Genetics Exam 4

translation definition

biological polymerization of amino acids into polypeptides from the base sequence of mRNA

translation requirements

amino acids, mRNA, ribosomes, tRNA

ribosomes

have a key role in expression of genetic information, consist of ribosomal proteins and ribosomal rna, small and large subunits

rRNA genes

repetitive DNA present in clusters at various chromosomal sites

tRNA

coordinate mRNA codons with corresponding amino acids

what complements tRNA anticodons

mRNA codons

tRNA stability and size

small and very stable

where are tRNA transcribed from

DNA

two-dimensional cloverleaf structure of tRNA

internal base pairing forms stems and loops

three-dimensional structure of tRNA

anticodon loop and amino acid binding site are at opposite ends of the folded molecule

charging tRNA

anticodon:nucleotide triplet in tRNA that complimentarily base-pairs to a codon triplet in mRNA

tRNA job

carries amino acid corresponding to its anticodon

tRNA charging

Chemical reaction in which an aminoacyl-tRNA synthetase attaches an amino acid to its corresponding tRNA.

initiation requires

-small and large ribosomal subunits
-mRNA molecule
- GTP
- charged initiator tRNA
-Mg2+
-initiation factors

shine delgarno sequence

- ribosomal binding site in bacterial and archaeal messenger RNA
- generally located around 8 bases upstream of the start codon AUG.
- helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the start codon.

initiation complex

a complex of protein factors, mRNA, met-tRNA, and the small and large ribosomal subunit which is required to start translation

elongation definition

lengthening of growing polypeptide chain by one amino acid

sites of ribosome

A site, P site, E site

elongation process

1. the sequence of the second triplet in mRNA dictates which charged tRNA molecule will become positioned at the A site. Peptide bond links the two amino acids together.
2. At the same time, the covalent bond between the tRNA occupying the P site and its amino acid is hydrolyzed (broken). The dipeptide remains attached to the end of the tRNA still residing in the A site.
3. the uncharged tRNA moves transiently through the third site on the ribosome, called the E (exit) site. the entire mRNA-tRNA-aa2-aa1 complex then shifts in the direction of the P site by a distance of three nucleotides
4. the third triplet of mRNA is now in a position to accept another specific charged tRNA into the A site
5. repeat

termination of translation

- occurs when the codon in A-site is a stop codon
- release factor places a water molecule on the polypeptide chain and thus releases the protein
- tRNA is released from ribosome, and ribosome dissociates into subunits

polysomes

-mRNAs with several ribosomes translating at once
- as mNA passes through ribosome, it is free to associate with another small subunit

why is translation more complex in eukaryotes?

- ribosomes are larger and longer lived than in bacteria
- 5' end of mRNA capped with 7-methylguanosine at maturation, which is essential for translation
- Poly(A)tail is added to 3' end
- requires more factors for initiation, elongation, and termination than in bacteria
- ribosomes are not free-floating but associated with endoplasmic reticulum

one gene-one enzyme hypothesis (old)

each gene contains the information needed to make an enzyme

Scientists that came up with one gene-one enzyme hypothesis

Beadle and Tatum

one gene-one polypeptide hypothesis

The premise that a gene is a segment of DNA that codes for one polypeptide.

sickle cell anemia

recessive genetic disease: afflicted individuals are homozygous for Hbs hemoglobin allele (erythrocytes become elongated under low oxygen tension)

how are normal and sickle cell hemoglobin chemically different

differ by one amino acid

polypeptide

amino acid polymer, precursor to protein

protein

polypeptide(s) folded up into a functional three-dimensional conformation

amino acid structure

a carboxyl group, amine group, and R group

R group function in an amino acid

determines the type of amino acid
ex. nonpolar R group = hydrophobic
polar R group = hydrophilic

peptide bond

bond holding amino acids together in a polypeptide

primary level of protein structure

sequence of amino acids

secondary level of protein structure

alpha helix (coil) and beta-pleated sheet

tertiary level of protein structure

three-dimensional conformation

quaternary level of protein structure

Composed of more than one polypeptide chains

protein folding

The physical process by which a polypeptide folds into its characteristic three-dimensional structure, which is essential to the protein's function.

what mediates protein folding

chaperones

misfolded proteins

*nonfunctional*
-can accumulate and be detrimental to cells and organisms containing them

prions

aggregates of misfolded protein causing transmissible brain disorders in mammals

examples of prions

Mad Cow Disease
Scrapies
Chronic Wasting Disease
Feline Spongiform Encephalopathy
Creutzfeldt-Jakob Disease

immunoglobulins

bind with specific antigens in the antigen-antibody response

transport proteins

movement of molecules across membranes

hormones and their receptors

regulate various types of chemical activity

transcription factors

regulate gene expression

enzymes

involved in biological catalysis (lower energy of activation)

which is the most diverse and largest group of proteins

enzymes

Three types of point mutations

silent, missense, nonsense

missense mutation

A point mutation in which a codon that specifies an amino acid is mutated into a codon that specifies a different amino acid.

nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

Silent/Same Sense Mutation

The codon is altered but the coded amino acid does NOT change

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

dominant mutation

one mutant allele (heterozygous genotype) is sufficient to cause phenotypic change

recessive autosomal mutation

unlikely to result in a detectable phenotype
- two mutant allele (homozygous genotype) is required to cause phenotypic change

neutral mutation

the majority of mutations occur in noncoding regions
- neither beneficial or detrimental (cannot be selected for or against)

somatic mutations

Mutations that occur in body cells, aren't passed to offspring, and don't affect the gametes

germ-line mutation

a mutation occurring in gametes; passed on to offspring

autosomal mutations

mutations within genes located on the autosomes

X-linked and Y-linked mutations

occur within genes located on the X and Y chromosome

spontaneous mutations

random change in the DNA due to errors in replication that occur without known cause

How do spontaneous mutations occur?

DNA polymerase occasionally inserts incorrect nucleotides, misincorporated nucleotides may persist after proofreading, uncorrected mispairing errors predominantly lead to point mutations

replication slippage

If loop occurs in template strand during replication, DNA polymerase misses looped out nucleotides, and small insertions and deletions occur

where is replication slippage more common?

repeat sequences (hot spots)

Tautomeric shifts

- Can change the bonding structure, allowing non complementary base pairing
- may lead to permanent base-pair changes and mutations

depurination and deamination

- DNA base damage leads to new base pairing and mutations
- common causes of spontaneous mutations

oxidative damage to DNA

Due to by-products of normal cellular processes
Exposure to high-energy radiation
Superoxides (O2 )
Hydroxyl radicals (OH)
Hydrogen peroxide (H2O2)

induced mutations

DNA damage caused by chemicals and radiation

mutagen

natural or artificial agents that induce mutations

examples of mutagens

fungal toxins, cosmic rays, UV light, industrial pollutants, medical X rays, chemicals in tobacco smoke

UV light creates what in DNA?

pyrimidine dimers

pyrimidine dimers

extra bonds formed between thymine or cytosine in DNA (cause of mutations)

ionizing radiation

enough energy to dislodge electrons from atoms, forming ions; capable of causing cancer (gamma, X-rays, UV)

energy of radiation varies with wavelength

short wavelength = increased energy

free radicals

naturally occurring, highly reactive chemicals that form in the presence of oxygen, can directly or indirectly affect DNA

proofreading and mismatch repair

DNA polymerase "proofreads," removes and replaces incorrectly inserted nucleotides
if proofreading fails, mismatch repair becomes activated

mismatch repair process

mismatches are deleted, cut, and removed. Correct nucleotide is inserted by DNA Polymerase

How are incorrect nucleotides recognized?

strand discrimination on DNA methylation
- enzyme recognizes DNA sequences and adds methyl group to adenines
- newly synthesized strand of replication remains unmethylated
- mismatch repair recognizes unmethylated strand and repairs

link between mismatch repair and cancer

a strong link

Postreplication repair

- responds after damaged DNA has escaped repair and has failed to be completely replicated
- protein directs recombination exchange with corresponding region on undamaged parental cell
- gaps can be filled in by repair synthesis (DNA polymerase and DNA ligase)

Base and nucleotide excision repair

Exonuclease recognizes and cuts distortion/error.
DNA polymerase inserts complementary nucleotides in missing gap.
DNA ligase seals final "nick."

base excision repair

DNA repair that first excises modified bases and then replaces the entire nucleotide

nucleotide excision repair

repairs pyrimidine dimers

NER and Xeroderma Pigmentosum

rare genetic disorder due to defects in NER pathways, affected individuals exhibit severe skin abnormalities, skin cancers, and developmental and neurological defects, 2000-fold higher rate of cancer

the Ames test

Test in which special stains of bacteria are used to evaluate the potential of chemicals to cause cancer

transposons

(jumping genes) short strands of DNA capable of moving from one location to another within a cell's genetic material

how were mobile genetic elements found in corn

Ac-Ds system (activator and dissociation)
- movement of Ds gene is dependent on Ac gene

Human transposable elements

-Half of human genome is composed of transposable elements
-LINEs and SINEs: long interspersed elements and short interspersed elements
-0.2% of detectable human mutations may be due to transposable element insertions
Transposons may contribute to variability that underlies evolution.

inducible enzymes

bacteria adapt to environment by producing inducible enzymes only when specific substrates are present

constitutive enzymes

Enzymes are continuously produced regardless of chemical makeup of environment

repressible system

Presence of specific molecule inhibits gene expression
Abundance of end product in environment represses gene expression

operon

a cluster of genes under control of a common regulatory region (promotor and operator)

three genes of lac operon

lacZ, lacY, lacA

lacZ

encodes B-galactosidase

B-galactosidase

breaks down lactose into glucose and galactose

lacY

encodes lactose permease

lactose permease

facilitates the uptake of lactose into the cell

lacA

encodes transacetylase

transacetylase

may be involved in the removal of toxic by-products of lactose digestion from the cell

I gene

codes for repressor protein which regulates transcription

polycistronic mRNA

molecules of mRNA that code for multiple proteins