biochem unit 0 trial

How many properties of living organisms can we recognize?

We can start by recognizing five properties of all living organisms.

What is the first property of living organisms?

(1) They're complex and highly organized; true at macroscopic and microscopic dimension; they're not "simple" organisms, structures or cells.

What is the second property of living organisms?

(2) They're composed of functional structures. Whether looking at the whole octopus, the tentacles, or a cell from the tentacle, we see a number of structures that all have some functional importance.

What is the third property of living organisms?

(3) They're actively engaged in energy transformations; that is, they must obtain energy (either from the sun or from food), use the energy to make new copies of themselves as well as carry out chemical reactions, and release wastes.

What is the fourth property of living organisms?

(4) They are capable of (at least some) self-replication.

What is the fifth property of living organisms?

(5) They're composed of cells.

What is a cell made up of?

A cell is made of several of different types of biomolecules: proteins, lipids, carbohydrates, nucleic acids, a number of small molecules, ions, and of course water \= ingredients of a cell.

Is water in your body ever made within cells?

Some of the water in your body is made within your cells. Much of it has to be consumed.

What is the simplest unit of life?

Cells are the simplest unit of life.

How many universal features does a cell have?

5

What is the first universal feature of a cell?

Cells are composed of the same elements and same biomolecules.

What is the second universal feature of a cell?

Cells are surrounded by a lipid bilayer.

What is the third universal feature of a cell?

Most cells contain a genome comprised of DNA.

What is the fourth universal feature of a cell?

Cells are small (most bacteria are 1 - 10 mm, most plant and animal cells are 10 - 100 mm in diameter.)

What is the fifth universal feature of a cell?

**All cells are derived from pre-existing cells.

What is synthetic biology?

The branch of science that is attempting to synthesize a living cell from individual (non-living) components is known as synthetic biology.

What are the goals of synthetic biology?

The goals of synthetic biology include creating entirely new cells, but also reprogramming existing cells to carry out complex new functions that have never independently evolved in nature.

Do we know how the first cells came about?

How the first cells came about in nature (the origin of life) still remains a mystery.

What are some of the important components of life?

Amino acids, nucleotides, sugars and other biomolecules.

Where did these important components of life come about from?

They came from other biomolecules.

Where did these molecules come from?

Well, in 1952 Miller and Urey did an experiment to try and find out.

What did Miller and Urey do in their experiment?

- They mixed together some of the gasses that they thought would be present on the early earth.

- After sealing this mixture inside of their apparatus, they sent an electrical spark (to simulate lightening) through the mixture......and waited to see what would happen

- After a few days, a dark brown goo had formed inside of their apparatus.

- The goo contained biomolecules, such as amino acids.

What did this experiment demonstrate?

The experiment demonstrated that many of the molecules necessary for the development of life could be formed from the simple molecular precursors (water, ammonia, hydrogen and methane) that were thought to be present on the early earth. In other words, naturally occurring processes could make at least some of the ingredients necessary for life.

Well what's the next step after forming these molecules?

As for the next step....putting these molecules, together, obtaining a source of energy, and compartmentalization.....no one really knows. The origin of life is still a mystery, but one that many of scientists continue to try and crack.

How many things do we need to "make" the simplest cell?

To "make" even the simplest cell we need 4 things.

What are the four major classes of molecules in cells?

The four major classes of molecules in cells are proteins (made up of amino acids), carbohydrates, lipids and nucleic acids.

What is the first thing needed to make a simple cell?

First, we have to have some specific molecules.

- proteins (made up of amino acids)

- carbohydrates

- lipids

- nucleic acids

- some other important organic and inorganic molecules

- water

What is the second thing needed to make a simple cell?

Second, we need a source of energy. It takes energy to combine molecules into larger structures that a cell needs to survive. Some cells also use energy to move about, to chase their food or to avoid being eaten by another cell. So a source of energy is pretty important. Unless you want to get eaten, but that's just weird

What is the third thing needed to make a simple cell?

Third, a cell needs a system for information storage. Perhaps the most important information a cell might need to have is the instructions for how to make a new cell. Other important information useful to a cell would be where to find food (nutrition) and how to avoid danger, like being eaten by another cell. Ouch!

What is the fourth thing needed to make a simple cell?

The fourth important "ingredient" necessary to make a cell is compartmentalization.

What does compartmentalization do?

Compartmentalization is what makes each cell unique - it is what separates one cell from another cell or from its environment. It helps keep all the good stuff inside (such as food, important proteins) and the bad stuff outside (such as chemicals that might damage the cell).

What else does compartmentalization help in?

Compartmentalization helps keep the cell unique.

How is compartmentalization maintained in cells?

In cells, the compartmentalization is maintained by the membrane made of lipid molecules that surround each cell.

What is the membrane doing in this case?

The membrane wraps around each cell like forming a barrier between the cell contents and the surrounding environment.

What is within the barrier?

Inside of the barrier lies the periplasm filled, with DNA, the proteins, the carbohydrates and other molecules the cell needs to survive.

What happens if the integrity of the membrane is broken?

Generally, if the integrity of the membrane is broken, all of the necessary components of the cell "leak out" into the environment and the cell dies.

What does a fundamental postulate of cell theory state?

A fundamental postulate of cell theory states that all cells are derived from another cell - we are all related!

Does this postulate account for how the first cell came into being?

No, this does not account for how the first cell came into being. Somehow, through a mechanism we still do not understand, a first cell emerged from where there were no cells before, and life was born!

So what happened once all of these "things" were together?

Once all of these things were together - specific molecules, a source of energy, and the information necessary to "self-replicate", the first cell came into being.

What is the name of the first cell that came into being?

It is known as the last universal common ancestor - LUCA.

Is every living organism derived from LUCA?

Every living organism on earth, dead, alive, or waiting to be born, is derived from LUCA. How, no one knows. But we do have some clues....

What are all living things on earth descended from?

All living things on earth (in the past, today, and into the future) are descended from a single organism, the last universal common ancestor (LUCA).

Was there something else before LUCA?

Before LUCA, there may have been other entities that resembled living organisms; we don't know if LUCA was the first, last or even only collection of molecules we would recognize as being alive. However, LUCA is our ancestor and the ancestor of all living things. LUCA, then, must have all of the minimal attributes of a cell.

Since all living things are derived from LUCA, does that make them all the same?

While all living organisms are derived from LUCA, they are each in their own way different.

What is one way of simplifying the study of life?

One way to organize life is based on the features of the cells that make up the organism.

What are the three domains of life?

The archaea, the bacteria and the eukarya.

- together the bacteria and the archaea are often called the prokaryotes

What is a unique morphological characteristic of prokaryotes?

prokaryotes lack a defined nucleus or most complex organelles

What is a unique morphological characteristic of eukaryotes?

Eukaryotes have more complex organelle structure, have an organized chromosomes and are often part of multicellular organisms.

What is the definition of self-replication?

self-replication: the ability to make copies of itself using pre-existing information.

Do cells resembles cells that they were derived from?

In general, cells closely resemble the cells from which they were derived.

A single bacteria, for example, divides producing two new bacteria. The new bacteria (which we call the daughters) closely resemble the parent. What property is this due to?

This is due to the property of inheritability - the parent bacteria has all the information needed to replicate itself.

Every time this info. is copied, is it perfect, like are there ever any mistakes in the process of replication?

Each time this information is copied, there is the small possibility that an error takes place, and the information is copied incorrectly.

Do these errors ever have an impact on the organism?

Sometimes these errors are benign, having no impact on the fitness of the organism. However, some errors in copying the information are more significant. As a result, the daughter does not exactly resemble the parent - it is different in some way; we call this variability.

What happens overtime with these mistakes that are now accumulating for generations?

Over time, such changes will accumulate and due to natural selection, give rise to new cells and organisms that barely resemble their ancestry. These "mistakes" are responsible for the diversity of life on earth.

Where is the information necessary for self-replication stored?

The information necessary for self replication is stored in an organism's genome.

What is the genome comprised of?

The genome is comprised of one or more molecules of deoxyribonucleic acid (DNA), a large biopolymer formed from nucleotide monomers.

Don't viruses also have a genome?

Yes, viruses also have a genome; the genome of viruses can be made of DNA or the related molecule Ribonucleic Acid (RNA). However, since viruses can not self-replicate, they are not considered living.

Finish the sentence: Even in a single organism...

there can be a wide array of cell types.

What are examples of different cells you might find inside of yourself?

An E. coli cell (a bacteria that lives in your gut), a white blood cell, a brain cell (neuron) and an epithelial cell.

These cells mentioned previously, they look quite different in appearance, is it just because of cosmetics?

The differences are not cosmetic; the differences in appearance correspond to different functional requirements for each cell.

Where else do we see this variability of difference in appearance?

Yeah, this variability is not limited to cells that make up our body. We see, for example, in examining prokaryotes that there are a wide variety of structures, each feature part of what makes an organism capable of surviving in its environment.

Why is there diversity in appearance of prokaryotes?

The diversity in appearance is reflective in the adaptations necessary for an organism (or cell) to thrive in its niche.

The prokaryote, Sulfolobus, where does it survive?

Sulfolobus, for example, only can survive in hot, boiling sulfuric acid. Places like that really exist.

The prokaryote, Haloquatraum, what is it?

Haloquatraum is the only square bacteria!

What is the prokaryote, Nanoarchaeum?

The smallest (known) living organism is the Nanoarchaeum. It is so small that it lacks many of the vital components necessary to sustain itself, living in a permanent symbiosis with the larger prokaryote to which it attached.

Where does the prokaryote, staphylococcus aureus live?

Staph bacteria normally colonize the skin and nose. Although this is a deadly, pathogenic virus when it enters your blood, we live in (relative) harmony with staph colonizing other parts of our bodies.

What is the prokaryote, treponema known for?

Treponema is the causative agent of syphilis.

Despite there being so much diversity within bacteria, what are the most common shapes that they take on?

Despite the tremendous diversity bacteria, most bacteria take on one of three shapes, COCCUS - BACILLUS - or SPIRILLUS.

What is the shape of a bacteria?

The shape of a bacteria is particular to its species.

What is the shape of a particular bacteria determined by?

The shape of a particular bacterial species is determined by proteins inside of the bacterial cytoplasm that arrange themselves into a "cytoskeleton".

Where and what does the cytoskeleton do?

Much like your skeleton, the bacterial cytoskeleton is inside of the bacteria, giving it shape and mechanical strength.

What is the main difference between your cytoskeleton and that of a bacteria?

However, while your skeleton is made of bone (mixtures of proteins and minerals), the bacterial cytoskeleton is made up entirely of proteins.

What do the proteins in a bacterial cytoskeleton form?

The proteins in the bacterial cytoskeleton form a filament -basically a long fiber or string made of many proteins are stuck together end to end.

So, what exactly determines the shape of a bacteria?

How these proteins stick to one another determines what the overall shape of the bacteria will be - So, the arrangements of the protein forming the cytoskeleton inside of the bacteria determine its outward appearance, just as your skeleton gives rise to your overall shape.

Is a true cell, typical?

Remember, no true cell is typical, but this approach will allow us to efficiently understand the basic principles of bacterial structure.

What are bacteria?

Bacteria are the most widespread of living organisms occupying water, soil, and air.

What is one common feature of bacterial cells?

One common features of bacterial cells is their small size. (usually 1.0 - 1.5 um wide and 2.0 - 6 um long).

What are other important features of bacteria?

Other important features of bacteria include a cell wall, plasma membrane, and the lack of internal membrane enclosed organelles.

What are some bacteria covered by?

Some bacteria are covered by a protective coat of molecules called a glycocalyx.

What exactly is the glycocalyx?

The glycocalyx is a layer of carbohydrates on the outside of many bacteria, and it comes in two varieties.

What two varieties does the glycocalyx come in?

When the glycocalyx is well structured and firmly attached to the rest of the bacteria it is called the capsule. When it can be easily removed, it is called the slime layer.

What does the glycocalyx do in terms of the immune system?

The glycocalyx helps protect the bacteria from the immune system, keeps it from drying out, and helps it attach to surfaces.

What is one thing that all living organisms have?

All living organisms have a plasma membrane, a double layer (bilayer) of lipids and proteins that enclose the cell.

What molecule makeS up the two layers of the plasma membrane?

The plasma membrane is made up of two layers of molecules, called lipids.

What does each lipid molecule have?

Each lipid molecule has two sides - one that dissolves well in water and the other that does not dissolve in water.

What does two layers of lipid molecules form?

Two layers of these lipid molecules form a membrane around the cell.

What side of a lipid faces which side of the cytoplasm within a bacteria?

The water-soluble sides of the lipids face the outside of the cell and the cytoplasm while the water insoluble portion of the lipids are clustered together.

Is the plasma membrane just a barrier around the cell?

The plasma membrane is not just a barrier around the cell - it also carries out the important function of allowing molecules to enter and leave the cell, as well as allowing the bacteria to stick to other cells (such as your cells).

By who are these additional functions of allowing the bacteria to stick to other cells and etc. carried out by?

These additional functions are carried out by 4 other molecules that are attached to the membrane and listed below.