ap bio unit 6: gene expression and regulation

structure of DNA backbone

phosphate and deoxyribose sugar

DNA nucleotide bases

Adenine + Thymine, Guanine + Cytosine

DNA purine bases (double ring)

Adenine, Guanine

DNA pyrimidine bases (single ring)

Thymine, Cytosine

Antiparallel structure

2 DNA strands run in opposite directions, going from 5’ to 3’.

5’ end

phosphate end

3’ end

sugar end

DNA function

stores and transmits genetic information

RNA backbone

phosphate and ribose sugar

RNA bases

adenine + uracil, guanine + cytosine

functions of RNA

mRNA and tRNA control protein synthesis, rRNA makes up part of ribosomes

3 components of a nucleotide

phosphate, sugar, nitrogen base

type of bonds that hold DNA strands together

hydrogen bonds

role and location of helicase

unzips the double helix by breaking the hydrogen bonds (moving into the replication fork)

role and location of topiomerease

an enzyme that moves ahead of helicase (on the double strand) and relieves the strand from supercoiling

function and location of single-stranded binding proteins

stabilizing the single strands and preventing them from joining together again

leading strand

the DNA strand that is synthesized continuously and moves toward the replication fork

why is the 3’ OH group necessary

it’s essential for adding a new nucleotide to the DNA strand. If it’s not present, DNA can’t continue replicating

leading strand synthesis

RNA polymerase (primase) puts a short RNA primer at the origin of replication (the 5’ end). Then, DNA polymerase adds nucleotide bases moving towards the replication fork.

lagging strand replication

• moves away from the replication fork in 5’ to 3’ direction

• RNA pol adds short RNA primer

• DNA pol adds nucleotides going away from replication fork

• DNA and RNA pol move back to begin a new fragment at the replication fork

• DNA pol I cuts out RNA primers and inserts remaining complementary nucleotides

• DNA ligase seals the backbone together

Okazaki fragments

Fragments of DNA formed on the lagging strandhyw

why can’t you going multiple Okazaki fragments together right after replication

the RNA primers are still in between the DNA fragments and the replication fork is in the way

role of DNA pol I

cuts out the RNA primers between fragments and inserts remaining nucleotides

role of DNA Ligase

seals the backbones of fragments together (covalent bond between phosphate and sugar) to create one complete strand

what does it mean that DNA replicates semi-conservatively

each newly formed DNA helix consists of one strand from the original DNA and one that is newly replicated

what does it mean that DNA replicates semi-discontinuously

one strand replicates continuously and one goes in fragments

where does transcription occur

inside the nucleus

what is transcription

turning DNA into an mRNA sequence, allowing the genetic information to be transported to the cytoplasm for protein synthesis and eventually gene expression

transcription initiation step one

transcription begins at the promoter. Eukaryotic promoters contain a TATA box, which marks the binding spot for RNA Polymerase and shows it which strand to transcribe

what is a transcription factor

proteins that regulate gene expression by binding to DNA sequences. They act as a “switch” to turn a gene on or off

second step of transcription initiation

transcription factors bind to the TATA box and help RNA polymerase attach in the right direction

third step of transcription initiation- transcription initiation complex

Transcription factors and RNA polymerase together create the transcription initiation complex. RNA polymerase unwinds the DNA and begins transcription

elongation step of transcription

RNA polymerase adds in complementary RNA base pairs (AUGC) in 5’ to 3’ direction

termination step of transcription

RNA reaches the termination site, RNA polymerase stops and the primary transcript (pre-mRNA) is cut free from the polymerase, 10-35 nucleotides downstream from the termination sequence. This signals the cell to start processing the transcript into mature mRNA

template strand/noncoding strand

the DNA strand that is transcribed (the one running 3’ to 5’ so that RNA pol can transcribe 5’ to 3’

nontemplate/coding strand

the one that is not transcribed and runs 5’ to 3’

overview of RNA processing

before the pre-mRNA leaves the nucleus, it has to be processed into mature mRNA ready for translation. post-transcriptional modifications involve 3 steps: adding the 5’ cap, adding the 3’ tail, splicing out the introns and stitching together the exons

adding the cap and tail

• on the 5’ end, a modified guanine called a 5’ GTP cap is added.

• on the 3’ end, 50-250 adenines are added, called the poly-A tail

• 3 functions:

• 1) helps mRNA export to the cytoplasm

• 2) keeps it from degrading

• 3) helps ribosomes recognize and attach to the 5’ end

splicing

• exons are the expressed coding regions

• introns interrupt the coding regions

• spliceosome cuts out the introns and stitches the exons together

alternative splicing

depending what sections are treated as exons, different sections of mRNA can be cut out. These will code for different proteins, and this is how we get 80k proteins from only 30k genes

what is translation

going from mRNA to a protein

where does translation take place

in the ribosome

explain mRNA and tRNA anticodon

the mRNA is the strand we created in transcription. tRNA are little segments of 3 nucleotides that base pair to the mRNA (this is called a tRNA anticodon). The anticodon codes for an amino acid.

translation initiation phase

a small ribosomal subunit scans the mRNA until it finds AUG (the start codon). a tRNA carrying the amino acid that the anticodon UAC codes for (methionine) binds to the start codon.

a large ribosomal subunit locks the tRNA, mRNA, and small subunit into place

translation elongation phase

1. ribosome reads the mRNA 3 codons at a time and brings in the tRNA that matches through the A site

2. peptide bond formation at the P site: tRNA attaches its amino acid to the growing protein (chain of amino acids)

3. translocation: empty tRNA (without amino acid) leaves through the E site, ribosome moves down to the next codon

translation termination phase

when a stop codon (UGA, UAG, UAA) enters the A site, a release factor binds the codon which releases the polypeptide and breaks apart the ribosome from the mRNA

redundancy

multiple different anticodons can code for the same amino acid

wobble

3rd letter of anticodon doesn’t really matter to determine amino acid

Chromatin

DNA and histones (looks like christmas string lights where histones are the bulbs)

heterochromatin

extremely densely packed chromatin that can’t be transcribed

euchromatin

loosely packed chromatin that can be transcribed

what chemical modifications could be made to remodel chromatin between hetero and euchromatin

Methylation: silences the gene and tightens DNA

acetylation: activates DNA by adding an acetyl group and opens up the gene, turning it on

epigenetics

the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself

regulatory sequences

pieces of DNA that interact with proteins to turn on or off transcription (don’t need to be close together)

activators

specific proteins that bind to enhancer regions and increase transcription by interacting with transcription factors and promoting binding to RNA polymerase

repressors

proteins that bind silencer regions and prevent activation