GIANT BIO UNIT

chapters 9 thru 13 lollll rip

bacteriophage

viruses that infect bacteria

transgenic

organism that contains DNA material from an artificially introduced source

chargaff’s rule

number of purines = number of pyrimidines

A bonds with what in DNA

T

T bonds with what in DNA

A

C bonds with what in DNA

G

G bonds with what in DNA

C

helical

spiral shape

antiparallel

two strands run in opposite direction

is DNA left or right handed

right

semiconservative replication

each strand of parental DNA acts as a template for a new strand

2 steps of dna replication?

helix is unwound, nucleotides added to existing nucleotides via phosphodiester bonds

what direction is template DNA read in by the replication enzymes?

3 to 5

during DNA synthesis, what side are the nucleotides added to

3’ end, the side with the free hydroxyl group

summarize the 2nd step of dna replication

dna template is read 3 to 5, therefore new strand is 5 to 3 (hence antiparallel)

dNTP

each carry three phosphate groups, during dna synthesis, 2 are released for energy, remaining one is used for the phosphodiester bond

role of pre replication complex

binds to specific site on dna molecule (the origin of replication aka ori), contains dna polymerase

role of dna polymerase

adds primer, to which it adds new nucleotides

what is primer

complementary to the dna template, synthesized by primase

leading strand aka

newly synthesized growing strand (oriented so it can grow continuously at its 3’ end as the fork opens up)

lagging strand aka

other new strand, made up of okazaki fragments (b/c the strand grows AWAY from the replication fork b/c the enzymes read from 3 to 5, while the lagging strand runs from 5 to 3)

what is the lagging strand made of

okazaki fragments

true or false each okazaki fragments needs its own primer

true, it must have its own in order to be synthesized by the primase

job of dna ligase

patch up all the tiny nicks left by dna polymerase as it removes the old primer and adds dna to the lagging strand

dna polymerase is processive meaning…

it catalyzes many sequential polymerization reactions each time it binds to a DNA molecule

what is a telomere

strings of repetitive sequences at the ends of their chromosomes (to prevent chromosomes from joining, b/c ligase might get confused and join 2 chromosome ends lmao cuz theres a gap when it gets damaged e.g.)

what does telomerase do

catalyzes the addition of any lost telomeric sequences

proofreading

occurs right after DNA polymerase inserts a nucleotide, removes incorrect base pair and tries again

mismatch repair

occurs after DNA has been replicated. looks for mismatched pairs that were missed in proofreading. portion of the dna including incorrect nucleotide -→ removed, dna pol adds correct sequence

pcr stands for

polymerase chain reaction

somatic mutations

occur in the body cells, passed onto daughter cells during mitosis

germline mutations

occur in sex cells, passed on to new organism at fertilization

silent mutation

doesn’t affect gene function (either not expressed or don’t have an affect on the encoded protein)

loss of function mutation

loss of expression of a gene or in the production of a protein that doesn’t work (mutations can prevent the gene from being transcribed, or transcribes too early)

gain of function mutation

protein with altered function (usually shows dominant inheritance)

conditional mutations

cause their phenotypes only under certain restrictive conditions. (the wild type phenotype is expressed under other permissive conditions)

point mutation

\+/- of a single nucleotide base or substitution of 1 base for another

chromosomal mutations

whole chromosomes can break & rejoin (there r 4 types: deletions, duplications, inversions, and translocations)

deletions

removal of genetic material

duplications

homolog chromosomes break at diff positions and then reconnect to the wrong partners (1 chromosome would have 2 copies, other would have none → deletion)

translocations

segments of chromosomes break off and become joined to diff chromosomes

spontaneous mutations

permanent changes in genetic material

induced mutation

mutation as a result of a mutagen

define transcription

info in a dna sequence is copied into a complementary rna sequence

define translation

the rna sequence created during transcription is used to create an amino acid sequence of a polypeptide

3 types of rna?

messenger RNA, ribosomal RNA, transferRNA

mRNA how is it created

rna strand produced in transcription is modified to create a messenger RNA, moves from nucleus to cytoplasm → translated into a peptide

ribosomal RNA purpose??

one of the rRNAs catalyzes peptide bond formation between amino acids, to form a polypeptide

what the heck is a ribosome

protein synthesis factory with multiple proteins and many rRNAs

tRNA what does it do??

mediates between mRNA and protein, can both bind a specific amino acid & recognize a specific sequence of nucleotides in mRNA (in summary it recognizes what amino acid should be added next to the growing polypep chain)

3 steps of transcription?

initiation, elongation, and termination

step 1 of transcription: initiation

needs promoter which tells where to start transcription & which 2 dna strands to transcribe & under what conditions

promoter contains what

a transcription initiation site

step 2 of transcription: elongation

after rna polymerase binds to promoter, rna pol unwinds dna and reads template strand 3 to 5. rna pol adds new nucleotides to 3 end of growing strand, catalyzes phosphodiester bonds

(therefore first nucleotide in the rna strand forms the 5 end, thus making the rna transcript antiparallel to dna template strand)

what’s different about adding nucleotides in elongation vs. dna replication?

uracil is paired with adenine instead of thymine

step 3 of transcription: termination

a certain sequence of bases tell the rna pol when to stop. new rna strand separates from dna template & rna pol

what is a coding region

dna sequences translated into proteins

introns =

intervening regions, do not code for anything, like filler

exons =

expressed regions that ARE transcribed

where do introns & exons appear

the precursor RNA or pre-mRNA

nucleic acid hybridization

used to find introns

what is rna splicing

removes introns, strings exons together

what is a consensus sequence

boundaries between introns and exons (no variation in DNA here)

what is a spliceosome

large RNA-protein complex that cuts the premRNA, releases introns, and joins ends of exons together

what is a 5’cap

added to the 5’ end of the pre mRNA as it is transcribed. molecule of GTP. facilitates the binding of mRNA to ribosome for translation & protects it from being digested by ribonucleases (enzymes that break down rnas)

what is a poly A tail

added to the 3’ end of the pre mRNA at the end of transcription. assist in the export of the mRNA from the nucleus + stability

start codon =

initiation signal for translation

stop codons =

termination signals for translation

missense mutation

result in change in the amino acid sequence

nonsense mutation

premature stop codon

frame shift mutation

happen b/c of insertion/deletion of 1 more more base pairs in the coding sequence. changes the whole expressed amino acid.

how exactly does tRNA do its job

it binds to a specific amino acid sequence, covalent attachment at the 3’ of dna. anticodon is complementary to the mRNA codon for the amino acid that tRNA carries.

what does the a in APE stand for

amino acid site where the charged tRNA anticodon binds to the mRNA codon, lining up the right amino acid to be added to the growing polypeptide chain

what does the p in APE stand for

polypeptide site, where the tRNA adds its amino acid to the polypeptide chain

what does the e in APE stand for

exit site, where the tRNA after giving up its amino acid, rests b4 being released from the ribosome & going back to the cytosol to grab another amino acid (process is then repeated)

proteolysis

cutting of polypeptide chain

glycosylation

addition of carb to protein to form glycoproteins