agents

what are point mutations

the addition, removal or substitution of one base

what are insertion mutations?

the addition of a base