Bio exam 4

How is a tRNA molecule 'charged'?

it is attached to the corresponding anti-codon of a tRNA molecule

what are the different sites of a ribosome?

A site, P site, and E site

what is the A site of a ribosome?

acceptor site for an aminoacyl tRNA; binds to the tRNA carrying the next amino acid

what is the P site of a ribosome?

peptidyl binds to the tRNA that is attached to the growing polypeptide chain

what is the E site of a ribosome?

exit site of tRNA

what occurs during initiation of translation?

mRNA attaches to ribosome; start codon signals the beginning of translation

what occurs during elongation of translation?

1. matching tRNA anticodon with mRNA codon

what occurs during termination of translation?

a stop codon is reached, attaching a release factor which disassociates the subunits of the ribosome and the mRNA strand

what bond is formed between the amino acids of the polypeptide chain?

peptide bond

what are the 2 ways eukaryotic translation differs from prokaryotic translation?

1. initiating amino acid in methionine

what is an RBS?

ribosome binding sequence

what is wobble pairing?

involves less stringent interactions between 3' base of the codon and 5' base of the anticodon;

what is a mutation?

heritable changes in genetic information

what is a point mutation? (single nucleotide variation)

a mutation that alters a single base

how do point mutations occur?

bases are substituted for one another, or there is a deletion or addition of a single base (or small number of bases)

what is base substitution?

one type of base is substituted for a different base.

what is a missense mutation?

when the base mutation alters the amino acid

what does it mean for a base substitution to be "silent"?

the mutated base still codes for the same amino acid

what does it mean for a missense mutation to be a transition or transversion?

transition: does not change type of base (purine to purine / pyrimidine to pyrimidine

what is a nonsense mutation?

occurs when a base is changed and the new codon is a stop codon

what does a nonsense mutation lead to?

the premature termination of translation

what is a frameshift mutation?

the addition or deletion of a base that shifts the reading frame

what does a frameshift mutation lead to?

the premature termination of translation

what is a triplet repeat expansion mutation?

contains triplet sequence of DNA that is repeated

where do triplet repeat expansion mutations occur?

coding region or in the noncoding transcribed DNA

what is a mutagen?

an agent that damages DNA

what is specific DNA repair?

targets a single kind of lesion in DNA and repairs only that damage

what is non specific DNA repair?

repair using a single mechanism to fix multiple lesions

what is photo repair?

specific to damage that is caused by photochemical reaction of DNA and UV light; removes dimers and restores bases

what repairs the damaged DNA in photo repair?

photolyase

what is photolyase?

an enzyme that uses energy from visible light to cleave dimers and restore bases

what is excision repair?

nonspecific repair mechanism that removes the damaged region and is replaced using DNA synthesis

what are the 3 steps of excision repair?

1. recognition of damage

what removes the damaged region of DNA in excision repair?

excision complex (names differ in different organisms)

how is damaged DNA resynthesized during excision repair?

DNA polymerase 2 replaces damaged DNA by using the undamaged strand as a template

what are other repair pathways?

error free and error prone

what is error prone repair?

last chance effort to save a cell that has been exposed to massive damage that it has overwhelmed the error free systems; SOS response

what is a chromosomal mutation?

an altered structure of a chromosome

what is deletion?

loss of a portion of a chromosome

what kind of mutation does deletion lead to? how?

a frameshift mutation because deleting a base or a series of bases will shift the reading frame

what is duplication?

produces an extra copy of all or part of a chromosome

what does the effect of duplication depend on?

location of the breakpoints (where duplication occurred)

what happens in the duplication region is not within a gene?

may have no effect

what is a tandem duplication?

a duplication that occurs next to the original

what is inversion?

segment of chromosome is broken in 2 places and reversed

what effects does inversion have?

may have no effect on phenotype if it does not break within a gene

what is translocation?

a piece of chromosome breaks off and attaches to

what problems does translocation cause?

causes problems during meiosis when 2 different chromosomes attempt to pair

what is the relationship between mutations and evolution?

no changes in genomes (mutations) = no evolution

what is a motif?

a protein that can turn genes on or off

why is gene expression regulated?

to ensure that the correct proteins are made when and where they are needed; cells adapt to their environment by gene expression

how do regulatory proteins bind to DNA?

they bind to the major grooves

what is an operon?

multiple genes that are used for a single transcription by a single promoter;

what regulates operons?

repressors

what is induction?

occurs when enzymes for a certain pathway are produced in response to a substrate; turns on gene expression

what is repression?

occurs when the bacteria doesn't need to produce enzymes; turns gene expression off

what is negative gene regulation?

a repressor protein binds to an operator to prevent a gene from being expressed

what is positive gene regulation?

when an activator protein binds to the operator (which changes the shape) and the operator can no longer bind to the strand; turning expression on

what is a general transcription factor?

A transcription factor that assembles at the core promoter and recruits RNA polymerase II to enable basal transcription; binds to sites on DNA to activate transcription

what is a specific transcription factor?

act in a tissue or time dependent manner to stimulate increased levels of transcription than at the basal level

what is an enhancer?

binding sites of specific transcription factors

what is an activator?

a protein that binds to an enhancer and stimulates transcription of a gene

what is DNA methylation?

the addition of methyl groups to certain bases in DNA

what is X chromosome inactivation?

process of one of the two X chromosomes being inactivated to equalize X chromosome expression

what is the region on the X chromosome that initiates inactivation?

Xist (X inactivation specific transcript)

what are histone modifications?

the methylation, phosphorylation, acetylation, ubiquitylation, and sumoylation of a histone

how do histone modifications impact gene expression?

alter the chromatin structure

what is chromatin remodeling?

chromatin remodeling complexes include enzymes that modify histones therefore changing the chromatin structure

What is ATP-dependent chromatin remodeling?

alter the relationship of DNA and histones;

What is mRNA degradation?

the transcripts that encode for regulatory proteins and growth factors contain specific sequences near the 3' end that make them targets for mRNA degrading enzymes. Then a sequence of A and U nucleotides near the 3' poly-a tail promotes the removal of the tail that destabilizes the mRNA which leads to the degradation by 3'-5' exonuclease. transcripts that contain sequences near the 3' end that are recognition sites for endonuclease which causes the transcripts to be digested quickly

what is protein degradation?

ubiquitin attaches itself to proteins that are folded incorrectly or nonfunctional and marks them for degradation. then proteasome degrades the proteins that have been marked/ubiquinated. once these proteins have fulfilled their role, they get polyubiquitinated and removed.

how to proteases degrade proteins?

by breaking the peptide bonds and converting proteins to amino acids

what is a proteosome?

large cylindrical complex where proteins enter at one end and exit as amino acids or peptide fragments

what happens as the proteasome degrades proteins?

to ubiquitinin chain is cleaved into units and can then be reused

what are small RNA's?

3 functions:

what are miRNA's?

MicroRNAs. They are small noncoding RNAs that regulate gene expression by base pairing to mRNAs

what are siRNA's?

small interfering RNA's that form perfect duplexes with target mRNAs and cause mRNA cleavage by the RNA-mediated interference pathway.

what is development?

the process of systematic, gene-directed changes through which an organism forms the successive stages of its life cycle

what is cell division?

a developing organism begins as a zygote that must undergo cell division to produce a new individual

what is differentiation?

as cells divide, changes in gene expression result in specialization of cells

what is pattern formation?

the development of specific structures in specific locations

What is morphogenesis?

formation of the body/anatomy

why was C. elegans used to study animal development?

transparent organism so individual cells can be followed throughout the 4 processes of development

what is cell determination?

a molecular decision to become a particular type of cell

what are the 2 ways cells become determined?

1. via differential inheritance of cytoplasmic determinants (maternally produced and deposited into the egg)

what is induction?

interaction between the 2 cell types that triggers a switch in the developmental path of these cells

what is a totipotent cell?

a cell that can give rise to any tissue in an organism

what is a pluripotent cell?

a cell that can give rise to all of the cells in an organism

what is a multipotent cell?

a stem cell that can give rise to a limited number of cell types

what is a unipotent cell?

stem cells that give rise to only a single cell type

what is reproductive cloning?

producing an individual using SCNT who is genetically the same as another

what is SCNT?

somatic cell nuclear transfer

what is therapeutic cloning?

uses SCNT to produce patient-specific lines of embryonic stem cells

How was Dolly cloned?

she was created using the technique of somatic cell nuclear transfer, where the cell nucleus from an adult cell is transferred into an unfertilized oocyte (developing egg cell) that has had its cell nucleus removed.

what is the basic structure of a virus?

core nucleic acid surrounded by a capsid

how do viruses replicate?

During attachment and penetration, the virus attaches itself to a host cell and injects its genetic material into it. During uncoating, replication, and assembly, the viral DNA or RNA incorporates itself into the host cell's genetic material and induces it to replicate the viral genome.

what are the steps of the lytic cycle?

attachment, penetration, synthesis, assembly, release

what occurs during attachment?

the virus surface proteins attach to a receptor site on the host cell's surface

what occurs during penetration?

viral genome is injected into host cytoplasm

what occurs during synthesis?

virus takes over cell's replication and protein synthesis machinery in order to synthesis new viral components