unit 6 - gene expression and regulation

what do nucleotides contain

5 C sugar, phosphate, nitrogenous base, A, T, C, G

complementary strands

two strands of DNA; if you know the order of one you know the order of the other because they correlate

antiparallel

the strands run in opposite directions; 5’ end is always opposite 3’ end of the other strand

how many hydrogen bonds are there between A-T?

2

how many hydrogen bonds are there between C-G?

3

what are chromosomes like in prokaryotes?

circular, they only have one

what are chromosomes like in eukaryotes?

linear, they have many

histones

protein DNA is wrapped around

euchromatin

when genetic material is loose

heterochromatin

when genetic material is fully condensed into coils

what is the first step in DNA replication

unwinding the double helix by breaking hydrogen bonds

helicase

unwinds double helix and breaks hydrogen bonds

replication fork

where the DNA that is being replicated opens up

topoisomerase

cuts/rejoins helix to prevent tangling; manages super-coiling

DNA polymerase

enzymes that add nucleotides to the newly built DNA strand; can only add nucleotides to the 3’ end

RNA primase

initiates replication by adding a short strand of RNA nucleotides

RNA primer

the short strand of nucleotides added to start replication

leading strand

nucleotides are added continuously using DNA polymerase

lagging strand

the strand made discontinuously

in what direction is the lagging strand built

the opposite direction of the way the helix is opened; can only built until the previously built stretch

okazaki fragments

the small fragments that make up the lagging strand

DNA ligase

links together fragments to make a continuous strand

semiconservative

half of the replicated DNA molecule is the old one, and the other strand is newly replicated

telomeres

ends of DNA molecule

transcription

process of making RNA from DNA

where does transcription occur

in the nucleus

translation

process of making a protein from an RNA

where does translation occur

in the cytoplasm

messenger RNA (mRNA)

temporary RNA version of a DNA ‘recipe’ that is sent to the ribosome

ribosomal RNA (rRNA)

produced in nucleus, makes up some of the ribosome,

transfer RNA (tRNA)

brings amino acids to the ribosomes, brings right amino acids to the right places at the right times

how does tRNA know when to bring amino acids

reads messages from mRNA

what are the three phases in transcription

initiation, elongation, termination

what starts off transcription

unwinding and unzipping DNA strands with helicase

promoters

where transcription begins

RNA polymerase

builds RNA and adds nucleotides to the 3’ side

what happens when an RNA is finished replicating the template DNA

it separates from template DNA

exons

regions that express code and will be turned into proteins

introns

noncoding regions of DNA that get spliced out

splicing

the vital removal of introns before RNA leaves the nucleus

spliceosome

does the splicing

translation

turning an mRNA into a protein

codons

a group of 3 nucleotides that the order of mRNA nucleotides will be read in

what does each codon represent

an specific amino acid

anticodon

nitrogenous bases that are complementary to the codon in the mRNA

start codon

special first ‘AUG’ in an mRNA that begins translation

elongation

addition of amino acids that are linked to one another by peptide bonds as more are brought and synthesized to the mRNA

stop codons

stops further synthesis of polypeptide

transcription factors

can either encourage or inhibit the unwinding of DNA; makes it easier or harder for RNA plymerase to move to the start site

epigenetic changes

changes to the packaging of DNA that changes the ability of transcription material to access a gene

what is an example of epigenetic changes

modifying a histone protein; tighter wrap around histone → DNA is harder to access, looser wrap → easier access

operon

closely linked genes that make a single mRNA molecule during transcription

what are the four parts of an operon?

structural genes, promoter genes, operator, regulatory genes

structural genes

code for enzymes needed in a chemical reaction - transcribed at the same time to produce particular enzymes

promoter gene

region where RNA polymerase binds to begin transcription

operator

region that controls whether transcription will occur; this is where the repressor binds

regulatory genes

codes for repressor

repressor

specific regulatory protein that can attach to operator and block transcription; if it binds to operator → transcription doesn’t occur, if it doesn’t bind → RNA polymerase goes to the operator → transcription occurs

trp operon

continuously ‘turned on’ and is ‘turned off’ only in high levels of the amino acid (tryptophan)

how does post transcriptional regulation get rid of cells

cell makes an RNA, decides it shouldn’t be translated into a protein. It then makes a double stranded RNA when

how does post transcriptional regulation hold cells for later

cell makes the protein and doesn’t need it yet- binds with other proteins, phosphorylation, pH changes

fertilization

causes zygote to go through a series of cell divisions

how do mutations occur

DNA is damaged and can’t be repaired or because DNA damage is repaired incorrectly, radiation, reactive chemicals

base substitutions

a single nucleotide is substituted for another

nonsense mutations

cause original codon to become a stop codon, results in early termination of protein synthesis

missense mutations

cause original codon to be altered and produce a different amino acid

silent mutations

codon that codes for the same amino acid is created

intertions/deletions

gain/loss of DNA or a gene

frameshift mutation

change in codon sequence used by ribosome, has bad consequences

duplications

result in an extra copy of genes

what are duplications mutations caused by

unequal crossing over during meiosis or chromosome rearrangements

inversion

changes occur in the orientation of chromosomal regions; can be harmful if it involves a gene or an important regulatory sequence

translocations

2 different chromosomes break and rejoin in a way that causes the DNA sequence/gene to be lost/repeated/interrupted

transposons

gene segments that cut/paste themselves throughout the genome - presence can interrupt a gene and cause errors in gene expression

why are viruses considered nonliving

they need a host cell’s machinery to replicate

retrovirus

use reverse transcriptase to convvert RNA into DNA so they can be inserted into a host genome

recombinant DNA

generated by combining DNA from multiple sources to make a unique DNA molecule

PCR

makes large samples of DNA when only small samples are initially available; denatures DNA, adds primers in an order where copying strands know where to start, DNA is replicated until enough is made

gel electrophoresis

DNA fragments separated according to size and charge; smaller fragments are faster moving → go toward bottom, DNA’s negatively charged → goes toward positive pole

RFLPs

fragments from restriction enzymes

DNA sequencing

allows scientists to determine the order of nucleotides in a DNA molecule

are pyrimadines single ring or double ring?

single ring

which nucleotide bases are pyrimadines?

uracil, cytosine, thymine

are purines single ring or double ring?

double ring

what nucleotide bases are purines?

adenine, guanine

which end of a DNA strand has a phosphate attached/

5’

which end of DNA has an (-OH) group attached?

3’

what does rRNA do during transcription

base-pairing of anti-codons and codons in the ribosome; makes primary peptides as tRNA releases amino acids

poly-A tail

100-200 adenine nucleotides that are placed on the 3’ end to provide stability and export nucleus

GTP cap

modified guanine that protects the transcript, attached to 3’ end

DNA polymerase III

catalyzes 5’-3’ polymerization of DNA during replication and proofreads

DNA polymerase I

repair, removes primers, fills lagging strand

gene expression

instructions in DNA are transcribed and translated into a functional protein

regulatory sequences

stretches of DNA that can be used to inhibit/promote protein synthesis ; interaction of these with regulatory proteins controls transcription

inducible system

operon system is usually turned off; when regulatory protein is bound to operator, RNA polymerase can’t bind to the regulatory sequence and inhibits the transcription of genes that are a part of the lac operon

how are operons transcribed in prokaryotes

in a single mRNA

promoters

DNA sequences up from transcription start site where RNA polymerase and transcription factors bind to start transcription

what is horizontal acquisition of genetic information

exchange of genetic information between related organisms (primarily prokaryotes), increases variation

transformation

uptake of naked DNA

naked DNA

DNA not protected by proteins or other molecules