AP Bio - Unit 6

Central Dogma of Biology

DNA is transcribed into RNA; RNA is translated into proteins

DNA

primary source of hereditary material

RNA

Viruses use this nucleic acids to encode their genetic infomraiton

Pyrmidines

uracil, cytosine, thymine

single ring structure

Purines

adenine and guanine

double ring structure

Prokaryotes

have circular chromosomes

Eukaryotes

have multiple linear chromosomes

Plasmids

small extra-chromosomal, double stranded, circular DNA molecules

Double Helix Benefits

• stores information for a long time

• helps protect information from damage

• helps detect when damage has taken place since the base pairing will become disrupted

RNA Structure

• exists for short periods of time

• oxygen in ribose makes the sugar much larger and more electronegative than deoxyribose

  • RNA is more reactive than DNA

Evidence of common ancestry

all organisms use the same basic code to tell ribosomes how to construct proteins

S phase

when DNA is replicated

Conservation Replication Theory

both strands of the template DNA molecule stayed bonded and intact while serving as a template for a brand new and identical double-stranded DNA molecule

Dispersive Replication Theory

original DNA helix breaks into fragments, each fragment serving as a template for a new DNA fragment

• daughter molecules would have alternating segments of old and new DNA in each of their two strands

Semiconservative Replication

results in a DNA molecule containing one original strand and a newly synthesized complement

5’ End

phosphate terminus; terminal phosphate group on the end of each DNa strand3’ End

3’ End

hydroxyl terminus; terminal hydroxyl group on the end of each DNA strand

5’ to 3’

direction that nucleotides can be added

Leading Strand

will always be synthesized continuously/in one long strand

Lagging Strand

will always be synthesized in Okazaki fragments, discontinuously

Helicase

unwinds the DNA strands by destabilizing thee hydrogen bonds between individual nucleotide bases

Single Strand Binding Protein

bind to unpaired DNA strands, preventing re-pairing

Topoisomerase

relaxes supercoil at the replication fork; moves ahead of helicase

Replication Fork

the ‘v’/location where the two strands are separated

Primase

an enzyme that adds a complementary primer made for RNA on the template strand that serves as a starting point for replication

• gives DNa polymerase an exposed 3’ hydroxyl group so that it can start adding nucleotides

DNA Polymerase

synthesizes the new strand of DNA by fusing new nucleotides to the sugar-phosphate backbone creating two double helices out of one

• attaches to 3’ end of the template strand and builds in the 5’ to 3’ direction

RNA Primers

must be broken down; leave a small gap in the DNA strand that must be filled in with free-flaoting nucleotides in the cytosol

Ligase

joins DNA fragments on the lagging strand

Transcription

the process in which an enzyme directs the formation of an mRNA molecule

• DNA strands are separated; one is template strand and other is coding strand

  • gene being transcribed is always on the coding strand

RNA Polymerase

separates the strands and synthesizes mRNA in the 5’ to 3’ direction by reading the template int he 3’ to 5’ direction

• recognizes promoter regions, opens up a transcription bubble

Transcription Factors

proteins that mediate binding of RNA polymerase and initiation of transcription

• presence during development helps determine how a cell differentiates

Transcription Initiation Complex

made of transcription factors and RNA polymerase

Initiation

RNA polymerase binds tothe promoter of the DNA, which is located upstream of the gene to be transcribed

Elongation

RNA polymerase adds nucleotides to a growing RNA strand, creating a new mRNA molecule

Termination

RNA polymerase releases the newly synthesized RNA transcript and dissociates from the DNA template

Terminator

DNA sequence that signals the end of transcription

• poly-A tail in eukaryotes

Primary Transcript

pre-mRNA, unprocessed

mRNA

carries the genetic information from DNA to the ribosome

• information is used to direct protein synthesis at the ribosomal site

  • made of codons

tRNA

recruited by ribosomes to help create a specific polypeptide sequence as directed by mRNA

• made up of anticodons

  • after adding their amino acid, the empty molecule is ejected from the ribosome and recycled

rRNA

molecules are functional units of ribosomes responsible for protein ascreates primary polypeptides by releasing amino acids

GTP Cap

modified guanine nucleotide added to mRNA to protect the transcript; helps ribosome attach to mRNA; protects primary transcript from degradation

• added to the 5’ end

Poly-A Tail

100-200 adenine nucleotides added to mRNa to help with exporting from nucleus, protects against primary transcript from degradation

• added to the 3’ end

introns; exons

___ sequences of an mRNA primary transcript that do not code for amino acids

___ sequences of an mRNA transcriptt that do code for amino acids

Alternative Splicing

retaining exons in different variations

Spliceosome

cts of 5 small-nuclear-RNa molecules and their associated proteins bound into a complex that binds to each intron and connects the exons

Translation

process by which an mRNA sequence is used to generate a polypeptide

• occurs on ribosomes

• prokaryotes: only cytosolic ribosomes

  • eukaryotes: cytosolic or Rough ER ribosomes

Co-Transcriptional Translation

in prokaryotes, transcription and translation happen simultaneously

• benefits: fast response to environment, production of multiple copies of the same protein, rapid growth and reproduction

Virus

infectious particle consisitng only of genes packaged in a protein coat

• can’t express own genes —> don’t have the equipment to amke proteins

  • relies on host cell’s machinery

Retrovirus

introduces viral RNA, not DNA, into host cells

• once the enzyme converts viral RNA into viral DNA, DNA is integrated into host genome where it is transcribed and translated

Reverse Transcriptase

an enzyme that copies the viral RNA of a retrovirus into viral DNA

Common Ancestry

same basic genetic code allows DNa ot be inserted and still produced proteins

Initiation

rrNA in ribosome interacts with mRNA at start codon (AUG/methionine)

Initiation Complex

a structure formed by the union of various components necessary to start protein syntehsis including mRNA, tRNA, and ribosomal subunits

A-site

binds incoming aminoacyl-tRNA

P-site

holds tRNA carrying the growing polypeptide chain

E-site

where deacylated tRNAs exit the ribosome

Elongation

polypeptide chain gets longer as each tRNA brings a new amino acid

• tRNA in the A site brings in the next amino acid, and the ribosome catalyzes the formation of a peptide bond between the amino acid in the P site and the incoming amino acid in the A site

Termination

translation ends once stop codon is reached

• stop codons don’t code for an amino acid

Release Factor

protein that allows for termination by recognizing stop codons and facilitating release of newly formed polypeptides from ribosomes

hydrolysis of ATP and GTP

where energy for translation comes from

Regulatory Sequences

stretches of DNa that promote or inhibit protein syntehsis

Regulatory Proteins

assist with the promotion or inhibition of protein synthesis

Epigenetics

study of heritable changes in the gene function that occur without changes to the underlying DNA

Epigenetic Changes

involve reversible modifications of DNa or histones

Histone

proteins used to wrap DNA around

• slight chemical modification of DNA and ___ causes tight or loose packing of DNA

• Packing/unpacking regulates gene expression

  • If DNA is inaccessible, gene canot be read; will not be transcribed, no proteins will be made

Post-translational Regulation

changes to proteins after translation

• can affect protein’s function, location, or lifespan

Operon

a stretch of DNa with a promoter, opertator, and related group of genes that function in a pathway

Operator

a sequence that either inhibitsw or promotes transcription by binding with regulatory proteins

Coding Region

genes that will be transcribed downstream of operator

Regulatory Gene

codes for a repressor hat bidns to operator and blocks attchment of RNa polymerase to promotoerI

Inducer

molecule that inactivates a repressor protein

Inducible Operon

usually turned off, but turned on in the presence of particular molecules

• when regulatory protein is bound to operator, RNA polymerase cannot bind to other regulatory sequence and inhibits transcription of the gene

Inducers

molecules that can bind to the regulatory protein and cause it to change shape

• after binding to the regulatory protein, the protein changes shape, causing it to release from the operator

Repressible Operon

on byd efault, but turned off in the presence of particular moleculres

Corepressor

molecule that activates the repressor to turn a gene ‘off’

Differential Gene Expression

expression of different genes with the same genome

Eukaryotic Genes

can be regulated at many stages

Histone Acetylation

modifying histone proteins in chromosomes to promote transcription, opens up the chromatin structure

Transcription Factors for Regulation

bind to certain DNA sequences depending on signals a cell receives; can promote or repress transcription

Control Elements

segments of noncoding DNA that serveas binding sites for transcription factors

microRNA

small RNA molecules that bind to complementary sequences in mRNA molecules, blocking translation or degrading mRNA

Inhibition of Translation

different proteins can block translation by degrading ribosomes

Promoters

DNa sequences upstream of the transcription start site where RNA polymerase and transcription factors bind to initiate transcription

Terminators

sequences that signal the end of transcription

Enhancers

increase the level of transcription of a gene

Silencers

decrease the level of transcription of a gene

Negative Regulatory Molecules

inhibit gene expression by binding to DNA and blocking transcription

• RNA polymerase is blocked from binding to the promoter

Mutations

primary source of genetic variation

Point mutation

change in a single nucleotide of a gene

• silent mutation (no observable effect on phenotype)

• missense mutation (change of an amino acid)

• nonsense mutation (terminated early)

Insertion/Deletion

addition or loss of a nucleotide

Frameshift Mutation

when the number of nucleoties inserted/deleted is not a multiple o three, changes the triplet grouping of nucleotides read during translation

Mutagen

a physical chemical reagent that can cause mutations

Horizontal Transfer of Genetic Information

the exchange of genetic information between different genomes or between unrelated organisms

• primarily occurs in prokaryotes

• 3 types: transformation, transduction, conjugation

• all made possible through plasmids

Transformation

uptake of DNa from a cell’s surroudningst

Transduction

the transmissin of foreign DNa into a cell when a viral genome (phage) integrates with the host genome

• viral genomes can combine once integrated into the host producing a new combination virus

Conjugation

cell-to-cell transfer of DNA

transposition

the movement of DNA segments within and between DNA molecules

Bacterial Transformtaion/DNA Cloning

analysis of DNA by bacterial cells taking foreign DNa from external sources

Restriction Enzymes

enzymes that cut DNa molecules t a specific pointR

Restriction Site

preceise location that enzymes cut DNa molecules