130 Final Exam (all cards)

Semmelweis

(a physician - hospital transmission) found that physicians who did not disinfect their hands, generally transmitted infections from one obstetrical patient to another

How is one water molecule held together? How is a population of water molecules held together?

The bonds within a water molecule are covalent but the bonds that hold a population of water molecules are hydrogen bonds

What are ions, what are the two types?

negative or positively charged atom

Selective toxicity

the property of some antimicrobials agents to be toxic for a microorganism and nontoxic for the host

Ehrlick

theorized a drug (chemotherapeutic) that is specific for a target without affecting the host (also known as magic bullet theory) - He also found a chemotherapeutic agent called Salvarsan, the first effective treatment against syphilis.

Vaccine definition

use of organisms or fractions of organisms to induce immunity

Lister

(a physician) applied germ theory to medical procedures. He knew that phenol could kill bacteria so he started using it during the surgical treatment of wounds. Incidence of infections and death reduced and other surgeons quickly adopted to his techniques

The four macro/biomolecules found in living systems are?

Carbohydrate, protein, lipids, nucleic acids

More than 90% of a cell (or organism) is composed of just four elements. What are the four elements?

Carbon, hydrogen, oxygen, nitrogen (remember: CHON)

Typically, what is the relationship/ratio between the number of protons, neutrons, and electrons of an element?

- # of protons = # of electrons - Atomic mass --> protons + neutrons

What are the 2 types of cells on earth? What are the 3 domains of life on earth?

- 2 cells --> prokaryotes, eukaryotes 1. Bacteria — cell walls contain peptidoglycans (a protein-carbohydrate complex) 2. Archaea — cell walls lack peptidoglycans 3. Eukarya include... A. Protists (slime molds, protozoa, algae) B. Fungi (unicellular yeasts, multicellular molds, mushrooms) C. Plants (mosses, ferns, conifers, flowering plants) D. Animals (sponges, worms, insects, vertebrates

explain 4 functions of saccharides in a living system

- 4 primary functions: provide energy, stored as energy, build macromolecules, spare protein and fat for other uses - Structure & Chemistry **Macromolecules: polymers made of monomers --> Examples: saccharides, lipids, proteins, nucleic acids

What is the difference between an element and an atom?

- Atom: smallest unit of matter - Element: substance made of multiple atoms (same type of atoms)

What is atomic number and atomic weight

- Atomic number: number of protons in nucleus (if atomic number changes, so does the identity) - Atomic Weight: total number of protons and neutrons in an atom

Pros and cons of microbes

- Benefits of Microbes - less than 1% are pathogenic, oxygen and fossil fuel production, sewage treatment, decay matter, recycle elements, digestion, antibiotics, pest control, etc. - Negatives of Microbes - disease, spoilage, degradation

What is the difference between cis and trans unsaturated fats? Can chemists alter these, and why would they?

- Cis: H atoms are on the same side of the double bond - Trans: H atoms are on opposite sides of the double bond - Yes they can be altered —> trans fat - Partial hydrogenation of unsaturated fats makes trans fat (cis formation found in unsaturated fats is converted to trans form) **Trans fats give food better stability and longer shelf life

What is peptidoglycan, and where is it found?

- Composition —> polymer made of sugars and AA's; sugars are NAM and NAG (glucose derivatives) - Found in prokaryotes; bacteria are gram (+) or (-) based on cell wall architecture NOTES: - Function - protection, structure, support

What is a covalent bond? What is a nonpolar covalent bond? What is a polar covalent bond? Can you think of examples?

- Covalent Bond: electrons are shared by atoms - Nonpolar Covalent Bond: bond between atoms of the same electronegativity (CH4) - Polar Covalent Bond: bond between atoms of different electronegativity (H2O) NOTES: Charges - Ions: charged atoms that have gained or lost electrons - Cations: atoms that lose electrons and become positively charged - Anions: atoms that gain electrons and become negatively charged ions

explain structural features of a DNA double helix.

- Each strand is composed of paired nucleotides (G—C, A—T) that are deoxyribose - Each double helix contains a "backbone" that runs antiparallel (5' --> 3') - Backbone is made of sugars and phosphates - Double stranded helix - phosphodiester & hydrogen bonds keep strand connected

Compare and contrast an endergonic reaction with an exergonic one.

- Endergonic reaction: one that absorbs more energy than it releases (anabolism) - Exergonic reaction: one that releases more energy than it absorbs (catabolism)

What are exchange reactions? Can reactions be reversible? Why are they reversible?

- Exchange Reactions: part synthesis and part decomposition (example: AB + CD —> AD + BC) - Chemical reaction are reversible and are dedicated with a double headed arrow **They are a result from unstable reactants or products (want to be in equilibrium) and each direction may need special conditions --> Example: A + B <—> AB

Name agents that may damage the bacterial cell wall

- Exposure to lysozyme (a digestive enzyme) that is found in perspiration, tear, mucus, and saliva —> breaks NAM & NAG (breaks peptidoglycans essentially) **Lysozyme catalyze hydrolysis reaction of bonds between sugar units of the disaccharide of peptidoglycans - Antibiotics destroy bacteria by disrupting the formation of peptide bridges in peptidoglycans NOTES: - So is a G+ or G- more susceptible to these agents? **G+ because peptidoglycan layer is on the outside and G- had outer membrane that prevents antibiotics from getting in (G - cell is more impermeable; its multilayered)

Some microbes contain a glycocalyx/capsule, where is it, what is it made out of, and what is its function?

- Glycocalyx: substance that surrounds a bacterial cell **Contains capsule layer (firmly attached with structure) and slime layer (loosely attached & unorganized) - Location —> made inside the cells and then secreted to the surface - Composition —> made of polysaccharides, polypeptides, or both (its an EPS substance —> extrapolymeric substance) - Function —> protection against phagocytosis, keeps water and nutrients in, has ability to cause disease (S. pneumoniae)

What is an isotopes

- Isotopes: same element with different atomic masses and number of neutrons

Biogenesis Theory

- Living cells can only arise from pre-existing ones - Virchow challenged spontaneous generation but didn't have the evidence to prove it

functions of polypeptides in a living system.

- Make protein - Made of C, H, O, N, and sometimes S - Transport (cytoskeleton) - Cell-cell recognition - Receptor/pores/transporters - Hormones - insulin - Defense - complement, antibodies

What is the purpose of the membrane?

- Most important function is selective permeability ◦Large molecules and ions can't pass easily while small ones (O2, CO2, small sugars) that are easily dissolved in lipid can - Secondary functions —> nutrient breakdown, energy production

What are the three components in a nucleotide?

- Nucleotides - nitrogenous base (purine or pyrimidine), phosphate group, pentose sugar (ribose or deoxyribose) NOTES: - Nucleosides - pentose, nitrogenous base - Tips to Memorize Nitrogenous Bases **Easiest to fit pyramid into pyrimidines (simple shape) **Cytosine and thymine both have y in name like pyrimidine **Adenine & guanine don't have y so they are purines **Structure difference thymine has methyl group —> methyl end in thy and thymine start with thy

How are integral proteins different from peripheral ones?

- Peripheral Proteins on the inner and outer surface function as enzymes and in transport - Integral Proteins are channels which substances can exit and enter the cell

Concerning a typically phospholipid, which portion interacts with water, and which portion does not?

- Polar head (hydrophilic) interact with water - Nonpolar tail (hydrophobic) doesn't interact with water

What are the three main subatomic particles?

- Protons: positively charged particles - Neutrons: uncharged particles - Electrons: negatively charged particles

What is the difference between saturated and unsaturated fats, and where are they sourced in nature?

- Saturated fat has no double bonds (meats, dairy products) - Unsaturated fat has one or more double bonds (plant oils, salmon, seeds) - both are simple lipids

How does the shape of a protein relate to its function?

- Shape determines function and interactions **Shape determined by H-bonds on backbone and by R group chemistry

Draw and label an amino acid

- Structures attached to alpha-carbon —> carbonyl group (-COOH), amino group (-NH2), side group (R) - Acidic (+) and basic (-) AA's will always be polar

Compare and contrast a synthesis/anabolic reaction with a decomposition/catabolic one.

- Synthesis (anabolic) Reactions: when two or more atoms, ions, or molecules combine to form a larger molecule - Decomposition (catabolic) Reactions: when bonds are broken and molecules are broken into smaller parts **Example: AB —> A + B

What is a triglyceride, and specifically where would you find them in humans?

- Triglyceride: simple lipid; glycerol + 3 FA's -Found in fat cells, later used to make plasma membranes (the primary function)

What are hydrogen bonds and how do they arise?

- Weakest type of bond in biology, strongest interaction in chemistry - Hydrogen can attach to fluorine, oxygen, or nitrogen (FON) - Serve as a bridge between different molecules but don't bind atoms into molecules

What is viruses?

- acellular (they are not cells) - reproduce utilizing the cell mechanisms of other organisms - inert/non active outside living host

Robert Hooke

- cell theory -> living things are composed of cells - Created compound microscope (20x)

John Needham

- claimed microbes arised spontaneously on nutrient broths like chicken and corn broths - found that even after he heated chicken and corn broth, the cooled covered solutions still grew microorganisms - Flaws - capped after cooled, didn't boil long enough

Fleming

- discovered Penicillin by accident - He noticed that his culture plates had been contaminated by mold but there were some areas that were clear and bacterial growth was inhibited - He decided to isolate the mold and determine how much other bacteria it was able to kill off (a lot) - Essentially mold against bacteria

What is fungi?

- eukaryotes that are surrounded by a nuclear membrane - organisms cannot perform photosynthesis - Characteristics: uni/multicellular, chitin cell wall, eukaryotes, organic chemicals for energy - Examples: mold and yeast

What 2 compounds that are joined to form a lipid?

- fatty acid, glycerol NOTES: - Lipids are primary component of cell membranes - Made of C, H, O - Nonpolar, insoluble in water, amphipathic (hydrophobic and hydrophilic end) - Mono, di-, triglycerides —> made of glycerol and FA's; formed by dehydration - Sterols —> ex: cholesterol, hormones

Anton van Leeuwenhoek

- first to see live organisms - Created simple microscope (200-500x)

Germ theory

- idea that microorganisms might cause disease

How are monosaccharides linked together, and how are disaccharides broken down?

- linked together by dehydration reaction - broken down by hydrolysis - Figure: A = dehydration, B = hydrolysis NOTES: - Monosaccharide: simple sugar, linked by glycosidic bonds ◦ Examples: glucose, fructose, galactose, ribose, deoxyribose - Disaccharide: two or more monosaccharides ◦Example: lactose, sucrose - Carbohydrates - sugar and starches • Contain C, H, O ◦ Functions: energy, structure (cellulose, peptidoglycan, chitin), glycocalyx, cell recognition, component of NA's, and ATP ◦ Many are isomer —> same chemical formula, different structure

What is Helminths?

- multicellular eukaryotic animals also known as worms - Parasitic flatworms and roundworms = helminths

What is algae?

- photosynthetic eukaryotes - cells walls made of cellulose - Characteristics: uni/multicellular, cellulose cell wall, photosynthetic organism, indirectly pathogenic

Define the following: Levels of Protein Structure (primary, secondary, tertiary, quaternary)

- polypeptide primary structure: amino acid sequence - polypeptide secondary structure: regions (α/β) that are stabilized by hydrogen bonds - polypeptide tertiary structure: overall 3D structure of polypeptides **Holds shape by chemical interactions of R group, H-bonds, ionic and covalent bonds, and hydrophobicity - protein quaternary structure: structure of multiple polypeptides linked together

What is archaea?

- prokaryotes often found in extreme environments - Divided into 3 groups.... **Methanogens - make methane as a waste product from respiration **Extreme Halophiles - live in salty environments **Extreme Thermophiles - live in hot sulfurous water

Biogenesis

- proposed by Rudolf Virchow - He said that living cells arise only from preexisting living cells. There was no proof of this theory at the time so spontaneous generation continued until 1861. - Pasteur ended the debate with his broth experiment.

Francesco Redi

- proposed the idea that maggots or organisms do not arise spontaneously - demonstrated that maggots appear on decaying meat only when flies are able to lay eggs on the meat - Not spontaneous cause maggot came from the fly not the meat

Which subatomic particle gives an element its identity? Which subatomic particle gives an element its atomic number? Which subatomic particles give an element its atomic mass?

- protons - identify, atomic number - protons & neutrons for mass

What types of substances can readily dissolve in water (two answers here)? Conversely, what types of substances have a difficulty time dissolving in water?

Sugar and salt readily dissolve in water while oil has a harder time

Pasteur

- showed that microbes are present in the air - First poured beef broth into a long-necked flask. He then heated the neck of the flask, bent it into an S-shape , and boiled the broth for several minutes. He noticed that microorganisms didn't appear in the cooled solution due to bending the flask which prevented the entrance of microbes. (accounted for spontaneous generation factors) NOTES: Other findings • Founded aseptic techniques: ◦This is not sterile (free of microorganisms to begin with) --> Heat - kills, Air - allows travel/contamination, Transmission - can be managed, Fermentation - yeast converted sugars to alcohol, Pasteurization - milk heat kills bacteria, Silkworm - protozoan contamination ◦ Germ theory (with Koch & Lister) - microbes cause disease & specific microbes can cause a specific disease ◦Vaccinations - anthrax & sheep, rabies, cholera

What is eubacteria?

- single-celled prokaryotic microorganisms - unicellular, peptidoglycan cell walls, divide by binary fission - classified into 5 phylums - Chlamydias, Cyanobacteria, gram-positive bacteria, Proteobacteria, and spirochete

Lazzaro Spallanzani,

- suggested that microorganisms from the air probably entered Needham's solutions after they were boiled - showed that nutrient fluids heated after being sealed did not develop any microbial growth - Flaw: sealed before boiled so people claimed that there was no room for vital forces

What is protozoa?

- unicellular eukaryotic microorganisms that can contain pseudopods, flagella, or cilia - Examples: rhizopoda, entamoeba

Cell Theory

- was discovered by Hooke - theory that all living things are composed of cells

Compare and contrast DNA with RNA.

1 Strand of DNA (RNA essentially) - Single stranded - Phosphate group same - Sugar is ribose (not deoxyribose) —> has an additional oxygen on the 2 prime carbon DNA - Double stranded - Backbones run antiparallel - 2 strands held together by H-bonds - 3' and 5' end connected by phosphodiester bond - Deoxyribose doesn't have oxygen on 2 prime carbon

A. What are the four common DNA nitrogenous bases? B. What are the four common RNA nitrogenous bases? C. What is the difference between ribose and deoxyribose?

A. guanine, cytosine, adenine, thymine B. guanine, cytosine, adenine, uracil C. Ribose: 5 carbon sugar thats found in RNA, oxygen that attaches to each carbon. Deoxyribose: 5 carbon sugar thats found in DNA, lacks one oxygen (at 2' carbon)

What are the 3 most common morphologies of bacteria?

Coccus = spherical shape - Strep = make change - Staph = cluster Bacillus = rod shaped; gram negative (found in gut and soil) - Example: Campylobacter jejuni - common cause of food poisoning; E. Coli - #1 cause of UTI's; enterohemorrhagic = contains Shiga toxin that damages cells and causes bleeding but can be killed with heat Spiral

Human lipid bilayers are often composed of saturated fats, what other type of fatty compounds are found in eukaryotic membranes?

Complex Lipids - made of C, H, O, P, N, and/or S - Sterols - keeps membrane fluid; 4 rings + OH group ◦ Examples: cholesterol, estrogen, testosterone ◦ Fungi has ergosterol instead of cholesterol

What are flagella made out of, and what is their function?

Composition - made of flagellum protein - 3 major parts **Filament - that contains flagellin protein **Hook **Basal body - secures the flagellum to the cell wall and plasma membrane - Function —> adherence, motility, stereotyping/ID by H or O **Example of stereotyping: E. Coli O157:H7

Cytoplasm: function & location

Cytoplasm: the part which many substances are found (prokaryote & eukaryote) - Surrounds many substances within the cell but remains outside of the nucleus - Function: gives cells its shape

What are the consequences of changing an amino acid within a polypeptide?

Dysfunctional protein and genetic diseases (ex. Huntington's, sickle cell anemia)

Eubacteria examples

E. Coli, Escherichia, Streptococcus

How to name microorganisms

Each organism is named by genus (capitalized) and specific epithet (lowercase) NOTES: - Carol is Linnaeus created the system of scientific nomenclature

What subatomic particle gives an element its behavior or reactivity?

Electrons

How do atoms achieve stability, or a less reactive, lower energetic state?

Fill its valence shell by sharing, donating or accepting electrons (drives bond formation)

Functions of fimbriae or pili

Fimbrae - Used to make biofilms on liquids, glass, and rocks - Helps bacteria to stick on epithelial surface of the body (adherence) - Composition - pilin protein - Location - at poles or dispersed Pili - For DNA transfer and movement - Allow for passing of DNA = sex? - Composition - pilin protein Figure —> conjugation = bacterial mating of same or different strains - F+ makes, F- receives plasmid (genetic information)

Name some polysaccharides, and where would you find them in nature?

Glycogen - stored form of energy in animals Cellulose - makes up cell wall of plants Starches - plant energy source Chitin - yeast and Arthropoda

What is the difference between a Gram positive and Gram negative bacterium?

Gram Positive (sphere shape) - Stain blue - Many peptidoglycan layers in cell wall = thick wall and structure - Periplasmic space (space between cell wall and plasma membrane) contains teichoic acid **Acid stabilizes wall during expansions - One layer membrane - Associated protein cross links = more rigid - Examples: S. aureus, Streptococcus pneumoniae Gram Negative (rod shaped) - Stain pink - Thin layer of peptidoglycans but multilayered - Periplasmic space contains enzymes and transport proteins - Outer membrane composed of phospholipids lipopolysaccharides, protein, poring, etc. - When gram negative bacteria die, they give off lipid A causing fever, dilated blood vessels, shock, and blood clotting

Give 2 examples of quaternary proteins.

Hemoglobin DNA Polymerase

What is a typical membrane composed of?

Made of phospholipids and proteins - Prokaryote membranes are composed of phospholipids while eukaryote membranes are composed of carbohydrates and sterols (cholesterol) **Phospholipid = polar part, phosphate group, glycerol —> form the phospholipid bilayer Membrane Proteins - Peripheral Proteins - Integral Proteins - Glycoproteins - Spanning proteins NOTES: - Plasma Membrane -> encloses the cytoplasm - Structure - lipid bilayer - Characteristics ◦ Fluid mosaic model: membrane isn't static; proteins can move in plasma membrane laterally ◦ Leaflets don't flip - phospholipids don't flip from one side to another

Water is unique in that it expands upon freezing, can you give one real-life example of this?

Making ice cubes - density changes upon freezing

amine/amino

NH2

Compare prokaryotic and eukaryotic cells

Prokaryote - One circular chromosome, not in a membrane - No histones - No organelles - Bacteria - peptidoglycan cell walls, archaea - pseudomurein cell walls - Divides by binary fission Eukaryote - Paired chromosomes, in nuclear membrane - Has histones - Has organelles - Polysaccharide cell wall - Divides by mitosis

What are the two cell types on earth?

Prokaryote and eukaryote

How is cholesterol similar to a monoglyceride, and how is it different?

Similarity: both had a hydrophobic and hydrophilic (OH part on cholesterol) end Difference: cholesterol is made in the body, monoglyceride is a simple lipid and cholesterol is a sterol

Explain simple passive diffusion, facilitated passive diffusion, active transport, and osmosis (and types of solutions)

Simple passive diffusion: movement of molecules from high to low concentration - Used in cells to transport small molecules such as oxygen and carbon dioxide across cell membranes -Cell doesn't require energy Facilitated passive diffusion: larger molecules pass through a transporter (specific or nonspecific) - Cell doesn't expend energy because molecules are moving from high to low concentration Active transport: cell uses energy (ATP) to move substances across plasma membrane from low to high concentration - Go against concentration gradient so energy is needed Osmosis: movement of water across a selective permeable membrane from high to low concentration - Move either by simple diffusion or by using the integral membrane protein (aquaporins) ‣ Isotonic : cell concentration is in equilibrium (no net movement of water) ‣ Hypotonic : low solute concentration outside cell than inside (water moves into cell = burst) ‣ Hypertonic : higher concentration of solutes inside cell than outside (water moves out of cell = cytoplasm shrinks because remember: water moves from high to low concentration) ** Refer to pictures for examples

Fill in the blanks The core of all the amino acids are the same, but the __________ group is unique. The 4 chemistry groups of the R groups are ______, _____, ________, and ____.

The core of all the amino acids are the same, but the _____side_____ group is unique. The 4 chemistry groups of the R groups are ___oxygen___, ___nitrogen__, ____carbon____, and __hydrogen__.

What is microbiology?

The study of microorganisms and their relationship with each other, hosts, and the environment.

Fill in the blank. The suffix affixed to saccharides is __________. Monomeric building blocks of sugars are called _____________, and an example is ____________. ___________ is the common table disaccharide, ____________ is the milk disaccharide.

The suffix affixed to saccharides is ____sugar______. Monomeric building blocks of sugars are called ___monosaccharide__________, and an example is ___glucose_________. __Sucrose_________ is the common table disaccharide, ______lactose______ is the milk disaccharide.

Water is considered cohesive, meaning it exhibits self-affinity. Why is this?

Water is polar and forms hydrogen bonds with other water molecules NOTES: - Strong interactions = high specific heat and vaporization

If bacteria are placed in a hypertonic solution what will happen?

Water moves outside of cell causing the cytoplasm to shrink

Do different elements have different electronegativity values, and does this affect the covalent bonds that form?

Yes and yes - 0.0 - 0.2 —> NP Covalent - 0.3 - 1.4 —> P Covalent - 1.5 —> ionic **no need to memorize ranges

Types of microorganisms

bacteria, archaea, fungi, Protozoa, algae, helminths, viruses

Jenner

created an immunization against smallpox. He collected the cowpox (milder disease) blisters off of milkmaids and injected the substance into a healthy 8 year old volunteer. The volunteer got sick but was able to recover and never got smallpox or cowpox again.

Koch

discovered how bacteria cause disease and established the Koch's postulates which is a set of experimental steps determining the relationship between microbes with a disease. He said a specific germ causes a specific disease. He determined these steps based on his experiment dealing with anthrax, a disease that was destroying cattle and sheep in Europe. His postulates.... 1. Isolate microorganism from disease —> take swab and put on plate in pure culture 2. Infect a healthy subject (animal) with organism and has to cause same exact disease 3. Isolate microorganism again from previously healthy organism to determine that organism is cause of disease

Spontaneous generation

forms of life could arise from non living matter

Spontaneous Generation

hypothesis that life comes from non living matter (a "vital force" needed for life)

Fill in the blank. pH is a measurement of ______________ in a solution. The addition of an ____________ will increase the proton concentration in a solution. Consequently the pH value will go ______. The addition of a ____________ will decrease the proton concentration in a solution. Consequently the pH value will go ______.

pH is a measurement of ______H+________ in a solution. The addition of an ____acid________ will increase the proton concentration in a solution. Consequently the pH value will go ___down___. The addition of a _____base_______ will decrease the proton concentration in a solution. Consequently the pH value will go __up____.