BIOL 221 Lecture quiz 1

Robert Hooke

Looked at cork under a microscope (very crude microscope, given the time period) and discovered that life was made of smaller units which he named cells.

Anton van leeuwenhoek

 Used a more advanced microscope than Hooke to be the first person to observe microorganisms.

Louis Pasteur

Used a flask of broth with an open-tube top to observe microbial growth. When broth was in this flask, boiled, and allowed to sit, no growth occurred. However, when the same experiment was done but the flask was tilted to collect dust that was in the tube, microbial growth did occur. He showed that growth could only come from other life as well as determining what causes fermentation, discovering that some organizations can live with and without oxygen, and developed the process of pasteurization to remove microorganisms from food.

Ferdinand Cohn

Discovered endospores that can’t be killed by boiling.

What are the steps in the scientific method? What is the importance of having controlled groups?

Steps:

1.     Ask question

2.     Do background research

3.     Construct hypothesis

4.     Test with an experiment

5.     Analyze results and draw conclusions

6.     Report results

7.     Try again (if necessary)

 

Control groups are important because without them you wouldn’t know what is causing a result. A control group is present to prove that the independent variable that is changed is what is causing a change in the dependent variable. For example, if trying to determine if a fertilizer for plants is effective, a control group with no fertilizer must be present to compare the results and prove the effectiveness of the fertilizer, otherwise no conclusion can be determined about the fertilizer.

What are the similarities and differences between prokaryotes and eukaryotes? Although not alive, what things are smaller than bacteria?

Differences:

-        Prokaryotes have smaller cells than eukaryotes.

-        Prokaryotes are also single-celled organisms while eukaryotes are multi-celled organisms.

-        Prokaryotes have no mitochondria, nucleus, or nuclear membrane while eukaryotes do.

-        Prokaryotes can survive in more extreme environments than eukaryotes.

-        Prokaryotes have a cell wall while eukaryotes do not.

Similarities:

-        Have a cytoskeleton.

-        Can be all be found in non-extreme environments.

Viruses, viroids, and prions are all smaller than bacteria, even though they are not alive.

What is a phage (bacteriophage)? Why should we consider using phage to treat infectious diseases? What are some of the arguments against using phage?

A bacteriophage is a virus that infects bacteria. Phage can be considered to treat infectious diseases because they can kill harmful, infectious bacteria that cause diseases. This, in theory, would cure a bacterial infection. However, using this method is not the most effective because a specific phage is needed for different bacteria. It is also not efficient and only works about 50% of the time. On top of this, the phage must be grown in a lab by having it infect a bacteria culture, so if not all bacteria in that culture are dead before the phage is given to a patient it can just cause more bacterial infection. Finally, the phage killing the bacteria can produce toxic byproducts which can be harmful to health.

What is a strong chemical bond? Give an example. What are the types of weak chemical bonds? How are the weak bonds different from each other? How could you predict the type of chemical bond that will form between two atoms?

A strong chemical bond is a chemical bond that cannot easily be broken, such as a covalent bond. Weak chemical bonds include ionic bonds, hydrogen bonds, and van der Waals interactions. These bonds are all different from each other because the interactions in each bond are slightly different and they have different requirements. The ionic bond is caused by an electron transfer between two atoms with extremely different electronegativities which forms a cation and anion that have an electrostatic attraction. A hydrogen bond is an electrostatic attraction between a partially positive hydrogen atom and a strongly electronegative atom. Van der Waals interactions can happen between any two atoms just because of the naturally occurring dipole moment which causes an induced dipole and an electrostatic interaction between these dipoles. You can predict the type of chemical bond between two atoms by looking at the difference in the atom’s electronegativities. If two atoms have similar electronegativities, they will form a nonpolar covalent bond. If there is a large difference in the atom’s electronegativities, an ionic bond will be formed.

What are the differences between hydrophilic, hydrophobic and amphipathic materials? What is the hydrophobic effect and why does it occur? What does pH measure?

Hydrophilic materials are those that are attracted to and can interact with water. These are materials that tend to have more polar covalent bonds and contain electronegative atoms such as oxygen or nitrogen. These allow for hydrogen bonding with water. Hydrophobic materials don’t have many or any polar covalent bonds, so they don’t really interact with water. Amphipathic materials have both a polar and nonpolar portion, so the polar portion can interact with water while the nonpolar portion cannot. This causes micelles to form. The hydrophobic effect is when a hydrophobic material is exposed to water so it will repel the water away from itself, and the water will instead interact with other water molecules and not the hydrophobic material. This causes the water to surround the hydrophobic material instead of interacting with it. This occurs because of this repulsion between the polar water and the nonpolar hydrophobic material. pH measures the amount of hydronium ions (H3O+) present in solution.

Algae

Eukaryote that contains chloroplasts for photosynthesis, some of them have cilia

Bacteriophage

Virus that infects bacteria specifically

Archaea

Prokaryotes that tend to have extreme lifestyles and no peptidoglycan in their cell wall

Bacteria

Prokaryotes with a cell wall containing peptidoglycan

Biogenesis

Hypothesis for where microbes come from: life must come from preexisting life

Cytoskeleton

In all cells to help maintain structure of the cell

Endomembrane system

Eukaryotic system that can import and traffic materials in the cell, the reason why eukaryotes are not diffusion-limited

Endospore

A seed-like part of some bacteria that is resistant to more harsh environments due to it’s outer layers

Endospore coat

Third layer of the endospore that helps protect it from environment

Endospore cortex

Second layer of endospore that helps protect it from environment

Endospore core

Inner layer of the endospore that contains DNA and ribosomes

Eukarya

Multicellular organisms, have large cells, cells have a nucleus, have membrane-bound organelles

Kingdom-specific infection

Viruses can only infect one kingdom, no one virus can infect multiple

Membrane-bound organelle

Organelles that are surrounded by a lipid membrane

Pasteurization

Technique to remove microorganisms from food

Peptidoglycan

Component of bacteria cell walls but not archaea cell walls, what differentiates the two

Prion

Infectious proteins, altered form of normal proteins that has an abnormal 3D shape (misfolded protein)

Prokarya

Single-celled organisms, small cells, no membrane-bound organelles, no nucleus, contain cell wall

Protozoa

Eukaryotes that do endocytosis to feed and have cilia

Endocytosis

Folding cytoplasmic membrane inward to bring in nutrients from the environment

Spontaneous generation

Hypothesis of where microbes come from: life can exist from nonliving material

Viroid

Infectious RNA molecules

Virus

Infectious microorganisms that are non-living (no metabolism), contain nucleic acids, proteins, and some of them contain lipids

What are the domains of life?

Bacteria, archaea, eukarya

What are some uses of microbes?

Making food, making chemicals, bioremediation, genetic engineering, medical applications

What does “diffusion-limited” mean with prokaryotes?

Prokaryotic cells can’t get too big because they are limited by how fast important materials can move through the cell

Louis Joblot

Put hay in water and the water got cloudy with microbes. Came up with a couple hypotheses: microorganisms grow on hay, settle from air, or spontaneously arose from decaying hay, concluded that even microorganisms need parents

John Needham

Said all organic matter needs air, poured broth into clean (but not sterile) bottles, covered them, and observed microbial growth

John Tyndall

Physicist who studied light but dust was a problem for him so he developed a box that removed dust from the air and produced “pure air”. He noticed that food didn’t spoil in this “pure air” so something in the dust must be causing the growth

Fungi

Yeasts or molds

Acid

A substance that can donate a proton

Amphipathic

A molecule that has both a hydrophilic and hydrophobic portion

Aufbau principle

Electrons fill lowest energy orbital first and then will go up from there

Autohydration

Hydrogen transfer from one water to another

Base

A substance that can accept a proton or donate an OH-

Cohesion

Molecules interact with other molecules of the same substance through hydrogen bonding

Electronegativity

An atom’s affinity for it’s electrons, how tightly it holds on to them

Heat capacity

The amount of energy needed to raise the temperature of a substance

Hydrogen bond

An electrostatic interaction between a partial positive hydrogen (that is covalently bonded to an electronegative atom) and an electronegative atom with lone pairs of electrons

Hydrogen bond acceptor

The electronegative atom (not H atom) involved in hydrogen bonding

Hydrogen bond donor

The hydrogen atom involved in the hydrogen bond

Hydrophilic

Attracted to and interacts with water

Hydrophobic

Repelled by and does not interact with water

Hydrophobic effect

When a hydrophobic material is exposed to water, the water will interact with itself instead of that material, so the water will just surround the material, but not interact with it

Ionic bond

A bond formed when one atom donates an electron to another, causing the donor to become a cation and the acceptor to become an anion, which makes an electrostatic interaction

Induced dipole

When an atom with a dipole moment is close to another atom, which induces a dipole in this other atom

Micelle

When an amphipathic substance is placed in water, the hydrophobic portions will cluster together to avoid the water and interact with each other, and the hydrophilic portions will be facing out to interact with the water

Neutral

No net charge

Neutron

Part of an atom that contributes mass but is neutrally charged

Nonpolar covalent bond

A covalent bond between 2 atoms with similar electronegativities so there is no dipole

Nucleus

The center of the nucleus that contains protons and neutrons

Orbitals

Space surrounding the nucleus where electrons float around

pH

A measure of how many hydronium ions (H3O+) are in a solution

pOH

A measure of how many hydroxy (OH-) ions are in a solution

Polar covalent bond

A covalent bond between two atoms with different electronegativities, so the more electronegative atom holds the shared electrons closer and has a partial negative charge while the less electronegative atom has a partial positive charge

Strong bond

A bond that is difficult to break, like a covalent bond

Valence electron

Electrons involved in bonding

van der Waals interactions

An interaction between atoms due to an induced dipole that causes an electrostatic interaction

VSEPR

A system of determining the geometry of a molecule

Weak bond

A bond that can be easily broken such as an ionic bond, hydrogen bond, or van der Waals interaction

Buffer

A solution of weak acid and it’s conjugate base that resists changes in pH

What is used to build proteins? What is the name of the covalent bond between the units in a protein? What is meant by primary, secondary, tertiary, and quaternary structure in proteins?

Amino acids are linked via a peptide bond to form proteins. Primary protein structure is the sequence of amino acids in a polypeptide chain. Secondary protein structure is formed by hydrogen bonding to give alpha-helices which are twist-looking structures and beta-pleated sheets which are flat looking structures. Tertiary structure is the 3D shape of the polymer which is stabilized by different interactions including van der Waals interactions, hydrogen bonding, salt bridge (ionic), and disulfide bonds. Quaternary protein structure is the interactions between proteins, it is a larger structure made of multiple protein subunits.

If you observed a chemical diagram of a compound, how would you know that it is a carbohydrate? What is the name of the covalent bond between the sugars in a disaccharide, oligosaccharide, or polysaccharide? What is the difference between the alpha versus beta linkages in carbohydrates?

If looking at a chemical diagram of a compound, I would determine it is a carbohydrate by looking for the ring structure and the one carbon atom in the molecule that is bonded to two oxygen atoms. The covalent bond between sugars in a disaccharide, oligosaccharide, or polysaccharide is called a glycosidic bond. An alpha-glycosidic bond forms when the 2 hydroxyl’s involved in forming the glycosidic bond are on the same side of the ring. A beta-glycosidic bond forms when the 2 hydroxyl’s involved in forming the bond are on opposite sides of the ring.

What are the three components found in any nucleotide? How are DNA nucleotides different from RNA nucleotides? What is the name of the covalent bond between the nucleotides in DNA and RNA? How is this bond formed?

The three components of every nucleotide are a sugar (ribose or deoxyribose), a phosphate group, and a base (adenine, guanine, cytosine, thymine, or uracil). DNA nucleotides have deoxyribose as the sugar where RNA has ribose as the sugar. Deoxyribose and ribose are different because ribose has one more oxygen than deoxyribose. The covalent bond between nucleotides in DNA and RNA is a phosphodiester bond which is formed between the 5’ end of one nucleotide and the 3’ end of another. DNA and RNA are synthesized in the 5’ to 3’ direction.

What is the difference between a triglyceride and a phospholipid? What is the name of the covalent bond that joins fatty acids to the backbone? What is the difference between saturated, cis-unsaturated and trans-unsaturated fatty acids? How do phospholipids assemble to form a biological membrane?

A triglyceride has a glycerol attached to three fatty acids while a phospholipid has a glycerol attached to two fatty acids and one phosphate. An ester bond is the covalent bond that joins fatty acids to the glycerol backbone. Saturated fatty acids have no C-C double bonds, or every carbon is attached to two hydrogens. Cis-unsaturated and trans-unsaturated fatty acids both have at least one C-C double bond (or two hydrogens removed). The difference is that cis-unsaturated fatty acids have the chain on either side of the double bond on the same side of the bond while trans-unsaturated fatty acids have the chain on either side of the double bond on different sides of the bond. Phospholipids are amphipathic so they have a polar head group (the phosphate) and a nonpolar tail (the fatty acids). The nonpolar tails will interact with one another and align so that there is a layer of these nonpolar tails, with the polar heads facing out on either side of the membrane. This minimizes unwanted interactions between polar head groups and nonpolar tails, and maximizes interactions of polar heads groups with each other and nonpolar tails with each other as well.

5’ phosphate

The 5’ end of DNA

3’ hydroxyl

The 3’ end of DNA

Adenine

A purine that pairs with T or U using 2 double bonds

Alpha glycosidic bond

Glycosidic bond between two monosaccharides that have their OH groups on the same side of the ring

Alpha helix

A twisting secondary protein structure formed by hydrogen bonds

Amino acid

Building blocks/monomers of proteins

Antiparallel

The 5’ end of one DNA strand must be complementary to the 3’ end of the other

Beta glycosidic bond

A glycosidic bond that forms between two monosaccharides that have OH groups on opposite sides of the ring

Beta-pleated sheet

A secondary protein structure that forms flat sheets by hydrogen bonding

Biological membrane

Structure formed by the amphipathic structure of phospholipids where the nonpolar fatty acid tails clump together in the middle of the membrane and the polar phosphate heads face out of the membrane on both sides of it

Carbohydrate

A macromolecule used for storage of energy that is made up of monosaccharides

Chiral carbon

A carbon atom that has 4 different groups attached to it, so it can have stereoisomers

Cis-unsaturated fatty acid

A fatty acid that has a C-C double bond where the chains are on the same side of the double bone

Cytosine

A pyrimidine that pairs with G using 3 hydrogen bonds

Dehydration synthesis

Formation of a polymer from monomers by releasing a water molecule

Deoxyribose

Sugar found in DNA nucleotides

Double helix

The structure of DNA which has two strands that twist around one another

Ester bond

The bond that forms between a glycerol backbone and a fatty acid in a triglyceride (dehydration synthesis)

Fatty acid

Hydrocarbon chain (7-21 C’s long) with a carboxyl group at the end

Guanine

Purine that pairs with C using 3 hydrogen bonds

Hydrolysis

Breaking a polymer down into monomers by using a water

Lipid raft

A section of the biological membrane where there is a dense collection of phospholipids due to the specific fatty acids on those phospholipids

Nucleotide

Building block of nucleic acid, made of a sugar, a phosphate group, and a base

Peptide bond

Bond formed between amino acids in polypeptide synthesis (dehydration synthesis)

Phosphodiester bond

Bond formed between nucleotides to form DNA (dehydration synthesis)

Phospholipid

A lipid that has a glycerol backbone attached to two fatty acids and one phosphate group