AP biology chapter 16 and 17

pathogenic

virulent(harmfully spreads)

Transformation

change in genotype and phenotype due to assimilation of foreign DNA

bacteriophage

a virus that infects bacteria; used in molecular genetics research

DNA

polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate

chargaff’s rules

the base composition of DNA varies between species

In any species the number of A and T bases are equal and the number of G and C and equal

to show when another attachment for DNA happens

what is the point of the 3 prime or 5 prime for a DNA molecule?

it deduced that the DNA was a helical (double helix) and that A’s do pair with T’s and C’s pair with G’s.

why is Rosalind Franklin’s photo 51 so important?

Anti parallel

when there are two lines, but one is exactly the same, but flipped upside down, which is what DNA is.

Purine

A and G (double ring) always paired with a single ring; being called a complimentary pair

pyrimidine

T ad C (single ring), paired with the double ring

The parent molecule(template) unwinds, and two new daughter strands are built based off of the base pairing rules (each will be half original/half new)

what happens in DNA replication?

semiconservative replication

each daughter molecule will have one old strand(derived from the parent) ad or newly made

origins of replication

where the two DA strands are separated, opening up a “replication bubble”

Primase

enzyme that brings in primer RNA; the RNA sits a little bit across the open DNA strand, being antiparallel, waiting for DNA Polymerase 3 to bring in complimentary pairs

DNA Polymerase III

brings in complimentary DNA nucleotides to build DNA strands

Binding proteins

when DNA “is unzipped”, they help to keep DNA strands from tieing back up

Leading strand

continuously, moving toward the replication fork; the continuous strand that does not have any fragments going toward the replication fork

lagging strand

• DNA polymerase must work in the direction away from the replication fork
  

• The strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase

DNA Helicase

Breaks Hydrogen Bonds and unzips DNA

Troposmerase

corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands

Replication Fork

a Y-shaped region where new DNA strands are elongating

mismatch repair

DNA polymerases repair enzymes correct errors in base pairing

• DNA can be damaged by exposure to harmful chemical or physical agents such as cigarette smoke and X-rays; it can also undergo spontaneous changes

nucleotide excision repair

• a nuclease cuts out and replaces damaged stretches of DNA

Telomeres

Eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends; they do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules

Gene expression

the process by which DNA directs protein synthesis, includes two stages: transcription and translation

one gene–one enzyme hypothesis

based off of the bread mold experiment and how when exposed to radiation, they were lacking an enzyme necessary for synthesis of arginine; each gene dictates production of a specific enzyme

one gene- one polypeptide

Many proteins are composed of several polypeptides, each of which has its own gene

RNA

the bridge between gees and the proteins for which they code; single stranded, and made out of ribose(different 5-carbon sugar than DNA)

Transcription

the synthesis of RNA under the direction of DNA; also the sythesis(producing) of mRNA; Using DNA to make RNA

Translation

synthesis of a polypeptide, using the information in the mRNA

Ribosomes

are the sites of translations

• In prokaryotes, translation of mRNA can begin before transcription has finished

• In a eukaryotic cell, the nuclear envelope separates transcription from translation 
  Eukaryotic RNA transcripts are modified through RNA processing to yield finished mRNA

What is the difference between prokaryotes and eukaryotes with transcription and translation?

primary transcript

initial RNA trascript from any gene prior to processing

central dogma

the concept that cells are governed by a cellular chain of Command: DNA → RNA → protein

20

how many amino acids does all living organisms have?

triplet code

the flow of information from gene to protein is based off of this: a series of nonoverlapping, three-nucleotide words;

• The words of a gene are transcribed into complementary non overlapping three-nucleotide words(ex: CCG)of mRNA

• These words are then translated into a chain of amino acids, forming a polypeptide

template strand

provides a template for ordering the sequence of complimentary nucleotides in an RNA transcript(during transcription)

codons

• the mRNA base triplets, are read in the 5′ to 3′ direction; Each one specifies the amino acid (one of 20) to be placed at the corresponding position along a polypeptide

• Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to end translation

• The genetic code is redundant (more than one codon may specify a particular amino acid) but not ambiguous; no codon specifies more than one amino acid

Codons must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced

RNA polymerase

pries the DNA strands apart and hooks together the RNA molecules; The RNA is complementary to the DNA template strand(uracil substitutes for thymine or U with A).

with a terminator cell at the end

how does RNA polymerase stop in porkaryotes?

promoter

THE DNA sequence where RNA polymerase attaches; they also signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start point

Transcription unit

The stretch of DNA that is transcribed

• Initiation

• Elongation

• Termination

what are the three stages of Transcription?

Transcription Factors

• mediate the binding of RNA polymerase and the initiation of transcription

transcription initiation complex

The completed assembly of transcription factors and RNA polymerase II bound to a promoter

TATA box

type of promoter; crucial in forming the initiation complex in eukaryotes

RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10–35 nucleotides past this polyadenylation sequence

how does RNA polymerase II stop in eukaryotes?

RNA processing

• Enzymes in the eukaryotic nucleus modify pre-mRNA before the genetic messages are dispatched to the cytoplasm(before translation)

• During this, both ends of the primary transcript are usually altered

It turns into pre-mRNA

what happens to RNA polymerase II after transcription?

Its 5’ end receives a modified nucleotide 5’ cap; the 3’ end gets a poly-A tail; These modifications seem to facilitate the export of mRNA and they protect mRNA from hydrolytic enzymes, and help ribosomes attach to the 5’ end.

what is different with the pre-mRNA molecule at its ends?

introns

noncoding regions; the same noncoding stretches of nucleotides that lie between coding regions

exons

eventually expressed, usually translated into amino acid sequences

RNA splicing

removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence; ONLY EUKARYOTES DO THIS!

spliceosomes

RNA splicing is sometimes carried out by these molecules; consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites

Ribozyme

Catalytic RNA molecules that function as enzymes and can splice RNA

Three properties of RNA enable it to function as an enzyme

• It can form a three-dimensional structure because of its ability to base-pair with itself

• Some bases in RNA contain functional groups that  may participate in catalysis

• RNA may hydrogen-bond with other nucleic acid molecules

alternative RNA splicing

• Some introns contain sequences that may regulate gene expression

• Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing

• The number of different proteins an organism can produce is much greater than its number of genes

in between transcription and translation(to get ready for Translation)

what stage does pre-mRNA splicing take place in?

domains

the modular architecture of proteins consisting of discrete regions; different exons code for the different domain in a protein; exon shuffling may result in the evolution of new proteins