ap bio unit 3.2 - replication, transcription, translation, and mutations

14.1 Genes specify proteins via transcription and translation 14.2 Transcription is the DNA-directed synthesis of RNA 14.3 Eukaryotic cells modify RNA after transcription 14.4 Translation is the RNA-directed synthesis of a polypeptide 14.5 Mutations of one or a few nucleotides can affect protein structure and function

The replication of DNA is

semiconservative

origin of replication

the area of DNA that replication begins at (has specific sequence of nucleotides that allows starting proteins to attach to)

replication fork

the Y-shape formed by separating the two strands of DNA

helicase is responsible for

unwinding the helix at the replication fork

single-strand binding proteins

bind to unpaired DNA to keep the strands from pairing again

topoisomerase

relieves strain caused by unwinding on/around replication fork (keeps DNA strands straight and avoids supercoiling)

primer

is a sequence of 5 - 10 nucleotides made by primase; synthesis can’t start on its own and builds from the 3’ end of the primer

DNA polymerase

synthesizes new DNA by attaching complementary base pairs to the template strands

DNA ligase

joins phosphate backbones of fragments into a continuous strand

Describe prokaryotic chromosomes

single, circular DNA molecule

Describe eukaryotic chromosomes

linear DNA and many proteins

levels of chromosome packing in eukaryotes

1. DNA (double helix)

2. proteins called histones (+ charge) bind to phosphate backbones of DNA (- charge)

3. chromatin folds so histones form bead-like nucleosomes

4. fold into chromatin fiber as histone tails interact with other nucleosomes

5. fiber folds into “looped domains”

6. looped domains coil into condensed chromosomes

Interphase chromatin can be slightly condensed and packaged as well, called

heterochromatin, which is inaccessible to transcription because of its folding

euchromatin

“true chromatin”, less compact and not condensed; able to be transcribed

genes affect phenotypes by dictating the production of

polypeptides (that make up proteins)

differences between RNA and DNA

• ribose sugar instead of a deoxyribose sugar

• contains uracil instead of thymine, which is less stable (and therefore unsustainable for DNA)

transcription

the synthesis of RNA using DNA as a template

translation

the synthesis of a polypeptide using info from mRNA, occurs at the ribosomes

bacterial cells can begin translation while mRNA is still being transcribed because

they do not have nuclei

central dogma

Crick’s theory stating genetic information flows in one direction: DNA —> RNA —> proteion

how many nucleotides make up a unit of code that corresponds to an amino acid?

three (triplet code)

compared to the template DNA strand, the RNA molecule is

complementary and antiparallel

codon

a set of three nucleotides of DNA that codes for one amino acid

why is the genetic code redundant but not ambiguous?

several codons may code for the same amino acid, but will only code for that amino acid

how does genetic code support theories of evolution?

the genetic code is nearly universal, which suggests a shared common ancestor

RNA polymerase

• synthesizes RNA by attaching RNA nucleotides to template strand

• assemble in 5’ to 3’ direction

• able to start a chain from scratch (doesn’t need a primer like DNA polymerase)

transcription unit

section of DNA transcribed

phases of transcription

1. initiation - RNA polymerase binds to the promoter (eukaryotes: transcription factors form a transcription initiation complex and help RNA polymerase bind and initiate)

2. elongation - RNA polymerase reads DNA from 3’ to 5’ and synthesizes 5’ to 3’, adding bases to the 3’)

3. termination

   1. bacteria - reaches a terminator sequence + releases the transcript w/out modification

   2. eukaryotes - proteins cut off RNA from polymerase at a transcribed signal + pre mRNA goes through modification

modifications to eukaryotic pre mRNA

• 5’ methyl cap attached to 5’ end

• poly-A tail added to 3’ end

• facilitate export of mRNA from nucleus + help protect RNA from hydrolytic enzymes

• help mRNA attach to ribosomes

RNA splicing

removal of RNA that was initially synthesized that occurs in the nucleus; non-coding sections are cut and not translated

introns vs exons

introns are intervening sequences and are removed; exons are coding regions that are expressed

alternative RNA splicing

exons from the same gene are arranged in different combos which = more possible proteins formed from the same transcription

spliceosome

protein complex that removes introns, degrades them, and joins exons on either side of the intron together

ribozyme

RNA molecules that function as enzymes

where do amino acids added to the polypeptide come from?

in the cell’s cytoplasm or are taken in from surrounding solution

the anticodon of tRNA complements the

codon on mRNA; corresponds to one type of amino acid

what does a tRNA do after it has added its amino acid and exits the ribosome?

is reused and picks up another amino acid in the cytosol

aminoacyl-tRNA synthases

enzymes that help the tRNA and its amino acid bind

ribosomes contain these three binding sites used for translation:

• P site - holds tRNA adding to the polypeptide

• A site - holds the next tRNA in line

• E site - discharges tRNA after amino acid has been deposited

• polypeptide will exit through an exit tunnel

the small subunit of the ribosome allows

attachment of mRNA

ribosomes mainly rely on this for their structure and function

rRNA (ribosomal RNA, which act as ribozymes)

phases of translation

1. initiation - mRNA binds to small subunit and an initiator tRNA; mRNA is scanned until start codon so the initiator tRNA can bind to it

2. elongation - mRNA is read from 5’ to 3’ and amino acids are added one by one; rRNA forms peptide bonds between amino acids of A and P site & removes bond to tRNA; tRNA is moved A —> P, P—> E

3. termination - stop codon reaches A site and release factors hydrolyze bond between polypeptide and tRNA; polypeptide is released through exit tunnel

post-translational modifications

chemical changes to amino acids, removal of amino acids, change to polypeptides length; must be modified to become functional proteins and do specific jobs

point mutation

changes in a single nucleotide pair of a gene

genetic disorders/hereditary diseases are

when mutations have adverse effects on the phenotype

small-scale mutations include

• single nucleotide-pair substitution - replacement of one base and its complement

• insertion/deletion - addition or loss of nucleotide pairs in a gene

silent mutation

are not harmful b/c of redundancy of genetic code/translate to the same amino acid

missense mutation

mutations that change an amino acid to another

nonsense mutation

codon for amino acid is changed into a stop codon, ending translation prematurely

mutagen

physical or chemical agents that interact with DNA and can cause mutations (ex. X-rays, UV radiation, nucleotide analogs)