Bio 203 Exam 1

Why have cells remained so small?

"Cells are small because they need to keep a surface area to volume ratio that allows for adequate intake of nutrients while being able to excrete the cells waste. That is why the cell needs to be small. The smaller it is, the larger the surface area to volume ratio is." -- Some random website Surface area increasing while volume remains constant Can get things in and out of the cell easier

Compound

A substance consisting of two or more different elements combined in a fixed ratio. Ex: NaCl, H2O

Element

A substance that cannot be broken down to other substances by chemical reactions. Ex: gold, copper, oxygen, carbon

Structure of a protein dictates its activity- give an example to explain why this is true

An antibody structure. It's structure allows it to bind to the particular foreign substance on the flu virus and mark it for destruction. Endorphin receptor is protein. Structure allows receptor protein to bind to a particular pain-relieving signaling molecule (endorphin molecule).

Describe the four levels of protein structure and what contributes to each level.

Primary (linear chain of amino acids) → Primary structure of a protein is its sequence of amino acids. Determined not by random linking of amino acids but by inherited genetic information. Secondary (regions stabilized by hydrogen bonds between atoms of the polypeptide backbone) → Coils and folds of segments of polypeptide chains (collectively referred to as secondary structure) are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone. Tertiary (Three-dimensional shape stabilized by interactions between side chains) → Overall shape resulting from interactions between side chains (R groups) of the various amino acids. One type of interaction that contributes to structure is hydrophobic interaction. Disulfide bridges, covalent bonds, may further reinforce shape. Quaternary (Association of two or more polypeptides → some proteins only) → Overall protein structure that results from the aggregation of these polypeptide subunits. Ex: Collagen or hemoglobin

What are proteins? Polypeptides? Amino acids

Proteins → A biologically functional molecule made up of one or more polypeptides. Polypeptides → A polymer of amino acids held together by a peptide bond. Amino acids → Organic molecule with both an amino group and a carboxyl group.

Distinguish between RNA and DNA (composition, structure)

RNA → Ribonucleic acid; mRNA interacts with cell's protein-synthesizing machinery to direct production of a polypeptide, which folds into all or part of a protein; Sites of protein synthesis are cellular structures called ribosomes. DNA → Deoxyribonucleic acid; provides directions for its own replication; directs RNA synthesis and, through RNA, controls protein synthesis; Each chromosome contains one long DNA molecule, usually carrying several hundred genes. Information that programs all cell's activities is encoded in the structure of DNA.RNA → Ribonucleic acid; mRNA interacts with cell's protein-synthesizing machinery to direct production of a polypeptide, which folds into all or part of a protein; Sites of protein synthesis are cellular structures called ribosomes. DNA → Deoxyribonucleic acid; provides directions for its own replication; directs RNA synthesis and, through RNA, controls protein synthesis; Each chromosome contains one long DNA molecule, usually carrying several hundred genes. Information that programs all cell's activities is encoded in the structure of DNA.

Ribosomes

Complexes that make proteins; free in cytosol or bound to rough ER or nuclear envelope

What do all lipids have in common?

They all mix poorly, if at all, with water b/c they consist mostly of hydrocarbon regions.

Ionic bond

The attraction between a cation (positively charged ions) and an anion (negatively charged ions).

What is the formula for a monosaccharide with 3 carbons? 6 carbons? What type of bond holds monosaccharides together?

3 carbons → Trioses with a formula of C3H6O3 6 carbons → Hexoses with a formula of C6H12O6 Glycosidic linkage holds monosaccharides together → Covalent bonds formed from dehydration reaction.

Write out the chemical equation summarizing photosynthesis and identify the reactants and products.

6CO2 + 6H2O → (sunlight) C6H12O6 + 6O2 Reactants → CO2 and H2O Products → C6H12O6 and O2

What are the most common elements in the human body?

96.3% of body mass is made up of Oxygen (O), Carbon (C), Hydrogen (H), Nitrogen(N) Calcium (Ca), phosphorus (P), potassium (K), sulfur (S) make up the remaining four percent or so.

Hydrogen bond

Attraction between a hydrogen and an electronegative atom (usually oxygen or nitrogen atoms).

What are some of the common atoms found in biologically important compounds?

Carbon Hydrogen Oxygen Nitrogen Sulfur Phosphorus

Why is water such a versatile solvent?

Because of the polarity of the water molecule

What are the four main groups of macromolecules found in living things?

Carbohydrates Lipids Proteins Nucleic Acids

What are carbohydrates? Distinguish between monosaccharides and polysaccharides and give some examples of each.

Carbohydrates → Include sugars and polymers of sugars. Monosaccharides → Simple sugars, monomers from which more complex carbohydrates are built. Generally have molecular formulas that are some multiple of the unit CH2O. Ex: Glucose(classified as aldose), Fructose(isomer of glucose, classified as ketose) Disaccharides → Double sugars, consisting of two monosaccharides joined by a glycosidic linkage, a covalent bond formed between two monosaccharides by a dehydration reaction. Ex: Maltose (two glucose molecules) and Sucrose (table sugar, glucose and fructose are monomers) and Lactose (glucose and galactose) Polysaccharides → Macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages. Used for storage material or building material for structures that protect cell or organism. Ex: Starch, Glycogen, Cellulose

What are the "building blocks" for each of these macromolecules?

Carbohydrates → Monosaccharides Lipids → Fatty Acid Proteins → Amino acids Nucleic Acids → Nucleotides

Describe the following extracellular components (composition, general structure/functions):

Cell wall Extracellular structure of plant cells Protects plant cell, maintains shape, and prevents excessive uptake of water. Hold the plant up against the force of gravity Much thicker than plasma membranes. Microfibrils made of polysaccharide cellulose are synthesized by an enzyme called cellulose synthase and secreted to the extracellular space, where they become embedded in a matrix of other polysaccharides. Strong fibers in a "ground substance" (matrix). Extracellular matrix In animal cells Main ingredients are glycoproteins and other carbohydrate-containing molecules secreted by the cells. Most abundant glycoprotein is collagen, which forms strong fibers outside of the cells. Regulate a cell's behavior Structural support

What does cohesion refer to? Adhesion? Explain how these properties are important for water transport through a plant

Cohesion → Hydrogen bonds holding the substance together, multiple hydrogen bonds make water more structured than most other liquids. Cohesion contributes to transport of water and dissolved nutrients against gravity in plants. Water from the roots reach leaves through a network of water-conducting cells. Then, when water evaporates, hydrogen bonds cause water molecules leaving the veins to tug on the water molecules farther down. This upward pull is transmitted through the network all the way to the roots. Adhesion → Clinging of one substance to another Adhesion by hydrogen bonds to the molecules of cell walls helps counter downward pull of gravity.

What do amino acids all have in common? How do they differ?

Common Share a common structure Each has a side chain Differ Side chains are different Physical and chemical properties of side chain determine unique characteristics of amino acid, thus affecting its functional role in a polypeptide (ex: nonpolar side chains make amino acid hydrophobic)

Describe DNA structure and base pairing. Draw one 6 base strand of DNA and then the complementary strand.

DNA molecules have two polynucleotides (or "strands") that wind around an imaginary axis, forming a double helix. Held together by hydrogen bonds between the base pairs. Very long, with thousands or even millions of base pairs. Adenine (A) in one strand always pairs with thymine (T) in the other. Guanine (G) always pairs with cytosine (C)

Distinguish between a dehydration reaction and hydrolysis in regard to macromolecules.

Dehydration Reaction → Reaction in which two molecules are covalently bonded to each other with the loss of a water molecule. When a bond forms between two monomers, each monomer contributes part of the water molecule that is released during reaction. One provides a hydroxyl group (OH) while the other provides a hydrogen (H). Hydrolysis → Process that is essentially the reverse of the dehydration reaction. Means water breakage, so the bond between monomers is broken by the addition of a water molecule with a hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other.

why is water polar

Polar molecule because unequal sharing of electrons (polar covalent bonds between O and H) and water's V-like shape makes the overall charge unevenly distributed. Oxygen → 𝛅- (partial negative charge) Hydrogen → 𝛅+ (partial positive charge)

What does denaturation and renaturation of a protein involve? What types of conditions can contribute to these processes?

Denaturation → If the pH, salt concentration, temperature, or other aspects of its environment are altered, the weak chemical bonds and interactions within a protein may be destroyed, causing the protein to unravel and lose its native shape. This change is called denaturation. Protein transferred from aqueous environment to nonpolar solvent Chemicals that disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain a protein's shape. Can result from excessive heat. Renaturation → If the denatured protein remains dissolved, it may renature when the chemical and physical aspects of its environment are restored to normal.

What determines the chemical behavior of an atom

Determined by the distribution of electrons in the atom's electron shells. Depends mostly on the number of electrons in its outermost shell (valence electrons)

What is an isotope?

Different atomic forms of the same element Neutrons vary among isotopes while protons and electrons remain the same

Lysosomes

Digestive organelle where macromolecules are hydrolyzed

Why is carbon so versatile in creating large molecules

Electron configuration → With four valence electrons, each carbon atom acts as an intersection point from which a molecule can branch off in as many as four directions enabling carbon to form large, complex molecules Valence → Number of covalent bonds it can form. Electron configuration of carbon gives it covalent compatibility with many different elements

Explain electronegativity in covalent bonding. Distinguish between nonpolar and polar covalent bonds.

Electronegativity → The attraction of a particular atom for the electrons of a covalent bond Nonpolar covalent bond → Covalent bond between same two elements or elements with the same electronegativity. Electrons are shared equally. Polar covalent bond → Covalent bond when an atom is bonded to a more electronegative atom. Electrons of the bond are not shared equally.

What are some functions of nucleic acids? What are these polymers formed from?

Enable living organisms to reproduce their complex components from one generation to the next. Controls protein synthesis Made of monomers called nucleotides

Explain evaporative cooling. Provide an example of how this property benefits living organisms.

Evaporative Cooling → As a liquid evaporates, the surface of the liquid that remains behind cools down (its temperature decreases). Occurs because the "hottest" molecules (the ones with greatest kinetic energy) are the most likely to leave as gas. Contributes to stability of temperature in lakes and ponds and provides a mechanism that prevents terrestrial organisms from overheating. Ex: Evaporation of sweat from human skin dissipates body heat and helps prevent overheating.

Distinguish between each of the following types of lipids and give examples (name and function): fats, phospholipids, steroids

Fats → Constructed from two kinds of smaller molecules: glycerol and fatty acids. Ex: Adipose tissue which stores energy, cushions vital organs like kidneys, and insulates the body. Phospholipids → Similar to a fat molecule but has only two fatty acids attached to a glycerol rather than three. Third hydroxyl group of glycerol is joined to a phosphate group which has a negative electrical charge. Typically an additional small charged or polar molecule is also linked to phosphate group like choline. Ex: Bilayer which shields their hydrophobic fatty acid tails from water. Forms boundary between cell and external environment. Steroids → Lipids characterized by a carbon skeleton consisting of four fused rings. Ex: Cholesterol is common component of animal cell membranes and is precursor from which other steroids (like vertebrae sex hormones) are synthesied. Cholesterol is synthesized in the liver and is also obtained from the diet.

Distinguish between hydrophobic and hydrophilic and give an example of a substance with one property or the other.

Hydrophobic → Substances that are nonionic and nonpolar(or otherwise cannot form hydrogen bonds) actually seem to repel water. Ex: vegetable oil Hydrophilic → Any substance that has an affinity for water (doesn't have to dissolve to be hydrophilic) ex: Cotton, cellulose Colloid → A stable suspension of fine particles in a liquid

What does genomics refer to? Proteomics?

Genomics → Looking at problems by analyzing large sets of genes or even comparing whole genomes of different species. Proteomics → Similar analysis to genomics of large sets of proteins, including their sequences.

What is the endomembrane system?

Includes the nuclear envelope, the ER, the Golgi apparatus, lysosomes, various kinds of vesicles and vacuoles, and the plasma membrane Carries out a variety of tasks in the cell, including synthesis of proteins, transport of proteins into membranes and organelles or out of the cell, metabolism and movement of lipids, and detoxification of poisons. Membranes are related either through direct physician continuity or by the transfer of membrane segments as tiny vesicles (sacs made of membrane).

What are ions? cations? anions? Why are drugs often manufactured as salts?

Ions → Forms when an atom or molecule gains or loses an electron and becomes charged. Cation → Positively charged ion Anion → Negatively charged ion Compounds formed by ionic bonds are called ionic bonds or salts. Most drugs are manufactured as salts because they are quite stable when dry but can dissociate easily in water.

What are isomers

Isomers → Compounds that have the same number of atoms of the same elements but different structures and hence different properties Structural isomers have different covalent arrangements of their atoms Cis-trans isomers → Carbons have covalent bonds to same atoms but these atoms differ in their spatial arrangements due to their inflexibility of double bonds Enantiomers → Isomers that are mirror images of each other and that differ in shape due to presence of asymmetric carbon.

vacuole

Large vesicles derived from endoplasmic reticulum and golgi apparatus. Food → Formed by phagocytosis, for Contractile → Eukaryotes living in fresh water have it bc it pumps excess water out of the cell, thereby maintaining a suitable concentration of ions and molecules inside the cell. Central → Many plant cells contain this. Functions include storage breakdown of waste products, and hydrolysis of macromolecules; enlargement of the vacuole is a major mechanism of plant growth

Identify the ways that carbon skeletons can vary

Length → vary in length Branching → skeletons may be unbranched or branched Double bond position → skeleton may have double bonds which can vary in numbers and location Presence of rings → some skeletons are arranged in rings

Distinguish between the components of the cytoskeleton. Provide an example of structures they form and the roles of those structures with in the cell.

Microtubules → Thickest; hollow robes constructed from globular proteins called tubulins. Shape and support the cell and also serve as tracks along which organelles equipped with motor proteins can move. Guide vesicles from ER to Golgi apparatus and from Golgi to plasma membrane. Involved in separation of chromosomes during cell division. Make up flagella and cilia, which helps move the cells through water. Microfilaments(action filaments) → Thinnest; solid rods and are built from a globular protein called actin. Can form structural networks when certain proteins bind along the side of such a filament and allow a new filament to extend as a branch. Makes up the cortex, the semisolid consistency of a gel → outer cytoplasmic layer of a cell Intermediate filaments → Fibers with diameters in middle range; diverse class of cytoskeletal elements. Each type is constructed from a particular molecular subunit belonging to a family of proteins whose members include the keratins. More permanent fixtures of cells. Play an important role in reinforcing the shape of a cell and fixing the position of certain organelles. Nucleus sits within a cage made of intermediate filaments that extend into cytoplasm.

Endoplasmic reticulum (smooth and rough)

Network of membranous sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes; has rough (ribosome-studded) and smooth regions. Rough → Makes proteins Smooth → Makes lipids

Nucleus/ nuclear envelope

Nucleus is made up of nuclear envelope, nucleoli, and chromatin Nuclear Envelope → Double membrane enclosing the nucleus; perforated by pores; continuous with ER Nucleolus → Non Membranous structure involved in production of ribosomes; a nucleus has one or more nucleoli Chromatin → Material consisting of DNA and proteins; visible in a dividing cell as individual condensed chromosomes

Atomic Number

Number of protons, which is unique to each element

Explain the concern regarding ocean acidification. (What is it and how does it affect aquatic ecosystems).

Ocean acidification → Process of when CO2 dissolves in seawater, it reacts with water to form carbonic acid Alters delicate balance of conditions for life in the oceans pH drops due to this, which can decrease carbonate ion concentration as H+ ions react with it to create bicarbonate ions. Carbonate ions are needed for calcification which is production of calcium carbonate by many marine organisms including reef-building coats and animals that build shells. Coral reefs are sensitive and this change would cause the ecosystems to disappear, which would be a terrible loss to biological diversity.

Radioactive isotope and uses

One in which the nucleus decays spontaneously, giving off particles and energy. When the radioactive decay leads to a change in the number of protons, it transforms an atom to an atom of a different element. Ex: Carbon-14 atom decays, neutron decays into proton, transforms atom into nitrogen atom. Useful applications Radioactive Tracers → Diagnostic tools in medicine. The radioactive isotopes are incorporated into biologically active molecules, which are then used as tracers to track atoms during metabolism (chemical processes of organism). Also used in combination with imaging instruments like PET scanners Radiometric Dating → Use radioactive decay in fossils to date fossils. See the half-life of the isotope (the time it takes for 50% of the parent isotope to decay) and then scientists would measure the ratio of diff isotopes and calculate how many half-lives have passed since an organism was fossilized or a rock was formed. Diagnostic purposes

Golgi apparatus

Organelle active in synthesis, modification, sorting, and secretion of cell products

Peroxisomes

Organelle with various specialized metabolic functions; produces hydrogen peroxide as a by-product and then converts it water

What type of bond holds amino acids together?

Peptide bond → a covalent bond formed between two amino acids by a dehydration reaction.

Chlroplast

Photosynthetic organelle; converts energy of sunlight to chemical energy stored in sugar molecules

What determines the characteristics of amino acids and how does this impact the overall structure and function of a polypeptide?

Physical and chemical properties of side chain determine unique characteristics of amino acid, thus affecting its functional role in a polypeptide (ex: nonpolar side chains make amino acid hydrophobic) Extending from the backbone of polypeptide are different side chains of the amino acids. Polypeptides differ in length and each one has a unique linear sequence of amino acids. Chemical nature as a whole is determined by the kind and sequence of the side chains, which determine how a polypeptide folds and thus its final shape and chemical characteristics.

Identify and distinguish between the various forms of cell junctions: plasmodesmata, tight junctions, desmosomes, gap junctions.

Plasmodesmata → Cell walls are perforated with these channels that connect cells. Tight Junctions → Plasma membranes of neighboring cells are very tightly pressed against each other, bound together by specific proteins. Establish a barrier that prevents leakage of extracellular fluid across a layer of epithelial cells. Desmosomes → Function like rivets, fastening cells together into strong sheets. Intermediate filaments made of keratin proteins anchor desmosomes in the cytoplasm. Attach muscle cells to each other in a muscle. Gap junctions → Provide cytoplasmic channels from one cell to an adjacent cell and in this way are similar in their function to the plasmodesmata in plants. Consist of membrane proteins that surround a pore through which ions, sugars, amino acids, and other small molecules may pass. Necessary for communication between cells ins many types of tissues.

Chemical equilibrium

Point at which the reactions offset one another exactly. Forward and reverse reactions are still going (occuring at the same rate) but there are no changes in the concentrations of reactants and products (not equal, but at a particular ratio).

Cytoskeleton

Reinforces cell's shape; functions in cell movement; components are made of protein Includes Microfilaments, Intermediate filaments, Microtubules

Describe the difference between a saturated and unsaturated fatty acid.

Saturated Fatty Acid → If there are no double bonds between carbon atoms composing a chain, then as many hydrogen atoms as possible are bonded to the carbon skeleton. Such a structure is said to be saturated with hydrogen. Unsaturated Fatty Acid → One or more double bonds with one fewer hydrogen atom on each double-bonded carbon.

Covalent bond

Sharing of a pair of valence electrons by two atoms. Nonpolar covalent are those with the same electronegativity and polar covalent is when electrons are not shared equally due to electronegativity differences.

Electron shells

Shells around the nucleus that hold electrons, each with a characteristic average distance and energy level. Electron state of potential energy is called its energy level, or electron shell. Potential energy is energy that matter has based on location or structure.

Distinguish between prokaryotic and eukaryotic cells

Similarities All bounded by a selective barrier, called the plasma membrane (or cell membrane) Inside, semifluid, jellylike substance called cytosol, in which subcellular components are suspended. All cells contain chromosomes, which carry genes in the form of DNA All have ribosomes, tiny complexes that make proteins according to instructions from the genes. All have interior called cytoplasm (in eukaryotic cells, refers only to region between nucleus and plasma membrane) Through parts of cellular respiration Some have cell walls Both have organisms which can photosynthesize Prokaryotic → DNA is concentrated in a region that is not membrane enclosed, called the nucleoid Membrane bounded structures are absent in almost all prokaryotic cells. Not formless soup though bc some of them contain regions surrounded by proteins, within which specific reactions take place. Smaller Circular chromosomes Eukaryotic → Most of the DNA is in an organelle called the nucleus, which is bounded by a double membrane. Variety of organelles of specialized form and function. Much larger Linear chromosomes

What is an atom and how does it relate to elements?

Smallest unit of matter that still retains the properties of an element. Each element consists of a certain type of atom that is different from the atoms of any other element.

Distinguish between a solution, solvent and a solute

Solution → A liquid that is a completely homogeneous mixture of two or more substances (aqueous solution is one in which the solute is dissolved in water) Solvent → Dissolving agent of a solution (i.e. water) Solute → Substance that is dissolved in solution (i.e. sugar)

What is specific heat? How does water's high specific heat moderate costal climates?

Specific heat → Amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1 degree Celsius. Large body of water can absorb and store a huge amount of heat from the sun in the daytime and during summer while warming up only a few degrees. At night and during winter, the gradually cooling water can warm the air. This capability serves to moderate air temperatures in coastal areas.

What are two examples of the functional roles of carbohydrates?

Storing sugars for later use. Ex: Plants storing starch. Animals storing glycogen. Building strong materials from structural polysaccharides. Ex:cellulose that make up the tough walls that enclose plant cells. Chitin for the exoskeletons of arthropods.

Mitochondria

THE POWERHOUSE OF THE CELL Organelle where cellular respiration occurs and most ATP is generated

Atomic mass

Total mass of an atom, just slightly different from mass number b/c neutrons and protons each have a mass very close to 1 dalton.

Mass number

Total number of protons and neutrons

What are trace elements?

Trace Elements are required by an organism in only minute quantities. Some (like iron) are needed by all forms of life while others are required by only certain species Ex: Iron (Fe), Cobalt (Co), Boron (B), Fluorine (F)

What is a trans-fat and what are the health concerns related to consumption of this form of lipid?

Trans-fat → Process of hydrogenating vegetable oils produces not only saturated fats but also unsaturated fats with trans double bonds. Can contribute to coronary heart disease.

Distinguish between the size of cells/structures visible with the unaided eye, light microscope or electron microscope. What is the average range in cell diameter?

Unaided eye → 100 micrometers (10-4 meters) to 10 meters Light microscopy → 100 nanometers (10-7 meters) to just above 1 millimeter. (magnify effectively to about 1000 times the actual size of the specimen) Super resolution microscopy → 10 nanometers (10-8 meters) to just above 1 millimeter Electron microscopy → 1 nanometer (10-9 meters) to 100 micrometers (10-4 meters) Average range of cell diameter → Between 1 and 100 micrometers.

Dalton

Unit of measurement for atoms and subatomic particles (including molecules) in honor of John Dalton who developed atomic theory in around 1800. Same as atomic mass unit (amu)

Why is water less dense as a solid then a liquid and what importance does this characteristic have on living organisms?

Water less dense as solid than a liquid bc water expands instead of contracting and becoming denser when solidified like in other materials. Cause of this is hydrogen bonding. When water at 0 degrees Celsius, hydrogen bonds keep molecules far enough apart to make ice about 10% less dense than liquid water at 4 degrees Celsius. Important for living organisms because this allows ice to float, which doesn't freeze bodies of water. The floating ice insulates the liquid water below preventing it from freezing and allowing life to exist under frozen surface. The ice also provides habitat for animals like polar bears.

What does pH refer to? What is an acid? Base? A buffer?

pH → Defined as the negative logarithm (base 10) of the hydrogen ion concentration pH = -log[H+] Neutral aqueous solution at 25 degrees C→ -log(10-7) = -(-7) = 7 pH decreases as H+ concentration increases Acid → Substance that increases the hydrogen ion concentration of a solution. Base → Substance that reduces the hydrogen ion concentration of a solution Buffer → A substance that minimizes changes in the concentrations of H+ and OH- in a solution. Ex: carbonic acid-bicarbonate buffering system that consists of an acid and a base in equilibrium with each other in blood. Note: hydroxide (OH-) and hydronium (H3O+) and hydrogen ion (H+) Note: [H3O+][OH-] = 10-14