BIOL 211 Midterm 1 UOFC

Who was the first taxanomist, who made the 5 kingdom classification system?

Carolus Linnaeus

What was the 5-kingdom classification system based on?

Based on nutrition and morphology (appearance)

What are the taxanomy ranks (most general to least)?

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

What are the 5 kingdoms and whats unique about each?

Animalea are mobile,

Plantea are immobile,

Fungi have different cells to plants, Monera have no nucleus,

Protista have nucleus

How was molecular biology used to discover the 3-Domains?

Organisms started to be classified by their DNA as opposed to morphology, which allowed differentiation between archeae and bacteria, which were too similar looking to differentiate previously.

What was specifically looked at when differentiating one organism from another

Its nucleotide sequences, inside of its ribosomes.

What are the 3-Domains of life, and what are their characteristics?

Bacteria: Prokaryotic, Small, vast population

Archeae: Prokaryotic, small, little population, survive only in extreme climates

Eukaryotes: Eukaryotic, Large cells.

How were archeae found to be more closely related to eukaryotes then bacteria?

Scientists found the Asgard group of archaea, which were capable of creating protein which was previously believed to be exclusive to eukaryotic cells (and their ribosomes)

Describe the bacteria domain

1. They come in 3 different shapes, Cocci bacilli and spirilla

2. They are prokaryotic

3. their cell wall is made of peptidoglycan

4. Bacteria are small (1-5um)

5. Bacteria are single celled

Describe the Archeae domain

1. They are small (1-5um)

2. They live in harsh environments

3. They are prokayrotic

4. They are in less abundance compared to bacteria

5. Their cell was is made of pseudo-peptidoglycan

Describe the Eukarya domain

1. They are eukaryotic

2. Eukarya can be single celled or multi-cellular

3. Cell walls are as followed: Plants - Cellulose. Fungi - Chitin. Animal - No cell wall

4. They are large (10x the size of prokaryotic cells)

What are some key differences between eukaryotic cells and prokaryotic cells

1. They are different in size (eukaryotes are 10x larger then prokaryotic cells)

2. Eukaryotic cells have organelles (including an endomembrane system), which prokaryotic cells lack

3. Eukaryotic cells have nuclear membranes, whereas prokaryotic cells have their DNA floating around in their cytoplasm

4. Eukaryotes have multiple peices of linear dna, whereas prokaryotes have one peice of circular DNA

Why must prokaryotic cells be small?

They must be small in order to have a larger surface area to volume ration (SA:V) in order to diffuse nutrients into their cytoplasm with greater efficiency.

What allows a eukaryotic cell to be the size that it is (large)

It can be large due to its cell organelles, which can facilitate the diffusion of molecules and nutrients into itself, meaning it does not necessarily need a large surface area to volume ratio.

Specifically, eukaryotic cells have endomembrane systems, allowing them to diffuse nutrients into the cell at greater efficiency, allowing for larger size

What is vertical gene transfer?

The transfer of genes between members of the same species, such as what all humans do

What is horizontal gene transfer?

The transfer of genes between members of different species, which is what a lot of bacteria do

What is the endosymbiotic theory?

The theory that eukaryotic cells as we know them today came from bacteria and archaea partaking in a symbiotic relationship and evolving together, to create eukaryotic cells with mitochondria and chloroplasts

How did mitochondria come to be?

1. Archeae host cell was energy starved, bacteria could create energy

2. Bacteria began to live inside the archway, receiving protection in exchange for giving the archaea energy

3. Over millions of years, they evolved together and became a eukaryotic cell with mitochondria

How did chloroplasts come to be

1. Archeae host cell was energy starved, photosyenthetic bacteria existed and could make its own energy

2. Bacteria began living inside the archaea host cell as a means of protection, and gave the host cell energy it produced

3. over millions of years, they evolved together into a eukaryotic cell with chloroplasts

What evidence is there to support endosymbiotic theory?

1. Mitochondria and chloroplasts are the same size to bacteria

2. mitochondria share DNA more closely to bacteria then they do with their eukaryotes (mitochondria have 70S ribosomes, eukaryotes have 80S ribosomes)

3. Other endosymbiotic relationships exist

List and define the cytoskeleton parts which help a cell during mitosis

Microtubules: made of a-tubulin and b-tubulin, used for tearing apart chromosomes during cell dividsion

Intermediate filament: provides structural support to the cell

Microfilament: tears apart the cytoplasm of a cell when it divides

What is a centrosome?

The centrosome is a cell organelle close to the nucleus

It is made up of centrioles, and they are involved in cell division

Microtubules are also found on the surface of centrosomes

How do we classify organisms based on how they get energy and how they get carbon?

If they get energy through eating molecules, they are "chemo". If they get energy through eating inorganic molecules they are "litho", if they get energy through eating organic molecules they are "organo", if they get energy through consuming light, they are "photo"

If they get carbon inorganically, they are "auto"trophs

If they get carbon organically, they are "hetero"trophs

What is an isolated, closed, and open system

An isolated system is one where no matter or energy can get in or out,

a closed system is one where matter cannot get out, but energy can travel freely

an open system is one where both matter and energy can travel freely

What is the first law of thermodynamics

energy cannot be created nor destroyed, it can only be changed

What is the difference between potential and kinetic energy

Potential energy is stored energy, whereas kinetic energy is the energy of motion/action

Where would the electron have to be to have the highest energy?

farhest away from the nucleus

Which type of bonds have the highest energy and why

non-polar covalent bonds have the highest energy, due to the fact that the electrons are the farthest away form the nucleus it could be

How is an electrochemical gradient supplying energy to other molecules?

A gradient has potential energy due to the concentrations of molecules on either side. Because of this, when a molecules move from one side to another, the energy changes

What is enthalpy, and what does it mean to have a negative or positive enthalpy

Enthalpy is the heat of a reaction

Negative enthalpy is exothermic

positive enthalpy is endothermic

What is entropy, and what does it mean to have a negative or positive entropy?

Entropy is the dispersion of energy in the reaction

Positive entropy means energy gets more dispersed

negative entropy means energy becomes less dispersed

What is the second law of thermodynamics?

The total entropy of the universe must always increase

What determines spontaneity?

the entropy of the system. A positive entropy means it is spontaneous, a negative entropy means it is non-spontaneous

What is free energy, and what does it mean for it to be positive or negative

Also known as Gibbs free energy, this is the energy available to do work

Positive G means it is endergonic, which is non-spontaneous

Negative G means it is exergonic, which is spontaneous

What is chemical equilibrium

When the forward reaction rate equals the backwards reaction rate

What happens to the gibbs free energy when the reaction gets closer and closer to reaching equilibrium

The gibbs free energy slowly decreases, until it reaches 0.

0 gibbs free energy means the reaction has reached equilibrium.

How do cells avoid reaching equilibrium, and why do they avoid reaching equilibrium

They avoid equilibrium in order to continue doing work, so they can keep making new molecules and being useful. They avoid equilibrium by increasing the amount of reactants, so that the reaction may always proceed.

What is standard free energy

The free energy at standard conditions (E.G. 25 celsius, 7 pH, equal concentrations of products and reactants)

What is metabolism and its different types?

Metabolism is the sum amount of reactions occurring.

Catabolism - breaking down complex molecules (proteins into amino acids)

Anabolism - building of complex molecules (amino acids into proteins)

What is a connected reaction?

A connected reaction is when the product of the first reaction becomes the reactant of the second reaction.

A --> B

B --> C

--------

A --> B --> C

What is a couples reaction?

When 2 reactions happen at the same time, one of which is endergonic and the other is exergonic. The exergonic one helps the endergonic one to react, by giving it energy. Coupled reactions are expressed by squiggly arrows, or by the exchange of Pi (phosphorus) in a chemical equation

What makes ATP so good at energy storage and distribution

ATP has 3 phosphates which are very high in energy due to its strong repulsive force with the surrounding oxygen atoms.

This means that once ATP reacts, and inorganic phosphate gets released and so does a large amount of energy

How many unique functional groups does an amino acid have?

3 unique functional groups

carboxyl group, amino group, R group

How are amino acids linked together to form peptides

They are linked by peptide bonds, which is the bond between nitrogen and carbon (N-C)

What makes an R group hydrophobic

If the R-group is non-polar, it is hydrophobic

(purely for memory: non-polar = non-water, therefore hydrophobic)

What makes an R groups hydrophilic

If the R-group is polar, it is hydrophilic

(purely for memory: polar = water therfore hydrophilic

What is a peptide

A polymer of amino acids

What is a polypeptide

More then 10 amino acids joined together to form a peptide

What is a protein?

A polypeptide folded into a 3D shape

What is the primary structure of a polypeptide

The primary structure refers to specifically the amino acids which make up that polypeptide

What is the secondary structure of a polypeptide

The secondary structure is the 2D shape which a polypeptide can get into. These shapes are helices and sheets, and are supported by the main chain carbons exhibiting hydrogen bonds

What is the tertiary structure of a polypeptide

The tertiary structure refers to the 3D shape of a polypeptide, which makes it into a protein. These are created by the hydrophobic/philic nature of the R-groups. Hydrophobic R-groups tend to stay away from water inside of the structure, while hydrophilic ones are on the outside of a protein

What is the quaternary structure of a polypeptide

The quaternary structure of a protein is made when more then one polypeptide joins together to create a larger protein.

Homo___er: means all the proteins are the same in the bundle

Hetero___er: means all the proteins are different

the blanks in those words refer to how many proteins are in each mass (E.G. Homotrimer, heterotetramer)

What is the activation energy of a reaction

The energy barrier this reaction must overcome in order to react. Activation energy is measured from the transition state to the reactants on a graph

How can we speed up a chemical reaction?

1. Increase the temperature, so molecules move faster and collide faster

2. increase the concentration of reactants so they can collide more and react more

3. add a catalyst such as an enzyme in order to force a reaction to completion quicker

What is the main purpose of an enzyme in a chemical reaction?

They increase the reaction rate and decrease the activation energy. They do not, however, change the gibbs free energy, and they do not get consumed in the reaction

What are the differences between the lock and key model and the induced fit model of an enzyme?

The lock and key model says that an enzyme has a specific shape which can facilitate a substrate in its active site. This is false

The induced fit model states that an enzyme can mould to fit the shape of its substrate, which is what actually happens.

What do enzymes do to a substrate to help them react better?

They bring the substrate closer together and in the correct orientation,

enzymes help form the transition state of the substrate to further speed up the reaction,

What happens when you double the enzyme concentration to a substrate solution

doubling the enzyme concentration, provided there is enough substrate, would mean that the reaction rate is also doubled.

what happens to the reaction rate when adding more and more substrate?

The reaction rate increases, but eventually plateau's when all the enzymes are taken up by substrate and the reaction cannot go any faster

What effects does temperature and pH have on enzyme activity

Having too much or too little temperature can denature the enzyme, as most (if not all) enzymes have a specific temperature they work best in.

Having too much or too little pH also causing the enzyme to denature for the same reason as above

to denature means to have the bonds of the enzyme get broken apart and the enzyme no longer functioning as it should

What is a reversible competitve inhibitor

Another molecule which competes with the substrate for the enzymes active site. Whichever concentration is highest between the competitor and the substrate will win out that enzyme.

for example, at equal concentrations, the reaction may slow because the substrate competes with the competitor. However, when adding a lot of substrate, that substrate will win against the competitor and the reaction rate will continue as it once had

What is a reversible noncompetitve inhibitor

A non-competitve inhibitor is a molecule which binds to the enzyme, but not at the active site. This means that all the substrate can still bind to the active site, business as usual. However, the other molecule which binds to another section of the enzyme may denature that enzyme, and deem it unusable.

The substrate cannot outcompete the molecule in this case

What are regulatory (allosteric) enzymes

These are enzymes which are regulated by the cell in order to either speed up or slow down the enzyme. At the end of a reaction mechanism, an allosteric activator or inhibitor may be formed, which binds to the enzyme but not at the active site

Allosteric activator: this is a molecule which binds to the enzyme (not at its active site) which forces the enzyme to speed up

Allosteric inhibitor: this is a molecule which binds to the enzyme (not at its site) in order to inhibite its work.

The cell regulates these actions in order to either have more or less of a certain product being made by the enzyme, depending on the cells need

What is a lipid and what are the 3 main groups of lipids?

A lipid is a non-polar (hydrophobic) molecule made up of hydrogen and carbon

The groups are as follows:

1. Triglycerides - A source of energy

2. Phospholipids - Main component of a cell membrane

3. Sterols - Another component of a membrane

What is the structure of a triacylglycerol like?

A triacylglycerol has 3 tails made of fatty acids, and they are bonded to 3 glycerols by ester linkages.

What is the structure of a fatty acid like and whats the difference between a saturated and unsaturated one

A fatty acid is a long chain of hydrocarbons with a carboxyl group at one end.

Unsaturated = Lacking in hydrogen, therefore double bonds are present

Saturated = having a lot of hydrogen, therefore no double bonds present

What is the structure of a phospholipid like?

A phopholipid has 2 parts. It has a fatty acid tail as the bottom part, which makes the bottom hydrophobic. At the top, it has phosphate and choline which makes it hydrophilic. This property of being both hydrophobic and philic is called being amphipathic.

What kind of structures can a phospholipid form in water

It can form a ball-like Micelle, with the heads all pointing out and tails pointing in

It can form a liposome, which is the same ball-like structure, but with the their being 2 sets of heads and 2 sets of tails

It can also form a phospholipid bilayer, which has the head on each end the the tails inside.

What does the fluid mosaic model describe

fluid - A membrane is fluid, and the phospholipds in it can move freely, laterally along the membrane

mosaic - A membrane is composed of other parts such as proteins (integral and peripheral)

What is fluidity and what increases it?

Fluidity is how easily a substrate can diffuse through the membrane (aka how fluid it is).

Fluidity can be increased by:

1. having lots of unsaturated fatty acids in order to create gaps in the membrane

2. Adding sterols to seperate the fatty acids from being too close

3. Increasing the temperature will also increase the fluidity

4. A shorter chain length of the fatty acids will increase the fluidity

How is it that unsaturated fatty acids are more viscous then the saturated counterparts

When fatty acids are saturated, they are straight and ca pack more closely together. They exhibit a lot of vander waal interactions, similar to velcro. When the fatty acids are unsaturated, they will have gaps between them due to the double bonds changing the shape of the fatty acid.

What do sterols specifically do to a membrane?

If a membrane is too fluid, the sterols will enter the membrane in order to close the gaps of the membrane

If a membrane is too viscious, the sterols will enter to seperate the fatty acid tails a little

Sterols are regulatory

Which molecules can diffuse easily through a bilayer and which cannot

Small, non-polar molecules can diffuse quickly and with easy

Small, polar molecules can diffuse across but slower

Large, polar molecules cannot diffuse unless they get help from protein.

Ions cannot diffuse unless a protein helps them

In which direction does diffusion work.

From high concentration to low concentration of solute

How does water diffuse via osmosis?

from low concentration of solute to high concentration of solute, in order to make each concentration on each side reach equilibrium.

What are the 3 different types of tonicity?

Hypertonic = when a substrate has a higher concentration then the thing being compared too

Hypotonic = When the substrate has a lower concentration compared to the thing being comapred too

Isotonic = When the substrate has an equal concentration compared to the thing being compared.

What is facilitated diffusion?

Facilitated diffusion is how larger molecules can move from high to low concentrations, via the use of a protein. Facilitated diffusion does not use any energy.

What is primary active transport

Primary active transport requires energy (ATP) in order to take molecules from low concentrations and put them into high concentrations. This also uses a protein.

What is secondary active transport?

Same thing as primary acive transport, except it does not need energy in order to diffuse molecules. Instead, energy is taken from other sources.

What is symport in secondary active transport.

When 2 molecules are being diffused through in the same direction, except one goes with the concentration gradient and the other goes against.

the first molecule going with the concentration gradient is what gives the second molecule enough energy to diffuse through against its own concentration gradient

What is anti port in secondary active transport?

Antiport is when 2 molecules diffuse across at the same time, but in 2 different directions. The main concept is the same as symport though

One molecule moves with the concentration gradient, the other one moves against it.

The movement of going with the gradient is what supplies the second molecule with enough energy to cross the membrane against the concentration gradient