genetics exam 3

chapters 8, 9, 10, and 11 +practice exam

Template Strand (Noncoding/Antisense Strand)

The DNA strand that is used as a template by RNA polymerase to synthesize the complementary RNA transcript.

Coding Strand (Nontemplate/Sense Strand):

The DNA strand whose nucleotide sequence corresponds to the sequence of the RNA transcript (with uracil replacing thymine).

Promotor

A double-stranded DNA sequence located upstream (5') of the gene that binds RNA polymerase and transcription factors to initiate transcription.

Transcription Start Site (+1)

The first nucleotide of a gene that is transcribed into RNA

Pribnow Box (-10 Consensus Sequence)

A conserved AT-rich bacterial promoter consensus sequence located approximately 10 base pairs upstream of the start site 5’-TATAAT-3’.

-35 Consensus Sequence

A conserved bacterial promoter sequence located 35 base pairs upstream of the start site 5’-TTAGAC-3’

Holoeznyme

In bacteria, the fully active RNA polymerase complex consisting of the core enzyme 2 alpha, 2 beta, 1 w, plus the sigma subunit

Intrinsic Termination

A bacterial transcription termination mechanism where an mRNA hairpin loop followed by a poly-U string causes RNA polymerase to stall and dissociate.

Rho-Dependent Termination

A bacterial termination mechanism requiring the rho (p) protein to catch up with a paused RNA polymerase and unwind the DNA-RNA hybrid.

TATA Box (Goldberg-Hogness Box)

A core eukaryotic promoter consensus sequence (5’-TATAAA-3’) located around position -25 that binds TFIID.

Preinitiation Complex (PIC)

An assembly of general transcription factors (TFIID, IIA, IIB, IIF, IIE, IIH) and RNA polymerase II poised at a eukaryotic promoter.

Enhancer

A cis-acting DNA sequence that increases transcription of a gene, often located far away, functioning via DNA looping and protein bridges.

Silencer

A DNA regulatory element that binds proteins to repress transcription by inducing structural bends or blocking activation.

5' Capping

The addition of a 7-methylguanosine residue to the 5' end of eukaryotic pre-mRNA via a unusual 5’ - 5’ triphosphate linkage to protect and stabilize the transcript.

Polyadenylation

The enzymatic cleavage of eukaryotic pre-mRNA downstream of an AAUAAA signal and the addition of a string of 20 to 200 adenine residues (poly-A tail).

Intron

A noncoding intervening sequence within a pre-mRNA transcript that is removed during RNA splicing

Exon

A segment of a gene/pre-mRNA that remains part of the mature mRNA and is translated into protein.

Spliceosome

A large dynamic macromolecular complex composed of snRNPs (U1, U2, U4, U5, U6) that removes introns from pre-mRNA.

Lariat Structure

A lariat-shaped looped intermediate formed during pre-mRNA splicing when the 5' end of an intron attaches to the branch point adenine.

Alternative Splicing

A regulatory process where different combinations of exons are joined together, allowing a single gene to encode multiple distinct protein

Chromatin

important for gene regulation in eukaryokes

3 types of eukaryotic polymers

RNA pol I: transcribes ribosomal RNA genes

RNA pol II: transcribes protein coding genes and most small nuclear RNA genes

RNA pol III: transcribes tRNA genes

What transcribes miRNA and siRNA

miRNA: RNA pol II

siRNA: RNA pol III

Aurthor Kornberg

won 1959 Nobel Prize in physiology/Medicine for finding the mechanism behind biological synthesis of Dson)NA/RNA - isolate DNA polymerase

Roger D Kornberg

(son) won 2006 nobel prize in chemistry for research in eukaryotic transcription — cells copy info from DNA > RNA

what bond forms beteen adjacent nucleotides to form RNA strands

phosphodiesterbonds

what is necessary for the formation of new phages (bacteria)

RNA transcription

mRNA

only RNA that undergoes translation, made by protein producing genes, is short lived between DNA and protein, is followed by post transcriptional processing

types and function of funcitonal RNA’s

doesn’t encode proteins, and helps / cell functions

1. siRNA

2. miRNA

3. tRNA

4. telomerase RNA

5. snRNA

ribosomal RNA (rRNA)

combines numerous proteins to form ribosomes

transfer RNA (tRNA)

responsible for binding an aminio acid and depositing it for inclusion into a groing protein chain

telomerase RNA

provides a template for synthesis of repetative DNA telemere sequences

small nuclear RNA (snRNA)

in the nucleus of eukaryotes and plays a role in mRNA processing

micro and small interfering RNA (mRNA and siRNA)

in plant and animal cells, used in post transcriptional regulation of mRNA

transcription

synthesis of a single stranded RNA molecule by RNA polymerase

4 stages of transcription in bacteria

1. promoter recognition

2. transcription initiation

3. chain elongation

4. chain termination

promoter

upstream (5’ end) to the start of transcription (+1 nucleotide)

controls acess of RNA polymerase to the gene

coding region

portion w/ the info needed to synthesize the protein product

termination region

downstream (3’ end) to the coding segment of the gene

regulates cessation of transcription

Rifampicin stops the formation of which bond? what does it stop synthesizing?

1. stops formation of the phosphodiester bonds

2. bacteria is unable to synthesize mRNA,tRNA, and rRNA

Bacterial RNA polymerase is composed of and binds to what?

1. composed of RNA polymerase core

2. binds to the sigma factor

eukaryotic transcription

• genes have introns and exons

  • introns get removed

• their protiens form chromatin

how many RNA polymerases are present in eukaryotes

3 that transcribe different genes

RNA polymerase core binding with sigma subunit forms

a holoenzyme

alternative sigma subunits

alters core enyme conformation to facilitate association with different promoter regions

promoter (bacterial transcription)

double stranded DNA sequence that is the RNA polymerase binding site; also binds other transcription proteins

where is bacterial promoter located

a short distance upstream of coding sequence (withing +1 nucleotides)

why i RNA polymerase attracted to promoters

cause of consensus sequences

promoter consensus sequences

written in single stranded shorthand form, 5’ to 3’ on the coding strand

what binds to the consensus sequences at -10 and -5

RNA polymerase

how does RNA polymerase initiate transcription

3 steps

1. form closed promoter complex

2. forms open promoter complex

3. holoenzyme shifts downstream to initiate at the +1 site

closed promoter complex

holoenzyme loosy attatches to promoter sequence, then tightly binds

open promoter complex

holoenzyme unwinds around 18 bp of DNA around the -10 position

when does the sigma subunit dissasociate from the core enzyme in transcription

after the first 8-10 nucleotides have been joint

what happens when transcription of a gene is completed

the 5’ end of RNA trails off the core enzyme, then the core enzyme dissasociates from the DNA, shortly after one round of transcription is initiated a second one begins

types of transcription termination mechanisms

1. intrinsic termination

2. rho-dependant termination

intrinsic termination

mechanism dependant on repeating sequences

• has an inverted repeat followed by a string of adenines

  • forms a stem-loop structure → “hairpin”

• ends with a series of U’s to slow down and destabalize

  • causes polymerase to release the transcript

Rho-Dependent termination

requires termination sequence and rho-protein

• rho protein bind to mRNA causing eperation of mRNA and RNA polymerase

• “rut-site” is included in the termination sequence

  • after rut site is transcribed,Rho protein will bind to the site

  • Rho will along DNA till polymerase is released from DNAse f

Codon

A sequence of three consecutive nucleotides on an mRNA molecule that specifies a particular amino acid or a stop signal.

Shine-Dalgarno Sequence

A purine-rich sequence in the 5' UTR of bacterial mRNAs (5’ - ACCAUGG - 3’) that facilitates recognition by the preinitiation complex

Peptidyl Site (P Site)

The ribosomal site that holds the tRNA carrying the growing polypeptide chain

Aminoacyl Site (A Site

he ribosomal site that binds an incoming charged aminoacyl-tRNA.

Exit Site (E Site)

The ribosomal site from which uncharged tRNAs leave the ribosome after peptide bond formation.

Degeneracy (Redundancy)

The property of the genetic code where most amino acids are specified by more than one codon

Third-Base Wobble

Flexibility in base pairing between the 3'-nucleotide of an mRNA codon and the 5'-nucleotide of a tRNA anticodon, allowing fewer tRNAs to recognize multiple codons.

Aminoacyl-tRNA Synthetase

An enzyme that catalyzes the specific attachment (charging) of an amino acid to its corresponding tRNA

Polycistronic mRNA

An mRNA molecule that encodes multiple different polypeptide chains, common in bacteria and archaea (found in operons)

Monocistronic mRNA

An mRNA transcript that encodes a single polypeptide chain, typical of eukaryotes

Polyribosome (Polysome)

A cluster of multiple ribosomes simultaneously translating a single mRNA molecule.

Karyotype

An organized visual display of a species' chromosomes arranged by size, shape, and banding pattern

Euploid

An organism or cell with a complete, balanced multiple of the basic chromosome set (n, 2n, etc)

Aneuploidy

A condition in which the chromosome number is not an exact multiple of the haploid set (e.g., trisomy, monosomy)

Nondisjunction

The failure of homologous chromosomes or sister chromatids to separate properly during meiosis or mitosis.

Autopolyploidy

• The presence of three or more complete sets of chromosomes derived from within the same species.

Allopolyploidy

Polyploidy resulting from the combination of chromosome sets from different species (hybrids followed by chromosome doubling)

Paracentric Inversion

A chromosomal inversion in which the inverted segment does not include the centromere

Pericentric Inversion

A chromosomal inversion in which the inverted segment includes the centromere

Dicentric Chromosome

A chromosome possessing two centromeres, typically arising from crossing over within a paracentric inversion loop

Acentric Fragment

A chromosome fragment lacking a centromere, which is lost during cell division

Reciprocal Balanced Translocation

A structural rearrangement where pieces of two nonhomologous chromosomes break off and switch places with no net loss of genetic material.

Robertsonian Translocation (centric fusion)

The fusion of two acrocentric chromosomes near their centromeres, reducing the total chromosome count.

Pseudodominance

The sudden phenotypic expression of a recessive allele due to the deletion or inactivation of the dominant allele on the homologous chromosome

Point Mutation (Localized Mutation)

A mutation affecting a single base pair or a small localized region of DNA.

Transition Mutation

A base-pair substitution where a purine replaces a purine, or a pyrimidine replaces a pyrimidine.

Transversion Mutation

A base-pair substitution where a purine is replaced by a pyrimidine, or vice versa.

Synonymous (Silent) Mutation

A base-pair change that alters a codon but does not change the amino acid sequence due to code redundancy.

Missense Mutation

A base-pair substitution that results in a different amino acid being incorporated into the protein

Nonsense Mutation

A base-pair change that converts an amino acid-specifying codon into a premature stop codon

Frameshift Mutation

The insertion or deletion of one or more base pairs (not multiples of three), shifting the reading frame of the mRNA

Depurination

The spontaneous loss of a purine base (A or G) from a nucleotide, creating an apurinic (AP) site.

Deamination

The spontaneous or induced removal of an amino group (NH2) from a nucleotide base (e.g., cytosine converting to uracil)

Thymine Dimer (UV Photoproduct)

An aberrant covalent bond formed between adjacent thymine residues on a DNA strand caused by UV irradiation

Base Excision Repair (BER)

A repair pathway where a DNA glycosylase removes a damaged base, an AP endonuclease nicks the backbone, and DNA polymerase fills the gap.

Nucleotide Excision Repair (NER)

A repair mechanism (such as UV repair by UvrABC in bacteria) that removes a damaged single-stranded oligonucleotide segment and resynthesizes the gap

Mismatch Repair (MMR)

A repair system (utilizing MutS, MutH, and MutL in E. coli) that recognizes and corrects replication errors on the unmethylated daughter strand.

p53 Repair Pathway

A crucial cellular checkpoint pathway regulated by the p53 tumor suppressor protein that pauses the cell cycle for DNA repair or induces apoptosis if damage is severe

How do transcription and translation differ fundamentally between prokaryotes and eukaryotes in terms of spatial and temporal coupling?

In prokaryotes (bacteria), transcription and translation are closely coupled; ribosomes can attach to mRNA and begin translating while transcription is still ongoing because there is no nuclear membrane. In eukaryotes, transcription occurs inside the nucleus where pre-mRNA undergoes extensive processing (capping, splicing, polyadenylation), and mature mRNA must be exported to the cytoplasm before translation can take place.

Explain the biological significance of wobble pairing at the third position of the codon.

Third-base wobble relaxes strict complementary base-pairing constraints at the 3' base of the mRNA codon and the 5' base of the tRNA anticodon. This allows a single tRNA molecule to recognize multiple synonymous codons, reducing the total number of distinct tRNA genes required by a cell while maintaining complete translational fidelity

Why are heterozygous carriers of balanced reciprocal translocations often semi-sterile?

During prophase I of meiosis, translocation heterozygotes form a characteristic cross-shaped (tetravalent) synaptic structure. Depending on how these chromosomes disjoin at anaphase I (alternate vs. adjacent-1 or adjacent-2 segregation), only alternate segregation yields gametes with a complete, balanced set of genes. Because adjacent segregation produces large duplications and deletions, roughly 50% of the resulting gametes are nonviable, leading to semi-sterility

Compare and contrast Base Excision Repair (BER) and Nucleotide Excision Repair (NER)

BER primarily targets single damaged or incorrect bases (such as uracil in DNA or oxidized bases) via DNA glycosylases that create an AP site before nick translation. NER handles bulky, helix-distorting lesions spanning multiple nucleotides (such as UV-induced thymine dimers) by recognizing the damage, cutting out an entire oligonucleotide segment (4–5 nucleotides on either side), and resynthesizing the gap.