CELL BIOL LAB 4: PROTEIN EXTRACTION AND SDS PAGE

Proteomics is the study

of proteins, particularly their structures and functions.

This term [Proteomics]was coined to make an analogy with ______,

genomics

Most importantly, while the genome is a rather constant entity, the proteome differs from cell to cell and is constantly changing through its biochemical interactions with the

genome and the environment.

[proteomics]One organism will have radically different protein expression in

different parts of its body, in different stages of its life cycle and in different environmental conditions.

The entirety of proteins in existence in an organism throughout its life cycle, or on a smaller scale the entirety of proteins found in a particular cell type under a particular type of stimulation, are referred to as the

proteome of the organism or cell type, respectively.

The large increase in protein diversity is thought to be due to

alternative splicing and posttranslational modification of proteins.

This discrepancy implies that protein diversity cannot be fully characterized by gene expression analysis alone, making proteomics a useful tool for

characterizing cells, tissues, and organisms of interest.

An international collaboration to achieve these goals is being coordinated by the

Human Proteome Organization (HUPO).

The term [_________]probably brings to mind Charles Darwin and the theory of Natural Selection and common descent.

evolution

As such, all species change gradually over time through

natural selection.

The environment selects organisms best suited to

survive and reproduce based on those differences.

Adaptations are the differences in

phenotypic (physical) characteristics such as the variations in finch beaks that are determined by a genetic component.

The genetic component is inherited from the parent in the form of

genes.

The discovery of the chemical structure of DNA gave us an understanding of how the triplet code of nitrogen bases allows the

synthesis of proteins (phenotypic expression) and how phenotypic adaptations are the result of changes in the DNA code (mutations).

However, current research in the field of proteomics is leading some scientists to question whether or not DNA is the

final determining factor in the synthesis of proteins and thus the determining factor in evolution.

The central dogma of molecular biology

(DNA > RNA > protein) has given us a comfortable explanation of how the information encoded by our DNA is translated and used to make an organism.

what does the central dogma describe?

It describes how a gene made of DNA is transcribed by messenger RNA and is then translated into a protein by transfer RNA in a complex series of events utilizing ribosomal RNA and amino acids.

this study is called the human genome project

In 1990, a massive research effort took place to sequence what was estimated to be the 100,000 genes that coded for each protein synthesized by humans (the human genome).

what was the estimated human genes and what about present day estimate?

100,000 human genes down to 25,000 human genes

how many genes does the c. elegans (nematode worm)have?

19,000

what is RNA editing?

form of posttranscriptional modification;

(rna editing)Higher eukaryotes can change the sequence of their messenger RNAs (mRNAs) by ____________________________, while lower eukaryotes ____________________

substituting bases in their primary mRNA transcripts at specific positions

insert and delete specific bases

(rna editing)These types of changes to the codons of mRNA can change _______________,_______________________, or ____________________

the amino acid sequence of a protein

create a new open reading frame where one did not originally exist

or introduce a new stop codon to create a truncated protein

(rna editing)These changes [to the codons of mRNA] can be regulated by the_______________,___________________________,_________________________________________

location of their expression, developmentally

and by the organism's environment,

and the resulting proteins can have very different functions

an example of a change in mRNA (rna editing)

Fasting rats produce 50% less of an edited form of apolipoprotein B (a protein involved in cholesterol metabolism) than rats on a high carbohydrate diet. This happens when a cytidine is substituted with uridine.

RNA editing is not limited to messenger RNA. In a number of yeast and higher eukaryotes, ___________ is also edited at the wobble positions of its anticodons

transfer RNA

Messenger RNA (mRNA) of higher eukaryotes has two types of sequence segments —

introns and exons.

Introns are portions of the code that are

removed or edited from the sequence to be transcribed into protein.

The remaining base segments, exons, move to the ribosome for

translation

Exons can be differentially

included or excluded in a process called alternative splicing to produce different mature mRNAs, which in turn generate distinct proteins.

This process (alternative splicing )can be used at _____________________or____________________

different stages in development or simply when a cell is signaled to alter its protein production.