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Is there a difference in cytoplasmic pH between prokaryotes and eukaryotes?

Is there a difference in cytoplasmic pH between prokaryotes and eukaryotes?



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The cytosolic pH in human cells is around 7.4, but fluctuates as the cell is replicating. Prokaryotes and eukaryotes are vastly different in many ways. One thing they share is cytoplasm. Is there any general difference in the pH between these two cytosolic spaces? Any pointers to a previous investigation into this would be hugely appreciated. Ideally I'm after a quantified numerical comparison from a peer reviewed reference, but given the obscurity of the question that might be a tall order!

Googling was to no avail. It's swamped with pH survival data.


In the article "pH of the Cytoplasm and Periplasm of Escherichia coli: Rapid Measurement by Green Fluorescent Protein Fluorimetry", by Jessica C. Wilks and Joan L. Slonczewski, the pH of E.coli cytoplasm was mentioned as 7.2 - 7.8. I just took E.coli's pH range as a common example of prokaryotes.

Reference link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1951819/


Is there a difference in cytoplasmic pH between prokaryotes and eukaryotes? - Biology

PART II. CORNERSTONES: CHEMISTRY, CELLS, AND METABOLISM

The discussion so far in this chapter has dealt with the process of aerobic cellular respiration in eukaryotic organisms. However, some prokaryotic cells also use aerobic cellular respiration. Because prokaryotes do not have mitochondria, there are some differences between what they do and what eukaryotes do. The primary difference involves the electrons carried from glycolysis to the electron-transport system. In eukaryotes, the electrons released during glycolysis are carried by NADH and transferred to FAD to form FADH2 in order to get the electrons across the outer membrane of the mitochondrion. Because FADH2 results in the production of fewer ATPs than NADH, there is a cost to the eukaryotic cell of getting the electrons into the mitochondrion. This transfer is not necessary in prokaryotes, so they are able to produce a theoretical 38 ATPs for each glucose metabolized, rather than the 36 ATPs produced by eukaryotes (table 6.2).


Prokaryotes vs. Eukaryotes: The Basics

All of known life on Earth is sorted into a classification system that begins with three categories called domains and spreads out with each descending rank. This is what is commonly known as the tree of life.

The organisms in Archaea and Bacteria are prokaryotes, while the organisms in Eukarya have eukaryotic cells.

The Archaea domain has subcategories, but scientific sources differ on whether these categories are phyla or kingdoms. They are:

  • Crenarchaeota
  • Euryarchaeota
  • Korarchaeota

The Bacteria domain used to continue directly down the tree into the single Monera kingdom. However, newer classification systems eliminate Monera and divide the Bacteria domain into the two kingdoms of Eubacteria and Archaebacteria, which is sometimes written as Archaea but should not be confused with the domain of Archaea.

The Eukarya domain is divided into four kingdoms. These are:

  • Plantae
  • Fungi
  • Protista
  • Animalia

All plant, protist, fungal and animal cells are eukaryotes. Most of them are multicellular, although there are some exceptions. In contrast, prokaryotes – bacteria and archaea – are single-celled organisms, with only a few exceptions. Prokaryotes tend to have smaller cell sizes than eukaryotes.


Comparing prokaryotes and eukaryotes

All life on Earth consists of either eukaryotic cells or prokaryotic cells. Prokaryotes were the first form of life. Scientists believe that eukaryotes evolved from prokaryotes around 2.7 billion years ago.

The primary distinction between these two types of organisms is that eukaryotic cells have a membrane-bound nucleus and prokaryotic cells do not. The nucleus is where eukaryotes store their genetic information. In prokaryotes, DNA is bundled together in the nucleoid region, but it is not stored within a membrane-bound nucleus.

The nucleus is only one of many membrane-bound organelles in eukaryotes. Prokaryotes, on the other hand, have no membrane-bound organelles. Another important difference is the DNA structure . Eukaryote DNA consists of multiple molecules of double-stranded linear DNA, while that of prokaryotes is double-stranded and circular.


4.3 Eukaryotic Cells

In this section, you will explore the following questions:

  • How does the structure of the eukaryotic cell resemble as well as differ from the structure of the prokaryotic cell?
  • What are structural differences between animal and plant cells?
  • What are the functions of the major cell structures?

Connection for AP ® Courses

Eukaryotic cells possess many features that prokaryotic cells lack, including a nucleus with a double membrane that encloses DNA. In addition, eukaryotic cells tend to be larger and have a variety of membrane-bound organelles that perform specific, compartmentalized functions. Evidence supports the hypothesis that eukaryotic cells likely evolved from prokaryotic ancestors for example, mitochondria and chloroplasts feature characteristics of independently-living prokaryotes. Eukaryotic cells come in all shapes, sizes, and types (e.g. animal cells, plant cells, and different types of cells in the body). (Hint: This a rare instance where you should create a list of organelles and their respective functions because later you will focus on how various organelles work together, similar to how your body’s organs work together to keep you healthy.) Like prokaryotes, all eukaryotic cells have a plasma membrane, cytoplasm, ribosomes, and DNA. Many organelles are bound by membranes composed of phospholipid bilayers embedded with proteins to compartmentalize functions such as the storage of hydrolytic enzymes and the synthesis of proteins. The nucleus houses DNA, and the nucleolus within the nucleus is the site of ribosome assembly. Functional ribosomes are found either free in the cytoplasm or attached to the rough endoplasmic reticulum where they perform protein synthesis. The Golgi apparatus receives, modifies, and packages small molecules like lipids and proteins for distribution. Mitochondria and chloroplasts participate in free energy capture and transfer through the processes of cellular respiration and photosynthesis, respectively. Peroxisomes oxidize fatty acids and amino acids, and they are equipped to break down hydrogen peroxide formed from these reactions without letting it into the cytoplasm where it can cause damage. Vesicles and vacuoles store substances, and in plant cells, the central vacuole stores pigments, salts, minerals, nutrients, proteins, and degradation enzymes and helps maintain rigidity. In contrast, animal cells have centrosomes and lysosomes but lack cell walls.

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 1, Big Idea 2, and Big Idea 4 of the AP ® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® exam questions. A Learning Objective merges required content with one or more of the seven Science Practices.

Big Idea 1 The process of evolution drives the diversity and unity of life.
Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry
Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.
Science Practice 7.2 The student can connect concepts in and across domains to generalize or extrapolate in and/or across enduring understandings
Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life and how these shared, conserved core processes and features support the concept of common ancestry for all organisms.
Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis.
Enduring Understanding 2.B Growth, reproduction and dynamic homeostasis require that cells create and maintain internal environments that are different from their external environments.
Essential Knowledge 2.B.3 Eukaryotic cells maintain internal membranes that partition the cell into specialized regions.
Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices.
Learning Objective 2.13 The student is able to explain how internal membranes and organelles contribute to cell functions.
Essential Knowledge 2.B.3 Eukaryotic cells maintain internal membranes that partition the cell into specialized regions.
Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively.
Learning Objective 2.14 The student is able to use representations and models to describe differences in prokaryotic and eukaryotic cells.
Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties.
Enduring Understanding 4.A Interactions within biological systems lead to complex properties.
Essential Knowledge 4.A.2 The structure and function of subcellular components, and their interactions, provide essential cellular processes.
Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices.
Learning Objective 4.5 The student is able to construct explanations based on scientific evidence as to how interactions of subcellular structures provide essential functions.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 1.15] [APLO 2.5][APLO 2.25][APLO 1.16]

Have you ever heard the phrase “form follows function?” It’s a philosophy practiced in many industries. In architecture, this means that buildings should be constructed to support the activities that will be carried out inside them. For example, a skyscraper should be built with several elevator banks a hospital should be built so that its emergency room is easily accessible.

Our natural world also utilizes the principle of form following function, especially in cell biology, and this will become clear as we explore eukaryotic cells (Figure 4.8). Unlike prokaryotic cells, eukaryotic cells have: 1) a membrane-bound nucleus 2) numerous membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, and others and 3) several, rod-shaped chromosomes. Because a eukaryotic cell’s nucleus is surrounded by a membrane, it is often said to have a “true nucleus.” The word “organelle” means “little organ,” and, as already mentioned, organelles have specialized cellular functions, just as the organs of your body have specialized functions.

At this point, it should be clear to you that eukaryotic cells have a more complex structure than prokaryotic cells. Organelles allow different functions to be compartmentalized in different areas of the cell. Before turning to organelles, let’s first examine two important components of the cell: the plasma membrane and the cytoplasm.


Difference between Prokaryotic and Eukaryotic Protein Synthesis

In prokaryotes protein synthesis begins even before the transcription of mRNA molecule is completed. This is called coupled transcription - translation.


2. Eukaryotic mRNA molecules are monocistronic , containing the coding sequence only for one polypeptide.
In prokaryotes individual bacterial mRNA molecules are polycistronic having transcripts of several genes of a particular metabolic pathway. ( Monocistronic vs polycistronic )

3. In eukaryotes, most of the gene have introns that separate the actual message for the synthesis of one protein into small coding segment called exons.
Prokaryotes do not have introns (Except Archaebacteria).

  • About ten initiating factors(IFs ) have been identified in reticulocytes an RBC. These are eIF1, eIF2, eIF3, eIF4 , eIF5, eIF6 ,eIF4B, eIF4C,eIF4D, eIF4F
  • Three initiating factors found in prokaryotes. PIF-1 , PIF-2 , PIF-3.

8. In eukaryotes 5’cap initiates translation by binding mRNA to small ribosomal subunit usually at the first codon AUG.
In bacteria translation begins at an AUG codon preceded by a special nucleotide sequence.

9. A poly A tail formed of about 200 adenine nucleotides is added at the 3’end of mRNA in Eukaryotes.
No poly A tail is added to bacterial mRNA.

10. In eukaryotes small subunit of ribosome(40 S) gets dissociated with the initatior amino acyl tRNA (Met-tRNA Met) without the help of mRNA. The complex joins mRNA later on.
In prokaryotes 30 S subunit first complexes with mRNA (30S-mRNA) then joins with f Met tRNA f-Met.


Similarities Between Prokaryotic And Eukaryotic Cells

For all their differences, prokaryotes and eukaryotes have a few similarities. They share some common structures (due to physics and evolution), and though their DNA is different, they even share some genetic features.

Both types of cells have five similarities:

  1. Both types of cells carry on all the necessary functions of life (adaptation through evolution, cellular organization, growth and development, heredity, homeostasis, reproduction, metabolism, and response to stimuli). However, they do these things in different ways.
  2. Both cells carry DNA and rDNA (ribosomal DNA)
  3. Both prokaryotic cells and eukaryotic cells have vesicles.
  4. Both prokaryotes and eukaryotes may be single-celled organisms. Amoebas, paramecia, and yeast are all single-cell eukaryotes.
  5. Both types of cells have vacuoles, storage units for food and liquid.

Structures Found In Prokaryotic And Eukaryotic Cells

All living organisms use cellular organization to create structures to conduct life processes. Cells organize into tissues, which organize into organs, which organize into amazing life forms like plants, fungi, dogs, ducks, and people.

Intracellular structures are common to both types of cells. Both prokaryotic and eukaryotic cells have:


Discussion and Conclusion

The fact that some prokaryotes have certain eukaryotic characteristics should not be unsettling for creationists. First of all, there is nothing in the Bible which distinctly characterizes eukaryotes as the sole organisms which have nuclear membranes. The distinction between eukaryotes on the one hand having a nuclear membrane and prokaryotes on the other hand having none is a man-made construct, and therefore subject to change. Second, the presence of MC-like proteins in certain species of bacteria highlights their functional modular nature, rather than their phylogenetic relationships. Third, what we can say, is that the forest of life is made up of a more colorful spectrum of organisms, including different kinds of bacteria which happen to have analogous features to eukaryotes. These characteristics include, besides internal membranes and endocytosis, things like straight chromosomes, DNA recombination, introns, extreme polyploidy, giant size, a dynamic cytoskeleton, intercellular signaling and even endosymbionts (Huber et al. 2002 Lane 2011). Yet these characteristics have never been observed to present all together at once in any one species. Furthermore, the evolutionary literature also talks about “the apparent absence of organisms resembling putative pre-eukaryotic evolutionary intermediates” (Aravind, Iyer, and Koonin 2006). Despite the analogous similarities between prokaryotes and eukaryotes described here, there still exist a large number of minute molecular-level differences between these two cell types. Makarova et al. (2005) describe this as a most dramatic evolutionary transition, second to the emergence of life itself. Sixty of these differences have been listed in Table 2 (after Cavalier-Smith, 2009). Furthermore, according to Makarova et al. (2005) there are 4137 eukaryotic genes (almost the same number of genes in the hypothetical last eukaryotic common ancestor, LECA) which are specific to eukaryotes compared to prokaryotes. Such a large number of genes really underlines the sharp distinction between prokaryotes and eukaryotes. The majority of these genes (41 out of 54 COG clusters, 77.4%) are involved in translation, which is a process which fundamentally affects cell function. Oddly enough, some evolutionists explain the emergence of eukaryote-specific proteins via the duplication and subsequent (unobserved) “drastic acceleration” (part of a process called nonhomologous replacement) of bacterial paralogs (Aravind, Iyer, and Koonin 2006), which has never been observed. Also according to some evolutionists, these eukaryotic proteins then freeze afterwards (Makarova 2005). As to what governs these phases of sequence acceleration followed by freezing is mere speculation, and has never been observed in nature. In sum, prokaryotes with different kinds of eukaryote-like structures show the vast diversity of the kinds of living things God created. Science changes with newer and newer discoveries and observations, and creation science is up to this task.

Table 2. List of eukaryotic cellular innovations (after Cavalier-Smith 2009)
AAA lysine biosynthetic pathway
Actin and actin-related proteins (Arps 1, 2, 3)
Arf1 and Sar1 GTPases
Calmodulin, Ca++ and inositol triphosphate second messenger systems.
Cell cycle resetting by anaphase proteolysis
Cell division by actomyosin not FtsZ
Centrin (Ca++ contractility)
Centrioles and δ, ε, and η tubulins
Centromeres/kinetochores
Chromatin condensation cycle: histone phosphorylation, methylation, acetylation heterochromatin
Cilia (nine doublets, dynein arms and centre pair spokes, ciliary transport)
Clathrin coats and adaptins
COPII coats
COPI vesicle coats
Delrin protein extrusion channel for ER-associated degradation (ERAD)
Dynein for sliding surface-attached astral microtubules and related midasin for ribosome export
Endosomes (early, late and multivesicular bodies)
Exocytosis and exocysts
Formins for positioning actomyosin
Four-module 30-subunit mediator complex regulating polII transcription
Golgi complex
Internalisation of DNA attachment sites as protoNE/roughER
Karyopherins
Lysosomes
Massive expansion of serine/threonine kinase controls
MCM replication licensing system controlled by cyclins
Meiosis and synaptonemal complex
Mitochondria
mRNA capping and export machinery
Nonsense-mediated mRNA decay
Nuclear envelope fusion and syngamy
Nuclear lamina
Nuclear pore complexes (NPCs)
Nucleolus and more complex rRNA processing (e.g. 5.8S rRNA)
Peroxisomes
Phagocytosis
Phosphatidylinositol/kinase signaling
Pinocytosis
Plasma membrane phosphatidylinositol anchor proteins
polyA transcription termination system
Post-transcriptional gene silencing, dicer and argonaut nucleases
Proteinaceous interphase nuclear matrix with bound DNA-topoisomerase II and its ability to reorganize as mitotic chromosome cores
Rab GTPases
Ran GTP/GDP cycle for directionality of NE export/import
Ras GTPases
Rho GTPases
Ribosome subunit nuclear export machinery
Separate RNA polymerases I, II and III
SNAREs
Sphingolipid synthesis
Spliceosomes and spliceosomal introns
SRβ of signal-recognition-particle receptor
Telomerases and telomeres
Trans-Golgi network
Tubulin: γ for centrosome and α and β for microtubules fixing it to cell surface
Ubiquitin and polyubiquitin labelling system
3+myosins
4-histone nucleosomes
13 kinesins
26S proteasomes with 19S regulatory subunit


Multiple Choice

Which is the location of electron transports systems in prokaryotes?

A. the outer mitochondrial membrane
B. the cytoplasm
C. the inner mitochondrial membrane
D. the cytoplasmic membrane

Which is the source of the energy used to make ATP by oxidative phosphorylation?

A. oxygen
B. high-energy phosphate bonds
C. the proton motive force
D. Pi

A cell might perform anaerobic respiration for which of the following reasons?

A. It lacks glucose for degradation.
B. It lacks the transition reaction to convert pyruvate to acetyl-CoA.
C. It lacks Krebs cycle enzymes for processing acetyl-CoA to CO2.
D. It lacks a cytochrome oxidase for passing electrons to oxygen.

In prokaryotes, which of the following is true?

A. As electrons are transferred through an ETS, H + is pumped out of the cell.
B. As electrons are transferred through an ETS, H + is pumped into the cell.
C. As protons are transferred through an ETS, electrons are pumped out of the cell.
D. As protons are transferred through an ETS, electrons are pumped into the cell.

Which of the following is not an electron carrier within an electron transport system?

A. flavoprotein
B. ATP synthase
C. ubiquinone
D. cytochrome oxidase


Which of the following processes occurs in prokaryotes but not in eukaryotes? a) translation in the absence of a ribosome b) transcription and translation occur simultaneously c) post-transcriptional splicing d) gene splicing.

1. Gene expression may be controlled by epigenetic mechanisms.

The base pair sequence of a gene is not solely responsible for the sequence of amino acids. A gene may have several allele/variants whose expression is controlled by multiple factors. Epigenetic processes such as DNA methylation, do not involve changes in the DNA sequence. Instead they influence the protein amino acid sequence by changes in the process of transcription or even translation.

2. The mutation introduced a stop codon into the middle of the mRNA molecule.

The protein will be shorter if the point mutation causes the creation of a stop codon in the interior of the mRNA strand. Thus, the remaining sequence after the mutation will no longer be used to create the rest of the protein.

3. Pre-mRNA is not edited, and is used as mRNA.

Because no introns and exons are included in the model, the pre-mRNA is not edited. During this step, the introns are removed from the DNA strand. However, due to the fact that the model does not define them and thus differentiate between them and the exons, the pre-mRNA will be used as mRNA.

4. The process of translation in the beetle is similar to other organisms, but involves a unique genetic code.

The processes of translation and transcription are identical in all organisms. The only difference is the DNA sequence itself, which is species or organism specific. Thus, as it is a new beetle species, its genetic code will be unique. However, it will be translated and transcripted in the same manner as that in all other species.Their mRNA will also have and use the same nucleic acids.

5. The removes introns from pre-mRNA.

The pre-mRNA includes both introns and exons. However, only exons are used in the protein synthesis, whereas the introns are removed during the pre-mRNA stage.

6. Each of many tRNA molecules contains an anticodon, and it binds to a specific amino acid.

The anticodon of a tRNA molecule is amino acid specific. Thus, it can bind to one or a few specific mRNA codons.

7. RNA contains uracil (U) instead of thymine (T).

Both DNA and RNA have phosphate groups bound to a nitrogenous base. However, the single stranded RNA has uracil instead of the thymine found in the double stranded DNA. Also, both RNA and DNA have cytosine and guanine.