What does the human gene H2AFY code?

 Question: What does the human gene H2AFY code? How many amino acids are present in isoform 1 of this protein?

Solution:

The human gene H2AFY codes for the protein Core Histone Macro-H2A1. In a subset of nucleosomes, it replaces the conventional H2A histones. It represents the transcription and inactivates the stable X-chromosome. Multiple transcript variants coding for different isoforms are formed because of alternative splicing. And expression of these isoforms is associated with different type of cancers and tumors. For example hepatocellular cancer.

372 number of amino acids are present in isoform 1 of this protein.

What is meant by the term “molecular clock”?

 Question: What is meant by the term “molecular clock”? What are the basic assumptions by which it is presumed to operate? How have data from molecular clock analyses been used?

Solution: MOLECULAR CLOCK:-

The molecular clock is defined as a technique that helps to detect the geological time or era in which two species or taxa diverged from the parent species. This technique uses the rates of molecular changes and other fossil characteristics to determine the geological time.

ASSUMPTION ARE OPERATION::

the molecular clock has become an essential tool in many areas of evolutionary biology, including systematics, molecular ecology, and conservation genetics. The molecular clock hypothesis states that DNA and proteinsequences evolve at a rate that is relatively constant over time and among different organisms. A direct consequence of this constancy is that the genetic difference between any two speciesis proportional to the time since these species last shared a common ancestor. Therefore, if the molecular clock hypothesis holds true, this hypothesis serves as an extremely useful method for estimating evolutionary timescales. This is of particular value when studying organisms that have left few traces of their biological history in the fossil record, such as flatworms and viruses.

The molecular clock is figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistorywhen two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA or amino acid sequences for proteins. The benchmarks for determining the mutation rate are often fossil or archaeological dates. The molecular clock was first tested in 1962 on the hemoglobin protein variants of various animals, and is commonly used in molecular evolution to estimate times of speciation or radiation.

It is sometimes called as gene clock or an evolutionary clock.

ANALYSIS USES ::

The molecular clock technique is an important tool in molecular systematics, the use of molecular genetics information to determine the correct scientific classificationof organisms or to study variation in selective forces. Knowledge of approximately constant rate of molecular evolution in particular sets of lineages also facilitates establishing the dates of phylogenetic events, including those not documented by fossils, such as the divergence of living taxa and the formation of the phylogenetic tree. In these cases—especially over long stretches of time—the limitations of MCH (above) must be considered; such estimates may be off by 50% or more.

Approximately how many prokaryotic cells live in 5 mL of fertile soil?

 Question: Approximately how many prokaryotic cells live in 5 mL of fertile soil?

Solution:  About 100 million prokaryotic cells.

Prokaryotic cells are super tiny and are the simplest single celled organisms. There are 100 million + in 5 mL of fertile soil. 

What is a molecular clock and why is it important when using molecular techniques to create a phylogeny?

Question: What is a molecular clock and why is it important when using molecular techniques to create a phylogeny?

Solution: Molecular clock is a hypothesis that predicts a constant rate of molecular evolution among species. It is also a method of genetic analysis that can be used to estimate evolutionary rates and timescales using data from DNA or proteins.
Molecular clocks are typically used in phylogenetic analyses, which aim to reconstruct evolutionary trees that show the relationships among species of interest. Internal nodes in the tree represent evolutionary divergence events. The timing of these events can be estimated using molecular clocks. A number of statistical methods are available for testing the molecular-clock hypothesis for a given set of DNA or protein sequences. When the molecular clock is rejected for a data set, one can use a statistical model to account for rate variation when estimating evolutionary timescales. When estimating evolutionary timescales in a phylogenetic analysis, the molecular clock needs to be calibrated.

In a phylogenetic tree, the species or groups of interest are found at the tips of lines referred to as the tree's branches. For example, the phylogenetic tree below represents relationships between five species, A, B, C, D, and E, which are positioned at the ends of the branches:

Define phylogeny and explain what we can learn from phylogenetic trees

Question: Define phylogeny and explain what we can learn from phylogenetic trees.

Solution: Phylogenetics is the branch of biology that deals with the study of evolutionary histroy and relationships between a indivisuals or group of organism. Phylogeny is the diagrammatic hypothesis that helps in visualizing the history of evolutionary relationship. Phylogenetic tree helps us to understand the ancestory, the differentiating characters, how evolution has occured and also how closely are two group of organisms related.

Question: What are synapomorphies and why are they important?

Solution: Synapomorphies is a shared derived character(apomorphy ) that is present in the ancestral species and its modified form by their decendants. Synapomorphies help in identifying the closest ancestor as well as how other species have evolved from the pre existing ones. For eg the verteberal column in mammals is conserved as the number of vertebrae are mostly constant but certain elephant species have more number of vertebrae thus giving information about the closest ancestor.

Question: Differentiate between homologous and convergent characters, reversals, and homoplasies.

Solution:

Homologous characters	Convergent characters
Different function	Same function
Similar fundamental structure	Different structure
Divergent evolution	Convergent evolution
eg. four limbs in tetrapods	eg. wings of bats, birds and insects

Reversals	Homoplasies
A character in a derived state reverts back to the ancestral state	Similar traits which are not derived from a common ancestor.
Eg. leg less lizard and snakes.(loss of limbs)	eg. origin of eye.

Question:  Explain what an outgroup is and why it is important.

Solution: A group of organisms who don't belong to the group of organism whose evolutionary relationship is being studied is called the outgroup. Outgroup helps in understanding those characters which are widely distributed in the population and thus have a primitive origin.

Question: What does parsimony mean and how is it used to develop phylogenies?

Solution: In making phylogenetic tress parsimony is applied and according to it the best hypothesis is one, which requires least number of evolutionary changes. Parsimony is important in identifying the outgroup and hence making the phylogenetic tree. Parsimony also tells us how closely are two group of organisms related.

Question: Differentiate between monophyletic, paraphyletic, and polyphyletic groupings.

Solution: a) Monophyletic : Includes the most recent common ancestor and all its decendants. Eg. Mammalia and Aves.
b) Paraphyletic : Includes the most common ancestor but not all its decendants. Eg. Pisces and Reptilia.
c) Polypheletic : Does not include the common ancestor of all the taxon. Eg. Agnatha for jawless lampreys and Insectivora(anteaters and armadillos)