F1 Exam #2 Test Info

genome

collection of all coding and noncoding DNA sequences in a cell

transcriptome

collection of all transcripts (mRNA) in a particular tissue at a particular time

proteome

collection of all proteins in a particular tissue at a particular time

exons and introns

coding and noncoding regions; no correlation to the size

dark matter

transposons and noncoding DNA

telomeres

• long sections of noncoding DNA sequences at the end of chromosomes

• don’t have genes and protect genome from shortening of chromosome that occurs during replication

• linear chromosomes

1. when you replicate DNA, the RNA primers at the 3’ end of each original strand is not replaced with DNA

2. leads to an unstable DNA/RNA hybrid so you lose part of that piece of DNA every time you replicate DNA

3. by having random sequences at the end of each strand, instead of losing genomic DNA, DNA is lost from the telomere instead

components of chromosome

DNA wrapped around histone proteins

helicase

breaks h-bonds between base-pairs and unzips the DNA double helix

RNA primase

synthesizes an RNA primer along the DNA strand to begin replication

ligase

creates the final phosphodiester bond between DNA fragments

order read and transcribed

read from 3’ to 5’ and transcribed from 5’ to 3’

how does dna polymerase detect base pairing errors

• base pairing specificcity determined by shape/geometry of nitrogenous bases

• one purine and one pyrimidine perfectly hbonded has distinct fit in active site

if one incorrect nucleotide is inserted dring replication does the error end up in one daughter celll or both

due to semi-conservative nature, only one daughter cell will have the error

differences in product of PCR vs DNA replication in cell

PCR: distinct length/sequence, billions of PCR products made during PCR cycle

DNA replication: different lengths, one copy of everything made in cell

differences in primers of PCR vs DNA replication in cell

PCR: designate to specific sequence to replicate

DNA replication: RNA primers, sythesized whenever replication begins so whole chromosome is copied

differences in DNA polymerase vs taq polymerase in PCR

taq polymerase: functions optimally at high temperatures, quick speed but less proofreading ability than DNA polymerase

DNA polymerase: would be denatured at high temperatures due to h-bonds breaking

coding strand

other complementary strand in DNA replication

template strand

DNA strand used during transcription to synthesize mRNA

units of gene, mRNA, protein

base pairs, nucleotides, amino aicsd

how to determine size of protein

• uncertain due to untranslated regions in mRNA

• if you have length of just exons, can divide by 3 and subtract 3 nucleotides for the stop codon

RNA polymerase vs DNA polymerase

RNA polymerase: can synthesize RNA polymers w/o primer, open double stranded DNA w/o heliase or topoisomerase

DNA polymerase: can’t do above

transcription factor

• must be specific to particular DNA sequence (DNA and r-group in amino acid sequence)

• bind to promoter region of a gene to recruit RNA polymerase and initiate transcription

• can regulate multiple genes beause some genes are involved in same process and need to be regulated together

if protein is nonspecific to DNA, what amino acids would be prsent in the protein

• would recognize the sugar-phosphate backbone of DNA

• basic amino acid with positive charge

regulatory transcription factor (activator)

binds to enhancer sequences and increases rate of transcription

small regulatory RNA function

in post-transcriptional regulation, the bind to completementary regions on an mRNA transcript and target it for degradation or to prevent translation

function of 5’ cap and 3’ polyA tail

prevents mRNA from being degraded, helps recruit/bind ribosome, helps with transport out of nucleus

can single gene produce different mature RNA transcripts

yes

• alternative splicing allows the cell to splice out exons for new products

DNA methylation in gene expression

• addition of methyl group on DNA (cytosine base on CpG site) inhibits gene expression

• when occuring on promotoer region can prevent transcription factor binding

• when occuring on histones, chromatin become more tightly coiled which prevents transcription factor from binding

• the old strand is methylated and helps DNA machinery determine onwhich strand the mutation is and which to be fixed

other mechanisms that prevent transcription factor binding

• histone deacetylation: removing acetyl groups from histones

  • removal of acetyl groups neutralizes the negative charge and allows positively charged histones to bind more tightly to negatively charged dna

• using silencer-transcription factor

• modifying transcription factor to prevent binding

glycosylation

addition of carbohydrate to a protein

addition of carbohydrate helps protein fold into proper form

ubiquitination

addition of ubiquitin molecule to protein

acts as a tag that marks protein for degradation

why is mRNA important for franslation

• mRNA has 3-nucleotide combination (codons) that translate into amino acid sequence

• initiation: ribosome looks for the first codon using tRNA which contains an anti-codon

• elongation: each new charged tRNA base pairs with codons to bring along next amino acid

rRNA function in ribosomes

• enzymatic function: catalyzes formation of peptide bonds

• stable 3D structure allows functional groups to interact with substrate (amino acids)

tRNA synthetase enzyme

charges tRNA with proper amino acid and determines which amino acid should go with which anticodon

mutations that can lead to a prematurely shortened protein

• SNP that changes regular codon to stop codon (nonsense mutation)

• frameshift: insertion of nucleotides not in multiples of 3 that causes a frameshift and a new stop codon to be created

genes

specific regions of chromosomes that code for a specific product

alleles

different forms of a gene

sources of genetic variation during meiosis

1. recombination/crossing over and unlinking of genes

2. segregation: homologous chromosomes are mixed and matched with different homologous chromosomes in the final game

3. independent assortment: homologous pairs of chromosomes align independently, so gametes receive different combinations of different members of each homologous pair

epistasis

a genetic phenomenon where the effect of one gene is masked or modified by one or more other genes

GWAS (genome wide association study)

• use SNPS

• SNPs are linked to genes relevant to stress tolerance

what can genes code for

tRNA, rRNA, small regulatory RNA

transposon

• can break out of genome in on location and glue into genome in another

eukaryotic cell vs bacterial cell genomes

eukaryotic: linear, telomeres

bacterial: circular, no telomeres, no introns, less dark matter

both: similar methods of compaction, DNA wrapped around histones

epigenetic mechanisms that results in diff transcriptomes and proteomes despite having same genome

• chromatin remodeling (histone modification)

• dna methylation: causes transcription factors to be less able to recognize promotor sequence and inability of transcription factors to bind to DNA

mecahnism that results in diff proteomes when genomes and transcriptomes are the same

post translational modifications: variation within proteome after protein is translated

multigenic

phenotype is dependent on many genes

homozygous

DNA sequence is same at two alleles for a gene on a homologous pair of chromosomes

mitochrondria genome

single copy, circular, small, wrapped around histone-like proteins

how are genes and mRNAs related

genes code for mRNAs and proteins

how does active site of DNA polymerase properly catalyze reaction and add new nucleotides

• specific for deoxyribose sugars on nuclotides and triphosphate nucleotides that bring energy for anabolic reaction

• not specific for given nitrogenous base but is specific for geometry of correct basepair with new nucleotide and template strand

components found in PCR mastermix

• DNA polymerase to build new strands of DNA

• dNTPs to serve as building blocks and energy for building new strands of DNA

• salts + divalent cations serve as cofactor for enzyme

reasons for uncertainty in inferring protein functionfrom gene sequence

don’t know which exons are removed by alternative splicing, post-translational modifications affect protein function, protein folding is difficult to predict

what can RNA do on its own vs not

open dna double helix, build phosphodiester bond to add correct ribonucleotide, separate mRNA from DNA template

CAN’T: find promoter (needs transcription factors) or proofread

causes of SNPs

machinery error (DNA polymerase error) or environmental (UV radiation, chemical mutagen)

unsaturated vs saturated fats

unsaturated: double bonds and kinked structure that creates space in between for movement (liquid oils)

capping enzyme

adds 5’ cap for stability, nuclear export, ribosome binding

splicing enzyme

removes introns (+ sometimes exons)polyA

polyA tail adding enzyme

adds polyA tail

acetylation of histones

loosens wrapping of DNA around histones making it less able to bind to acidic/negative phosphate groups on DNA (allos transcription in that region of DNA)

epigenetics

changes in chromatin structure (histone/DNA wrapping), results from environmental influence, stable over long periods of time and can be inherited

• changes in gene expression passed from one generation to the next without change in DNA sequence

• if methylation pattern is passed on during process of meiosis and gamete production then that patter is passed from parent to offspring

enhancer region

binds to transcription factors and helps factors to recruit RNA polymerase and start transcription

nonmendelian genetics

1. environmental influence

2. epistasis

3. multigenic traits

4. pleiotropy

5. incomplete/codominance

6. polymorphism

incomplete dominance

blend (spots)

codominance

both alleles are expressed fully

polymorphism

more than 2 alleles in population (more than 2 phenotypes possible in population)

pleiotropy

more than 1 trait controlled by 1 gene

epistasis

2 or more genes where 1 is transcription factor for other

multigenic traits

more than 1 gene for 1 trait

would it matter if there were mutations in the VDR promotor or introns?

promoters regulate transcription of gene so changing promoter might affect transcription and overall protein expression

introns are spliced out but position of introns is determined by sequence of genes and if there’s a mutation splicing might not occur completely and the intron might be included in the final mRNA

amino acid bonding

basic: protein, hydrogen acceptor, polar, ionic bonds

acidic: hydrogen donor, polar, ionic bonds

polar: hydrophilic, hydrogen bonds

nonpolar: hydrophobic

histone acetylation

• acetyl group added to N-terminal tail of histone protein which neutralizes their positive charge and decreses attraction between histones and negatively charged DNA which relaxes the chromatin structure and activates gene expression

how do cells translate from mRNA to protein

1. tRNA has specific amino acid attached to it based on the anticodon

2. the charged tRNA is created by tRNA synthetase

3. codon in mRNA is matched to an anticodon in tRNA

4. pairing of mRNA and tRNA occurs in ribosomes

5. ribosomes bind to caps/polyA and scan 5’UTR

6. ribozom (rRNA) builds the protein’s peptide bonds

copy number variants

• allows cell to increase gene expression (fish with more copies of FADS2 can make more DHA)

phosphorylation

phosphate group (polar, acidic) is added to a protein which can turn protein activity on or off

sumoylation

post-translational modification where small ubiquitin-like modifier protein is covalently attached to a target protein; regulates protein localization and activity

disulfide bond

covalently links “s” atoms of two different cysteine residues; important for protein structural integrity

lipidation

adds lipid to a protein chain; increases protein’s hydrophobicity

hydroxylation

adds hydroxl group to side chain of protein; stabilitizes proteins

differences in patterns of gene expression reasons

• histone acetylation

• dna methylation

• different transcription factors bind to the same regulatory sequences but are made at different times in different cells

• changes that destabilitize the mRNA: capping, polyA tails, small regulatory RNAs that degrade or block translation

• alternative splicing that creates different proteins

• post-translational modifications

meiosis I

homologous pairs of replicated chromosomes align and are separated

meiosis II

sister chromatids of replicated chromosomes are separate

independent assortment

different alignment of homologus chromosomes in memiosis I leads to different combinations of maternal/paternal chromosomes in gametes