Chapter !2 - Genomes are the Hub of Biology Code : KSI0011

<Index of Chapter 2>

Individuals, populations, the biosphere ; past, present , and future

Comparing genomes between species can reveal their relationships and how they achieve their similarites and differences. We share 96% of our genomes with our nearest relatives, the chimpanzees and many of our proteins are identical. This small amount of genomic change must account for the diffecences betwee humans and chimps. Indeed, genomics is essential to understnading and drawing species boundaries. As useful a concept as a species may be, there is consensus that it's definition is a very tricky problem. 

 

The central dogma, and peripheral ones

DNA makes RNA makes Protein.

In 1958, E.Crick proposed the central dogma of molecular biology

The central dogma - DNa makes RNA makes protein - describes not only a series of molecular events but a direction of information transfer. Information sensing and response are also essential for integration and coordination of the activities and expression patterns of many molecules. In this wa, cells can achieve stability and robustness.

 

Expression patterns

   - Regulation of gene expression

      > Most control takes place at the level of transcription. 

Promoters. 

Cpg islands

Modulation of local chromatin conformation

Hypersensitive

CpG islands are regions of high CG contents, rich in the dinucleotide sequence GC, that appear at the 5' ends of vertebrate genes. Methylation of C residues silences genes.

Ex . Control of beta-globin gene expression

Ex2. Mammalian females are X-chromosome -scilenced mosaics. (X-inactivation ) (Barr-body)

 

-Some mechanisms of refulation act at the lefvel of translation

-Antisense RNA 

RNA interference

Shine-Dalgarno sequences 

-> Another mechanism of translation control is the attachment of ligands to the Shine- Dalgarno sequences ribiosome. 

 

Some regulatory mechanisms affect protein activity

 

 

Trancription > Gene copy number / Promoter activity / Repression / arrenuation / Induction / DNA methylation & Chromatin remodeling

Translation > mRNA lifetime / Codon usage, tRNA levels / Ribosome binding / Alternative splicing / RNA interference

Post- translational modification > Protein turnover / Chemical modification (Phosphorylation) / inhibition / Allosteric change

 

   - Proteomics

Proteins are the executive branch of the cell. Some prtoeins are structuralm such as the keratins that form our hair and the outer horny layer of our skin. 

To carry out such a wide variety of functions, proteins show a great diversity of 3D conformations. This diversity in structure and function is nevertheless compatible with many common stuctural features

 

- Post - translational modifications 

 

   - Genomics and developmental biology

-Developmental toolkits

The mapping from genome to proteins is a static correspondence. But in fact, implementation of the genome is a dynamic process. both (1) in the short term as the response to internal and external stimuli, and (2) in the longterm, as the unfolding of programmes of development and differentiation. Evolution illuminates both the static and dynamic aspects of the implementation of the genome.

Genetics of behaviour / Sporadic 

- Genes and minds; neurogenomics

 

Populations

   - Single Nucleotide polymorphisms(SNPs) and haplotypes

   All people except for identical siblings have unique DNA sequences. Many of the differnces between and translocations. Comparisions between unrelated individuals reveal overall differences between Whole-genome sequencing .

Any change in DNA sequence is a mutation including substitutions insertions and deletions. 

Many of the differences between individuals have the form of individual isolated base substitutions, or SNPs. There are also many short deletions. 

Haplotype > are local combinations of genetic polymorphisms that tend to be co- inherited. 

Application of haplotypes to infer relationships between populations : The barbary macaques.

 

   - A clinically important haplotype : The major histocompatibility complex

MHC haplotypes control donor-recipient compatibility in transplants

-MHC haplotypes determine patterns of disease resistance

-MHC haplotypes influence mate selection

 

   - Mutations and disease

By what mechanisms can mutations affect human health 

Many diseases are caused directly by mutations. Many others have a genetic component and arise in the context of an interaction between genetics and lifestyle. 

 

Genetic Diseases- some examples of their causes and treatment

   -Haemoglobinopathies- molecular diseases caused by abnormal haemoglobins.

   -Phenylketonuria (PKU)

   -Alzheimer's diseases

   -SNPs and cancer

Species

Many modern biologists define a species as a group of similar organisms that interbreed naturally to produce fertile offspring. An alternative approach is to base species definitions on genomics sequences. This approach is extremely powerful even for higher organisms. and essential for prokaryotes. 

 

Why living things should be quantized into discrete species is a very subtle question. 

 

The biosphere - Extinctions

Extinctions

Extinction of the thylacine

Survival of Pere david's deer 

 

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