Eukaryotic Chromosome Structure and Genome Organization

• Chromosome packing
• essentially spools of DNA wrap around histone protein
• Each is linked to the next by small protein strand
• Nucleosomes coil together to form chromosomes

• Looser chromatin
• Gets transcribed

Tightly packed chromatin that is not transcribed

Chromosomes fragment from end or middle is lost as chromosome repeats

• If fragment detaches from a chromosome during a deletion event reattached itself
• If reattaches to the homologous chromosome, that chromosome will have two sets of identical genes in a particular region, and original chromosome where the deletion occurred will be too short

• Refers to the number of copies of a chormosome an organism has
• Haploid- one copy
• Diploid- two copies, humans

46 Linear chromosomes that are arranged in 23 homologous pairs

Two paired chromosome, are similar in length, but may not have the same alleles

The deleted fragment could also attach back into the chromosome from which it came but in reverse direction

• Common alteration in which the piece of DNA that breaks off attached to the end of another chromosome
• Usualy not the homologous chromosome, but to a chromosome that is not its pair

• The chromosome giving a piece of DNA also receives one back that is comparable in size from the receiving chromosome 
• In many cases these mistake render large group of genes useless

• Base sequence of DNA is transcribed to mRNA
• DNA double helix unwinds and is transcribed in a 5'-->3' direction, using only one DNA strand as as a template
• RNA transcription proceeds from only one DNA template called the anitsense strand
• RNA transcription doesnt require an RNA primer
• RNA poly both initiates the synthesis and catalyzes the addition of nucleotides

The two strands of DNA run in opposite directions to each other and are therefore anti-parallel, one backbone being 3′ (three prime) and the other 5′ (five prime). This refers to the direction the 3rd and 5th carbon on the sugar molecule is facing.

• are main molecules responsible for trancribtion with DNA and RNA codons
• Must bind to the promotor sequence before it can access the structural genes to be transcribed
• Transcription occurs until RNA poly reaches termination sequence

Set of three nucleotides

• Coding sequences of DNA
• 5% of eukaryotic DNA codes for proteins
• Exons EXIT the nucleus and go to ribsome for translation

• Several noncoding sequences or Junk DNA
• Makes up 95% of eukaryotic DNA
• Introns remain IN the nucleus

• Heterogenous nuclear RNA
• mRNA that is initially transcribed off a DNA template
• a 'precursor' molecule
• Contains both introns and exons
• During hnRNA introns are removed and exons are spliced together
• Therefore mRNA is only made up of exons

• Methylated guanines (G) are added to the 5' end of the mRNA
• Protects the 5'end against degradation and damage as mRNA travels through nuclear membrane and cell at start of protein synthesis and at ribosome for translation

• After being cleaved at a specific site the mRNA recursor receives a poly A tail made of 100-300 adenine nucleotides
• Similar to 5'cap poly A tail aids in stabilization and protection of mRNA transcript and later at translation

• Short Nucler RiboNuclearProteins
• are similar to histone proteins in that RNA winds ands wraps around them

Large ribonucleoprotein that forms during the excision of introns and spicing together of exons

• Pieces of DNA that can move form place to place within an organisms genome
• Some transpons can replicated themselves before they move, so insert themselves in new place and maintain attached

Move from central chromosome to plasmids or vice versa

• Transposons are always found between inverted repeats
• Nucleotide sequences that are upside down mirror images of each other

• Simplest Transposon
• Two inverted repeats and transposase gene
• Tell DNA where to go after detached from location

• Allow genes to move from chromosome to plasmid (in bacteria)
• Usually they return after replicated and transferred to another bacteria via plasmid
• *This is how bacteria can rapidly transfer antibiotic resistance to a colony

Are introns/junk DNA and enchancers

• Non coding regions of DNA that influence activation of genes
• RNA poly must bind to promotor 
• Enhancers are far upsteam from target genes and bring transcription factors into contact with promotor region and act to enhance transcription

• Hundreds of thousands of proteins that exert transcriptional control over genome
• Alll Help RNA poly find and bind to given promotor region
• Have a high rate of conserved DNA binding domain
• Allows it to attache to DNA nucleotides
• Most are specific for enhancer or promoter sequence

• Are A-T rich regions of DNA that are involved in positioning the start of transcription
• Regions of AT rich separate more easily because they form a double bond while C-G form a triple bond
• DNA unzips at these regions for RNA access

Other types of promotors that exist within introns of genes and usually occur in genes that encode rRNA and tRNA

• The attachment of methyl (CH3-) Groups to nitrogenous bases 
• When Methalized bases cannot be transcribed and are a way to inactivate certain genes at times

• Promotor regions rich in CG upstream of genes
• They remain unmethalyzes because they are the start to many genes
• If they become methylzed they turn off many sequences and block RNA poly from attaching
• CG islands are key to scientists that exons are nearby

• Regulated through selective methylation of DNA
• Maternal Alleles are methylated with certain patterns and paternal with another
• Allows differential expression of identical alleles depending upon which parent gives it

• Rapidly copied and multiple copies accumulate in genome
• Usually during embryonic development

• DNA forms a complex with a core of eight histone proteins
• Each sections of DNA and protein core comprise an individual nucleosome
• Each nucleosome is connected to another via linker DNA
• This thread forms a hollow helix called solonoid
• The solonoid interacts with other proteins to forms chromatin
• chromatin condenses to form chromosomes

• Solonoid interacts with other proteins and forms chromatin
• Chromatin condenses to form chromosomes

Thread of histone proteins forms a hollow helix

• Basic unit of DNA made up of:
• A nitrogenous base
• Sugar
• Phosphate group

• Adenine and Guamine
• Bases with two fused rings of N and C

• Thymine and Cyctosine
• Bases with single rings of N and C

• Two strands of DNA have antiparallel orientation
• One Strand is positioned in the 5'-->3' the other in 3'--->5' direction
• 5' Phosphate, and 3' hydroxyl groups are exposed at opposite ends
• Carbons in the sugar ring are numbered 1'-->5'
• A nucleotides phosphate group is attached to the 5' carbon of its own sugar and the 3' carbon of the next sugar

• usually at TATA rich regions where DNA can separate more easily
• Prokaryotes only have one region

Enzyme that catalyzes the separation of DNA Helix

• Each strand acts as a template for production of a new strand
• DNA synthesis begins at more than one location on each strand
• Synthesis will occur at these points with the enzyme primase

• Synthesis that proceeds in two directions because DNA poly can only synthesize in 5'-->3' direction
• On top strand DNA syntheis will begin at primer and proceed in the same direction as the movement of the fork (here: R)
• As more parent DNA is unwound, synthesis is continuous
• On the bottom strand DNA synthesis proceeds in the opposite direction of the fork (here:L)
• To stay consistent with 5'-->3' rule primase and DNA poly must jump back as more parental DNA is unwound and then move forward, not continuous

• RNA nucleotide that provides a free hydroxyl (OH) group and allows dNTP's to join
• At the end of replication RNA primers are cut out by DNA poly and replaced with DNA nucleotides

• RNA polymerase that makes an RNA primer that can be elongated
• Initiates the replication of DNA

• Primase initiates the replication of DNA and synthesis continues from the sites of origin at replication forks
• The two prongs replicate in opposite directions

• Each arriving nucleotide comes as a dNTP (deoxyribosenucleotide triphosphate) as it binds to a strand it loses two terminal phosphates
• This reaction releases energy and provides the E needed to attach nucleotides

• Enzyme the elongates DNA at replication forks
• Catalyzes the addition of nucleotides to the primer to make the new DNA stand and align nitrogenous bases in position opposite to the parent strand 
• Cannot add nucleotides to parent DNA needs RNA primer
• **Will only add nucleotides in one direction 5'-->3', so only to the 3' end

DNA synthesis always occurs in the 5'-->3' direction, and the parent strand is read 3'--->5'

• Fragments of DNA that were replicated discontinously 
• To stay consistent with 5'-->3' rule primase and DNA poly must jump back as more parental DNA is unwound and then move forward, not continuous

Because synthesis of the discontinuous strand lags behind synthesis of the continuous strand, the discontinuous strand is also known as the lagging strand and the continuous strand as the leading strand

Okazaki Fragments are connected to one another by DNA ligase

• Each daughter strand is synthesized according to a parent template
• Once complete there are two resulting daughter strands, one each wound with a side of the parent template
• The parent strand is therefore semi conserved in each daughter strand

• Antisense- the DNA strand the RNA uses as template
• Sense- the DNA strand that is not transcribed

• mRNA that has just been trancribed
• Contains a seq of exons and introns
• Introns are excised from primary transcript once a cap and tail have been added

• Regulate the super coiling of DNA into Chromosomes
• Aids in DNA unwinding for transcription and Replication

Topoisomerase I causes single stand breaks and ligations which affect the nature of coiling

Topoisomerase II causes double strand breaks

Fixes errors in replication when DNA poly adds wrong base, it usually cut out and replaced with correct base

When DNA poly corrects mistakes in a 3'-->5' direction

Errors that are corrected within a strand or middle of a strand

• are adjacent thymine nucleotides that become covalently bonded due to UV E and UV damage
• They prevent DNA poly from copying DNA beyond site
• UV specific nucleases cleave the dimer and insert two new thymines, which are sealed together with ligase.

• Pushes apart the double helix in a certain region and bind to a promoter sequence and beings to transcribe the structural genes
• 5'-->3'
• Must synthesize mRNA off 3'-->5'
• No proofreading function

Combination of all codons

• The process by which mRNA codons are translated into a sequence of amino acids
• Occurs at ribosome (Free and bound to ER)
• tRNA is used at ribosome to carry correct amino acids in place
• In cytoplasm in prokaryotes

• ER bound secrete proteins to ER lumen then golgi body
• Free ribosomes secrete proteins right into cytoplasm

Allows proteins designated for the nucleus to pass through the nuclear membrane and remain in the nucleaus

Tell ribosomes to remain bound to ER until after protein synthesis

• Initation
• Elongation
• Termination
• All require ATP and enzymes

Enzyme that loads tRNA with amino acids

A tRNA with an amino acid

• transfer RNA
• Specific for 1/20 amino acids
• Brings amino acid to sequence on mRNA (tRNA holds the complementary sequence, anticodon, of bases on one end and an amino acid on the other)
• Polypeptide chain is attached to carboxyl end

• Come from digestion of food or from the environment
• 20 naturally occurring amino acids
• Many different codons can code for the same amino acids

• Also called degenerate
• Many different codons can code for the same amino acids
• The idea is that the third base is not as important as the first two. 
• tRNA binds more tightly to the first two bases and the third is more varriable

• mRNA binds to the small ribosomal unit
• tRNA imitator carries the amino acid methionine and binds with initiator start codon (AUG)
• The anticodon of the initiator tRNA is UAC
• The Large ribosomal unit binds to small unit around mRNA
• Creates a complete ribosome with MET tRNA complex in the P site

• Two units
• Small Unit  (40S) goes under mRNA
• Large unit (60S) is U-shaped and goes around tRNA and amino acid, and locks to the smaller unit (80S)
• This locks mRNA in place
• This complex slides along mRNA

aminoactyl tRNA

• Petidyl tRNA
• First spot on small ribosome

Start codon/initiator

• H bonds for between mRNA codon in the A side
• Enzyme peptidyl trasnferase forms a peptide bond between the amino acids tRNA (aminoactyl tRNA) in the A spot to MET in the P spot
• Translocation-Ribosome moves three bases along mRNA in 5'-->3' direction
• tRNA from a moves to P and tRNA in P is expelled
• A is empty for new tRNA

Forms a peptide bond between the amino acids tRNA

• Ribosome moves three bases along mRNA in 5'-->3' direction
• Requires GTP

• Polypeptide synthesis stops when mRNA termination codon arrives in the A site
• Protein called a release factor binds to termination codon and adds a water molecule to the end of the protein chain 
• The poly chain releases from ribosome

• UAA
• UGA
• UAG

mRNA is read by multiple ribosomes at the same time

Sort signals as the end of the protein chains that direct protein to a certain location

Sort signals from the middle of proteins 3D structure

the ER lumen then golgi body

• into the golgi body
• They are then wrapped in a vesicle
• This vesicle merge with membranes and the proteins are dumped out

• Proteins that remin in ER have this signal added to their structure
• Group of four amino acids added to carboxyl terminal that restricts protein to ER lumen

Proteins that aid in the folding of new ER proteins

• The addition of sugars to protiens
• Usually glycosylation signals that proteins are destined for export out of the cell or for membranes
• Rarely do proteins in cytoplasm have sugars
• Makes proteins more resistant to being digested and form a selectively permeable layer above the cell

Cytoplasmic

• Most common sugar group added to a protein in ER
• Sugar is added to NH2 group of asparagine amino acid
• NH2 --> N linked

• A carboxyl terminal of a protein is changed to a GPI anchor  that allows proteins to eventually anchor in exterior of cell membrane
• It enters Golgi body and is packaged and the vesicle merges with cell membrane on excretion and the protein is stuck

Sugars are added to the carobxyl group (OH) off serine and thronine amino acids side chains

Proteins that coats vesicles carrying lysosomal proteins

• Inheritance, only possible in mutations found in sperm and egg cell can be inherited
• Mutagens

• external cancer causing agents
• EX: UV light, radon, asbestos

When a single base is substituted by another

• When mutations cause no change in function
• Can occur when:
• Mutations are in introns
• Mutations codes for same amino acid

• Involves change in the reading frame of mRNA
• Occurs when a base is inserted or deleted, the codons of mRNA are shifted
• Can render the whole structure non functional

Produces a premature termination of a protein chain, base is changed into a stop codon

• The first tRNA (initiator tRNA) carrier formyl methionine (fMert) instead of methionine
• mRNA does not need to be process (capping, tailing, splicing) in prokaryotes before translation
• Because no processing of mRNS is needed, and transcription occures in the same place (Cytoplasm) they can occur at the same time