Mutations and Gene Expression

Mutations

permanent alterations of an organism's DNA, only mutations that affect gametes will affect next generation

How are mutations caused?

Variety of factors: DNA damage due to radiations, uncaught mistakes in DNA replications, and DNA damage due to free radicals

T/F: DNA polymerase has a high error rate to start with

FALSE, DNA polymerase has a low error rate to start with because incorrectly matched bases are not favorable in shape and number/location of hydrogen bonds

Why else does DNA polymerase have a low error rate?

DNA polymerase proofreads itself as it copies DNA.

What does DNA polymerase do when an incorrect base pair is added?

The difference in shape causes DNA polymerase to pause and then the incorrect base is removed, allowing for a correct base to be added.

What can happen even after DNA polymerase has finished its job?

Mismatch repair can catch mismatched bases, get rid of incorrect nucleotide and the nucleotides around it, and then fill in with correct nucleotides.

What can mismatch repair do?

It can distinguish between the old parent strand and the new daughter strand to fix mismatches. In eukaryotes, this mechanism is less clear.

What are genes involved in mutation called?

mutator genes, they are important in cancer development.

T/F: all mutations have an effect on proteins

False, Not all mutations have an effect on proteins because there are large stretches of non-coding DNA, and even when the mutation is in the middle of a gene, there is redundancy in the genetic code.

Why are mutation important?

Mutations create genetic variation, which is important for evolution to occur.

What happens when mutations have negative effects?

They often create alleles that produce defective or missing proteins/enzymes (e.g enzyme no longer binds to a substrate correctly, not building a new macromolecule or not breaking one down)

What is a point mutation?

Affects only one or a few base fairs of DNA, point mutations are the least likely to have a large effect.

Silent mutation

new codon codes for same amino acid

missense mutation

if new codon codes for a different amino acid

nonsense mutation

if substitution creates a new, earlier stop codon

frameshift mutation

mutations that affect the reading frame, likely to have catastrophic effect on protein function, especially if the addition/deletion is near the beginning of gene sequence.

What do larger scale mutations involve?

parts or whole chromosomes

Polyploidy

the condition where a cell or organism has more than two complete sets of chromosomes

Aneuploidy

A genetic condition where cells have an abnormal number of chromosomes.

What does transcription use to polymerize RNA nucleotides?

RNA polymerase

How is RNA polymerase similar to DNA polymerase (used in DNA replication)?

Both use activated nucleotides to supply energy

Both have 5' to 3' directionality

Both use base pairing with a template strand

Both can proofread

What is the main difference of RNA polymerase and DNA polymerase?

RNA polymerase doesn't need primers because it doesn't require a free 3'-OH to attach nucleotides; uses ribonuclotides.

What are transcriptions three main stages?

Initiation, Elongation, and Termination

What is initiation?

attachment of RNA polymerase to a promoter sequence upstream of the gene and first addition of nucleotides

What is elongation?

nucleotides that are complementary to template strand are added to a growing RNA strand

What is termination?

end of transcription

How is initiation in prokaryotes different from initiation in eukaryotes?

Prokaryotes rely on the interaction between sigma and two sequences in the bacterial promoter (-35 and -10 boxes) to orient and bind the RNA polymerase

How is initiation different in eukaryotes?

Eukaryotes have promoters as well, their sequences are larger and more diverse; they are recognized by transcription factors, rather than by sigma in prokaryotes.

What signals does the termination of transcription rely on?

Bacteria use transcription-termination signals

Eukaryotes use after poly(A) signals

What do prokaryotes do even before transcription has terminated?

Post-Transcription: Prokaryotes can immediately begin translation as soon as the mRNA is long enough

Which organisms can usually increase translation rates with polyribosomes (multiple ribosomes attached to the same mRNA)?

both prokaryotes and eukaryotes

Why can eukaryotic cells add in the extra step of RNA processing before translation?

They have a nucleus which allows the alternation of RNA after transcription

What two components do the pre-RNA have?

non-coding DNA of introns removed and coding exons spliced back together

In order to avoid inserting introns with the gene, what enzyme must be used?

reverse transcriptase is used to make DNA from mRNA

must also add a bacterial promoter

What does the alternative splicing of exons do?

allows eukaryotes to make multiple different sizes and functions of proteins from the same DNA sequence.

why are the 5' cap and poly(A) tail added to a eukaryote?

To form a mature mRNA

Both serve to help bind ribosomes to mRNA as well as protect the mRNA from degradation by enzymes.

what are tRNAs with amino acids called?

aminoacyl tRNAs

What enzyme link the correct tRNAs with their Amino acid?

aminoacyl-tRNA synthetases

What does wobble pairing do?

Wobble pairing in the third position of the codon/anticodon pair allows for some tRNAS to be able to be used for more than 1 codon.

What happens during the initiation of translation?

1) the small subunit of the ribosome first binds to the mRNA

2) methionine tRNA binds to start codon

3) large subunit of ribosome binds last

What happens during elongation?

1) The next aminoacyl tRNA that corresponds to codon comes into the A site

2) a new peptide bond is formed between amino acid from A site and growing polypeptide chain in P site

3) ribosome moves on to next codon, ejecting "used" tRNA in the E site

What happens during the termination of translation?

When the ribosome hits a stop codon, a release factor is added.

Causes the ribosome and newly-synthesized polypeptide to detach from each other and from the mRNA.