Bio Ch 15/17 & 19-21

Chromosome theory of inheritance

States Mendelian genes have specific loci (sites) along chromosome & it is the chromosome that undergoes segregation & independent assortment.

Supported by Mendel experiments

Mendel Experiment

Chose fruit flies (inexpensive, convenient)

4 pair of chromosomes, easily distinguishable w/ light microscope

Spotted male fly w/ white eyes

Mated that mutant white eye male with red eye female (all F1 = while type (red eye) )

F2 has 3:1 (only in males showcasing sex linked)

Separation of homologs during Anaphase 1

Accounts for segregation of the 2 alleles of a gene into separate gametes

Random arrangement of chromosomes pairs during metaphase 1

Accounts for independent assessment of alleles for two or more genes located on different homolog pairs

SRY gene activation is important

On Y chromosome allows for correct development of male anatomical features

X-linked trait is due to

Recessive allele, females must be homozygous to phenotypically show

Duchess muscular dystrophy

Affects male (weakening bone/coordination)

Lacking key protein on X chromosome

Hemophilia

X linked , lacking protein required for blood clotting

Female mammals including human inherit

2 X chromosome

Does not mean they encode double

Infact almost all of one X becomes inactive

Barr Body

Inactive X cell on female condenses into this compact object

Most genes on this are not expressed until they’re in the ovaries where chromosome are reactivated to give rise to egg (resulting in female egg having active X after meiosis)

Linked genes

Genes located near each other on the same chromosome tend to be inherited together in genetic crosses

Morgan’s experiment w/ flies body color & wing size gene

Resulting flies had higher combination of traits seen in P generation

Concluding that they’re linked

Meiosis & random fertilization

Generate specific variation among sexually reproducing organism due to

Independent assortment

Crossing over Meiosis 1

Probability of any sperm fertilizing any egg

Matching offspring are called

Parental types

Non parental phenotypes amongst offspring have new combinations

Recombinant types

50% frequency of recombination in test cross is observed

For any 2 genes that are located on different chromosomes & thus cannot be linked

More than 50% frequency indicates

Genes are linked

Crossing over accounts for recombination of linked genes

Breaking physical connection between specific alleles of genes on same chromosome

Occurs while replicated homologous chromosomes are paired during prophase of meiosis 1

Genetic map

Ordered list of genetic loci along a particular chromosome

Linkage map

Genetic map based on recombinant frequencies

(Genes located ver far apart on same chromosome will NOT show linkage)

Nondisjunction

Members of a pair of homologous chromosomes do not move apart properly during meiosis 1 or sis.chromatid fail to separate during meiosis 11

One gamete receives 2 of the same while the other receives nothing

Aneuploidy

One or more chromosomes are present in extra or deficient copies

Nondisjunction can occur in

Mitosis, and if aneuploidy occurs during earlier embryonic development, this can be passed on to large numbers of cells having substantial negative impact

Polyploidy

More than 2 full sets of chromosomes

Important in plant

Errors in meiosis or radiation (etc) can cause changes

Deletion

Duplication

Inversion

Translocation

Deletion

Chromosomal fragments is lost

Duplication

Reattachment of extra fragmented segment to sis/non sis chrom

Inversion

Fragment reattaches OG chromosome in reverse orientation

Translocation

Fragment joins a non homologous chromosomes

Deletion & duplication are likely to occur in

Meiosis

translocation & inversion

Can alter phenotype bc gene expression can be influenced by its location

Nondisjunction in meiosis results in

Aneuploidy in gametes & resulting zygote

(Although number is high in human, most are miscarried, the ones that survive ~syndrome~ )

Down syndrome

Trisomy on 21

Genomic imprinting

Expressions of an allele in offspring depends on whether the allele is inherited from male or female parent

Occurs during gamete formation, silences a particular allele of a certain gene or activates it

Costs of methyl —CH3 groups being added to Cytosine ( silencing allele mainly/ few activation )

Critical for embryonic development

Extra cellular gene

Not all locate on nuclear chromosomes, some outside organelle

(Some on mitochondria, chloroplast, plastid DNA. = do not display Mendelian inheritance)

Defects in protein of mitochondria

Result in reduction of ATP, b/c of effect on oxi phosphorylation

Causing disorder (detrimental) only from female parents

Gene expression

Process of DNA directing synthesis of proteins (some cases RNA)

Garold postulated that symptoms of an inherited disease reflects on the inability to make a particular enzyme

Later named One gene- One enzyme hypothesis

Beagle & Tatum

Neurospora (bread mold)

Used haploid mold species to demonstrate relationship between gene and enzyme

Require minimal medium

To experiment used complete medium to investigate Argentine synthesis, using Argentine requiring mutant

Result = each mutant unable to carry out one step in pathways for synthesizing Arg (presumably bc it lacked enzyme)

Supporting the one gene one enzyme hypothesis

Not all proteins are

Enzyme

Transcription

Synthesis of RNA using information in DNA

Occurs in nucleus

(Protein coding gene resulting in RNA = mRNA)

Translation

Synthesis of a polypeptide using info in the mRNA

Site = ribosome

Both transcription & translation occur in prok & euk

In bacteria since there’s no compartmentalization it occurs at same time

In euk transcription occur in nucleus but must be transported to cytoplasm for translation

Primary transcript

Initial RNA transcript from any gene including those specifying RNA is not translated into proteins

Flow of info going one way = Central Dogma

DNA — RNA — PROTEIN

Triplet of nucleotide bases = smallest unit of nucleotide length that can code for AA

4³ = 64 (possible code)

Flow of information from gene to protein is based on the triple codes

Template strand

DNA strand that is transcribed, provides pattern

Ex: 3’ ACC 5’

mRNA

Carrier of info from DNA to cells protein synthesizing machinery

Complementary 5’ UGG 3’

Non template strand of DNA

Coding strand 5’ TGG 3’

Number of nucleotides

Is 3x those of AA

61 OUT OF 64 CODE FOR AA

There is redundancy in genetic code

But not ambiguity

Enzyme RNA polymerase

Pries 2 strands of DNA apart & joins together RNA nucleotides complementary to DNA template thus elongating RNA polynucleotide

Assembly in 5’ — 3’ (adding on 3’)

Can start chain from scratch without the need of pre existing primer

Transcription stages

Initiation

Elongation

Termination

Promoter

DNA seq, where RNA polym attaches & initiates transcription

In bacteria signal ending transcription

Terminator

Bacteria vs Eukarya RNA polymerase

Bacteria = 1

Euk = 3 (RNA pol 11 used for pre mRNA synthesis, while others transcribe RNA molecules that are not translated to protein

Binding of RNA pol to promoter

Determines where transcription start & what direction it will travel

In eukarya transcription factors

Help guide binding of RNA pol & initiation of transcription

Transcription initiation complex

Whole complex of transcription factors & RNA pol 11 bound to the promoter

Has crucial promoter DNA seq called TATA box

Elongation of RNA

Enzyme adding nucleotide to 3’ end

Termination of transcription

In bacteria = terminator which causes polymerase to detach from DNA & releases transcript

In eukarya = RNA pol 11 transcribes seq on DNA , called polyadenylation , which specifies a signal in pre-mRNA

(note although in eukarya this cleavage marks end of mRNA , RNA pol 11 continues to transcribe until enzymes catch up & it dissociate from DNA

Alteration of mRNA end

5’ end (synthesized first) receives 5’ cap (modified form of G add onto 5’end after transcription of the first 20-40 nucleotide)

3’ end also modified before mRNA exit nucleus , enzyme add 50-250 more A nucleotide forming a poly A tail

Important function of 5’cap & poly A tail

Facilitate export of mature mRNA from nucleus

Help protect mRNA from degradation by hydrolytic enzymes

Help ribosome attach to 5’ end of mRNA once it reaches cytoplasm

UTRs

Untranslated regions of 5’ & e’ , help ribosome binding

RNA splicing

In eukarya nucleus

Large portions of RNA primary transcript molecule are removed & remaining portions are reconnected

Non coding region of Nucleic acid lies between

Intron

Eventually expressed

Exons

In RNA splicing introns are

Cut out from molecule while exons are joined together , forming an mRNA molecule w/ continuous coding seq

Removal of intron is possible

Via protein complex = spliceosome

(They also join together exons

Showing RNA can act as catalyst)

Ribozymes

RNA molecule that functions as enzyme

Intron RNA function as ribozyme & catalyzes its own removal

3 properties of RNA functioning as enzyme

Region in RNA molecule that may base pair, In An antiparallel arrangement w/ a complimentary region elsewhere in same molecule

Some of bases in RNA containing functional groups that can participate in catalysis

Ability of RNA to HB with other Nucleic acid molecules adding specifity to it’s catalytic activity

introns have allowed

Single gene to encode more than one kind of polypeptide

Alternative RNA splicing

Genes giving rise to 2 or more diff polypeptide base on what segment is treated as exon

Introns increase

Probability of crossing over between exon of allele by providing more terrain for cross over

Tranfer RNA

Tranfer an AA from cytoplasmic pool of AA to a growing polypeptide in a ribosome

Key of translating genetic message into a specific AA is the fact each tRNA molecule enables translation of given mRNA codon into certain AA

Has complimentary stretches of nucleotide bases that can HB to each other

tRNA

Used repeatedly , & in eukaryotic it is made in nucleus & travels to cytoplasm

Aminoacyl- tRNA synthetases = allows for correct matching of tRNA & AA

(Uses ATP & releases charged tRNA)

Ribosome

Eukarya = larger can continue even after bacterial ribosome are inactivated

Facilitate coupling of tRNA anticodon w/ mRNA codons during protein synthesis

rRNA

Most abundant type of cellular RNA

Site in Ribosome

E= exit site (discharged tRNA leave ribosome)

P= peptidyl- tRNA binding site ( holds tRNA carrying growing polypeptide chain)

A= Aminoacyl tRNA binding site ( holds tRNA carrying the next aa to be added to chain)

Ribosome can be considered

One colossal ribozyme

Translation 3 stages

Initiation = bring mRNA , tRNA bearing first AA of polypeptide & 2 subunit of ribosome

(Binding to mRNA reaching AUG codon, binding to large subunit as well, completing initiation complex)

Proteins called initiation factors bring all components together (energy is expended)

tRNA sit in P & A is vacant for next

N terminus to C terminus (synthesis of polypeptide)

Elongation of translation

AA added one by one to previous AA at C terminus

Energy expenditure happens at 1 & 3 step

Step:

1st = codon recognition

2nd= peptide formation to carboxyl end

3rd= translocation from A to P & empty tRNA in P are released from E

Termination in translation

Stop codon reaching A site (UGA, UAA, UAG 5’ — 3’ )

Release factor protein shaped like Aminoacyl tRNA binds directly to stop codon in A site & release water (hydrolyzing peptide chain)

2 types of ribosome

Free = suspended in cytosol & mostly synthesize protein that stays in cytosol

Bound= attached to cytosolic side of ER or nuclear envelope, make proteins of Endomembrane system as well as the ones secrete into the cell

(These ribosome are identical and can alternate between free/bound)

Signal mechanism for targeting proteins to ER

Polypeptide synthesis begun in cytosol as free ribosome translate mRNA , there process continues to completion unless growing peptide itself cues ribosome to attach to ER

Polypeptide (marked by signal peptide which targets protein to ER)

Signal recognized by SRP , binds to receptors protein in ER , part of protein complex that forms a pore

SRP leaves , polypeptide synthesis resumes w/ simultaneous translocation across the membrane

Signal peptide is cleaved by enzyme in receptor complex

Rest of completed polypeptide leaves the ribosome & fold into final conformation

Mutations

Source of new gens/ changes to genetic info

Point mutation

Changes in a single nucleotide pair of gene

If in gamete , can be passed to future generations (ex:sickle cell)

Nucleotide pair substitution

Replacement of one nucleotide & its partner w/ another pair of nucleotide

Silent mutation

No observable affect on phenotype bc results in same AA

Missennse mutations

Substitution that changes one AA

To another

Nonsense mutations

Causes translation be terminated prematurely

Insertion & deletions

May alter reading frame, disastrous effect on resulting protein

Framehsift mutation

Wherever # of nucleotide inserted or deleted does not equal multiple of 3 (unless near every end, otherwise protein is non functional)

Mutations arise by

Error in DNA replication

Recombination

Mutagens interacting w/ DNA

Using CRISPR CAs 9

Gene editing

CAs 9 acts with guide RNA made from CRISPR region of bacteria genome

CAs 9 is Nuclease & cuts ds DNA molecules

Thus triggers repair system where there’s no undamaged DNA to use as template, repair enzymes introduce /remove random nucleotides

Technique is good in “knocking out” given gene to see what it does in an organism

Cas 9

Bacterial protein helping defend bacteria against virus that infect them (becateriopahges)

CRISPR CAS 9 has been modified

To repair gene w/ harmful mutations

By introducing functional segment along with the CRISPR system , so when it edits , the defective gene is corrected

Gene

Region of DNA that can be expressed to produce a final functional product , that’s either a polypeptide or RNA molecule

Virus

Infectious particle consisting of little more than genes packaged in a protein coat

CANNOT reproduce/carry out activities outside of host cell

Viral genomes

Can be diverse DNA/RNA , ds, ss