Bio Unit 1

What is biology?

What is biology?

The study of life

Characteristic of life: order

Living organisms have organized structures.

Characteristic of life: energy processing

obtaining fuel and using the chemical energy stored in the food to power work.

Characteristic of life: growth and development

inherited information carried by genes controls the pattern of growth and development.

Characteristic of life: response to the environment

responding to external stimuli

Characteristic of life: Evolutionary adaptation

adaptations that evolve over countless generations by reproductive success of those individuals with heritable traits that are best suited to their environments.

Characteristic of life: regulation

regulation of blood vessels which helps maintain a constant body temp, by adjusting heat exchange with the surrounding air

Characteristic of life: reproduction

Reproducing to make a new organism of the same kind

Levels of biology: molecules

chemical structure consisting of two or more units called atoms

Levels of biology: organelles

various functional components present in cells

Levels of biology: cells

life's fundamental unit of structure and function

Levels of biology: tissues

a group of cells that work together, performing a specialized function

Levels of biology: organ

body part that is made up of multiple tissues and has specific functions in the body.

Levels of biology: organism

individual living things

Levels of biology: population

all the species living within the bounds of a specified area that interbreed with each other

Levels of biology: communities

the array of organisms inhabiting a particular ecosystem is called a community

Levels of biology; ecosystems

all the living things in a particular area, along with all the nonliiving components of the environment with which life interacts, such as soil, water, atmospheric gases, and light.

Levels of biology: Biosphere

all life on earth and the places where life exists.

Core themes of biology

a. Life requires expression and transmission of genetic material

b.Life requires the transfer and transformation of energy and matter

c. New properties emerge at successive levels of organization,

Model organism

A non- human species that has been extensively studied and is easy to maintain and reproduce in a laboratory setting, as well as having specific experimental benefits.

Evolution

Evolution is a process of biological change where species accumulate differences from their ancestors as they adapt to different environments over time

Natural selection

Natural selection: the national environment consistently "selects" for the propagation of certain traits among naturally occurring variant traits in the population.

Three domains of life

bacteria, archaea, eukarya (protists, fungi, plants, animals)

What is the difference between a prokaryote and eukaryote?

Prokaryote: single called organism, few pieces of DNA, either a bacteria or archaea.

Eukaryote: nucleus, membrane bound organelles, endomembrane structures

What is the scientific method?

A process of inquiry that includes making observations, forming logical, testable explanations (hypotheses), and testing them.

Other than use of the scientific method, how else is knowledge gained in biology?

Theories? Idk

Macromolecule

large carbohydrates, proteins, and nucleic acids that are big.

Polymer

a long molecule consisting of many similar or identical building blocks linked by covalent bonds.

How are polymers made?

Polymers are made by a condensation reaction, where two molecules are covalently bonded to each other with the loss of a small molecule. If a water molecule is lost, it is known as a dehydration reaction.

How are polymers broken down?

Polymers are broken down by hydrolysis, the reverse of the dehydration reaction. Hydrolysis means water breakage, where the bond between monomers is broken by the addition of a water molecule, with a hydrogen attaching to one monomer, and the hydroxyl attaching to the other.

Example of condensation:

Carbohydrate and protein polymers are synthesized by dehydration reactions. One provides a hydroxyl group (OH-) while the other provides a hydrogen (H-). The reaction is repeated as monomers are added to the chain, making the polymer longer.

Example of hydrolysis:

digestion. The organic material in our food is in the form of polymers that are too big to enter the cells. In the digestive tract, enzymes attack the polymers, speeding up hydrolysis. The monomers are then absorbed into the bloodstream for distribution to all body cells

Criteria needed to identify a molecule as a monosaccharide

- have molecular formulas that are some multiple of the unit CH2O.

- have a carbonyl group > C = O

- multiple hydroxyl groups.

- size of carbon skeleton, which ranges from 3-7 carbons long.

Sugars, other than glucose:

Lactose, Galactose, Fructose, Sucrose

Starch

a polymer of glucose monomers, as granules within cellular structures known as plastids (including chloroplasts)

Glycogen

a polymer of glucose that is like amylopectin but more extensively branched. Vertebrates store glycogen mainly in liver and muscle cells. Breakdown of glycogen in the liver/muscles release glucose when the demand for energy increases. This stored fuel cannot sustain an animal for long, in humans, glycogen stores are depleted in a day, unless we eat

Cellulose

organisms build strong materials from structural polysaccharides. Cellulose is a major component of the tough walls that enclose plant cells. It is a polymer of glucose.

How are starch, glycogen, and cellulose the same? How are they different?

Similarities: they are all polysaccharides of glucose.

Differences: Starch is the main carbohydrate in plants, while cellulose is the main component of plant cell walls and glycogen is the main carb energy source in fungi and animals.

Fatty acid

combines with a glycerol molecule to compose a fat. A fatty acid has a long carbon skeleton, usually 16-18 carbon atoms in length. The carbon at one end of the skeleton is part of a carboxyl group, the functional group that gives these molecules the name fatty acid. The rest of the skeleton consists of a hydrocarbon chain. The nonpolar C-H bonds in the hydrocarbon chains of fatty acids are the reason fats are hydrophobic. Fats separate from water because the water molecules hydrogen bond to one another and exclude the fats

Triacylglycerol

A lipid consisting of three fatty acids linked to one glycerol molecule; also called a fat or triglyceride.

How is a phospholipid different from a triacylglycerol?

Like triglycerides, phospholipids have a glycerol backbone. But unlike triglycerides, phospholipids only have two fatty acid molecules attached to the glycerol backbone

Three functions of proteins

Fighting disease, producing euphoria, relieving pain

How are amino acids categorized?

They are categorized according to the properties of their side chains. One group consists of amino acids with nonpolar side chains, which are hydrophobic. Another group consists of amino acids with polar side chains, which are hydrophilic. Acidicic amino acids have side chains that are generally negative in charge due to the presence of a carboxyl group, Basic amino acids have amino groups in their side chains that are generally positive in charge.

Peptide

smaller versions of proteins that are made of short strings of amino acids. When two amino acids are positioned so the carboxyl group of one is adjacent to the amino group of the other, they can become joined by a dehydration reaction, with the removal of a water molecule. The resulting covalent bond is called a peptide bond.

Polypeptide:

a polymer of many amino acids linked by peptide bonds. The polypeotide has a repetitive backbone to whic the amino acid side chains are attached.

Primary structure of protein

a protein's sequence of amino acids. The primary structure is determined by inherited genetic information. In turn, the primary structure dictates secondary and tertiary structure, due to the chemical nature of the backbone and the side chains of the amino acids along the polypeptide. (example: Transthyretin - a blood prortein. It's made of 4 identical polypeptide chains, each composed of 127 amino acids. Each of the 127 positions along the chain is occupied by one of 20 amino acids.)

Secondary structure of proteins

coils and folds in patterns that contribute to the protein's overall shape. The secondary structure is a result of hydrogen bonds between the repeating constituents of the polypeotide backbone (not amio acid side chains.) Oxygen atoms have a partial negative charge, and the hydrogen atoms attached to the nitrogen atoms have a partial positive charge. Weak hydrogen bonds form between these atoms; because they are repeated over a long region of the polypeptide chain, they can support the shape of the protein

α-helix

a delicate coil held together by hydrogen bonding between every 4th amino acid. (example, α-keratin, the structural protein of hair, has the α-helix formation over most of it's length)

B-pleated sheet

two or more segments of the polypeptide chain lying side by side (called -strands) are connected by hydrogen bonds between parts of the two parallel segments. -pleated sheets make up the core of many globular proteins, as the case for Transytherin, and dominate some fibrous proteins. (ex. Silk protein of a spider's web. Many hydrogen bonds makes each spider silk thread stronger than a steel strand.)

Describe the basic structure of an atom. What is an atom made of?

An atom is the smallest unit of matter that still retains the properties of an element. They are made of neutrons, protons(+), and electrons(-). The protons and neutrons are packed tightly in the nucleus at the center of an atom.

Mass number = number of protons and neutrons.

Atomic = number of protons

Number of neutrons = mass number - atomic number

Approximately, how many elements are necessary in the human body? Which four are the most important?

Humans need 25 elements. The important four are oxygen, carbon, hydrogen, and nitrogen.

Isotope

Isotope - different atomic forms of the same element. All atoms of a given element have the same number of protons, but some atoms have more neutrons than other atoms of the same element, and therefore have greater mass.

What is the difference between a compound and a molecule?

A molecule is two or more atoms held together by covalent bonds. A compound is made by two or more different elements.

How many electrons can the first and second electron shells hold? What about the orbitals?

The first shell can hold up to 2 electrons, and the second shell can hold up to eight electrons.

The orbital is the three-dimensional space where an electron is found 90% of the time. The first shell has a 1s orbital, while the second shell has a 2s orbital, and three 2p orbitals.

Which shells have more energy? How many orbitals are part of the first and second shell and how many electron do they hold?

Shells 2 and 3 have the most energy.

The lone electron of a hydrogen atom occupies the 1s orbital, as do the 2 electrons of a helium atom. The second shell can hold up to 8 electrons, but with 2 shells in each orbital.

What happens to the valence shells (what is the valence shell?) of atoms when they form covalent bonds?

Covalent bond is the sharing of a pair of valence electrons by two atoms. When valence shells form covalent bonds, they share their electrons. For example, hydrogen. When two hydrogens share a covalent bond, they share their electrons, so the molecule has a complete valence electron shell.

How is an ionic bond (what is it and how is it formed?) different from a covalent bond?

Ionic bond: Cations(+) and anions(-) attract each other because of their opposite charges. The transfer of electrons in an ionic compound allows a bond to form because it results in two ions of opposite charge. Any two ions of opposite charge can form an ionic bond. The ions do not need to have acquired their charge by an electron transfer with each other.

Example: NaCl. Na gives an electron to Chlorine, so that Chlorine's electron shells are full. Na+ becomes more positive because it loses an electron. Cl- becomes negative because it gains a negative electron. In a covalent bond, two atoms share electrons, rather than one giving to the other.

What is a hydrogen bond and how do they form? What types of molecules are involved?

Hydrogen bond: noncovalent attraction between a hydrogen and an electronegative atom. When a hydrogen atom is covalently bonded to an electronegative atom, the hydrogen atom has a partial positive charge that allows it to be attracted to a different electronegative atom with a partial negative charge nearby.

In living cells, the hydrogen usually bonds with oxygen or nitrogen atoms.

What other type of non-covalent bond exists and how do they work?

Another non-covalent bond is in a van der Waals interaction. Electrons aren't always evenyl distributed, and they may accumulate by chance in one part of a molecule or another. This results in ever changing regions of positive and negative charge that enables all atoms and molecules to stick to one another. These interactions are individually weak and occur only when atoms and molecules are very close together. Example: van der waals allow a lizard to walk up a wall. The interactions between the lizard's foot molecules and the molecules of the wall's surface are so numerous that despite their weakness, they can support the lizard's body weight.

What is a chemical reaction?

A chemical reaction is the making and breaking of chemical bonds, leading to changes in the composition of matter. One example is the reaction between hydrogen and oxygen molecules that forms water.

What does it mean when a chemical reaction reaches equilibrium?

When a chemical reaction reaches equilibrium, it means that the products of the forward reaction become the reactants for the reverse reaction. Basically when the rate of the forward reaction equals the rate of the reverse reaction. The two opposite headed arrows indicate that the reaction is reversible. Equilibrium doesnt' meant that the reactants and products are equal in concentration, but only that their concentrations have stabilized at a particular ratio.

What is water? Describe the structure of water (including its asymmetrical shape and polarity).

Water is a polar molecule. The oxygen has partial negative charges because it pulls electrons toward itself. The hydrogen atoms have partial positive charges. Weak attractions between oppositely charged regions of water molecules, called hydrogen bonds, allow water molecules to bond to each other. Oxygen can form two hydrogen bonds. Each water molecule can hydrogen bond to several others, these associations are always changing.

Water has cohesive properties, meaning

hydrogen bonds holding water together. Water molecules stay close together as a result of hydrogen bonding. Even though the arrangement of molecules in a sample of liquid water is constantly changing, many of the molecules are linked by multiple hydrogen bonds. These linkages make water more structured than other liquids.

Water has adhesive properties, meaning

the clinging of one substance to another. Adhesion of water by hydrogen bonds to the molecules of cell walls helps counter the downward pull of gravity when transporting water throughout plants.

What is the difference between the cohesion and adhesion of water?

Cohesion is water being held together, but adhesion is water sticking to something else.

Water has high specific heat,

the specific heat is defined as the amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1 degree Celsius. The specific heat of water is 1 calorie per gram and per degree Celsius. Because of its high specific heat, water will change its temperature less than other liquids when it absorbs or loses a given amount of heat.

Water has high heat of vaporization

the heat of vaporization is the quantity of heat a liquid must absorb for 1 g of it to be converted from the liquid to the gaseous state. To evaporate 1g of water at 25 degrees C, about 580 cal of heat is needed, nearly double the amount needed- nearly double the amount needed to vaporize a gram of alcohol or ammonia.

Water has high surface tension

measure of how difficult it is to stretch or break the surface of a liquid. (example, a spider walking across water)

Evaporative cooling

as liquid evaporates, the surface of the liquid that remains behind cools down (its temperature decreases). This evaporative cooling occurs because the "hottest molecules," those with the greatest kinetic energy, are the most likely to leave as gas. Evaporation of sweat from human skin dissipates body heat and helps prevent overheating on a hot day or when excess heat is generated by strenuous activity.

Solid ice that is less dense than liquid

In liquid water, the hydrogen bonds constantly break and re-form. As a result, the water molecules can slip closer together. In ice, the hydrogen bonds are stable and the water moluecles are faterhter apart. This means that ice is less dense than liquid water, so it floats.

What does it mean to state that water "dissolves" substances?

Many compounds made up of nonionic polar molecules, such as the sugar in the sugar cube mentioned earlier are also water soluble. These compounds dissolve when water molecules surround each ofht esolute molecules, forming hydrogen bonds with them. Even if molecules as large as proteins can dissolve in water if they have ionic and polar regions on the surface. Many polar compounds and ions are dissolved in the water of such biological fluids as blood, the sap of plants, and the liquid within all cells.

What does it mean to state that water ionizes? What happens to water?

To state that water ionizes means that it produces hydronium (H30+) and Hydroxide (OH-). When water is ionized, it is separated into hydrogen and oxygen molecules using an electric current. It creates acidic water and alkaline water

In general terms, what is pH?

pH is a scale of the acidity levels of substances/solutions. This is based on the concentration of H+ and OH- ions.

What is an acid? What is a base? Why might a strong acid or base be harmful?

An acid is a solution that is highly concentrated in H+ ions. A basic solution is one that has a high concentration of OH-

Strong acids or bases can be corrosive and attack human tissues

What did the Urey-Miller experiment show?

Miller set up a closed system to mimic conditions thought at time to have existed on the early Earth. A flask of water stimulated the primeval sea. The water was heated so some vaporized and moved into a second, higher flask containing the "atmosphere" - a mixture of gases. Sparks were discharged in the synthetic atmosphere to mimic lightning. In the results, Miller identified organic molecules that are common in organisms, which included formaldehyde, hydrogen cyanide, and amino acids and hydrocarbons. The experiment showed that organic molecules may have been synthesized abiotically on the early Earth.

What is organic chemistry? What elements are most biological molecules made of?

- organic chemistry is the study of carbon compounds. Most molecules are made of carbon.

How many atoms can a carbon atom covalently bind to (in other words, how many pairs of electrons can be shared between a carbon atom and other atoms)? Why?

4 atoms - because 4 more bonds and electrons would allow the carbon to be stable with 8 valence electrons.

What is a hydrocarbon? What is a hydrocarbon skeleton?

A hydrocarbon is an organic molecule consisting of only carbon and hydrogen.

A hydrocarbon skeleton is made up of carbon atoms bonded to ecah other.

Disulfide bridges

covalent bonds that can further reinforce the shape of a protein. They form where two cysteine monomers, which have sulfhydryl groups (-SH) on their side chains are brought close together because of the folding of the protein. The sulfer of one cysteine bonds to the sulfer of the second, and the disulfide bridge (-S-S-) rivets part of the protein together. These different interactions can contribute to the tertiary structure of a protein.

Quarternary structure

the overall protein structure that results from the aggregation of these polypeptide subunits. Some proteins consist of two or more polypeptide chains aggregated (formed by the combination of many separate items) into one functional macromilecule.

Examples: collagen and hemoglobin

DNA

is structured in the form of a double helix. The two sugar-phosphate backbones run in opposite of 5' → 3' directions from each other; this arrangement is referred to antiparalle. The sugar phosphate backbones are on the outside of the helix, and the nitrogenous bases are paired in the interior of the helix. The two strands are held together by hydrogen bonds between the paired bases. Most DNa molecules are very long. A pairs with T, C pairs with G

RNA

Roughly L-Shaped, due to complementary base pairing of antiparallel stretches of RNA. In RNA, A pairs with U.

polar covalent bonds

unequal sharing of electrons

polar molecule

molecule with an unequal distribution of charge, resulting in the molecule having a positive end and a negative end

buffer

A solution that minimizes changes in pH when extraneous acids or bases are added to the solution.

organic chemistry

studying compounds containing carbon

What is an isomer? How are structural isomers, cis/trans isomers and enantiomers different from each other?

Isomers are compounds that have the same numbers of atoms of the same elements, but different structures and different properties.

Structural isomers -differ in the arrangement of covalent bonding partners

Cis-trans isomers differ in arrangement about a double bond.

Entiaomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands.

Hydroxyl group

OH-

Carbonyl

C=O

Amino group

-NH2

Sulfhydryl

-SH

phosphate group

-OPO3^2-

Methyl group

-CH3

Tertiary structure of protein

overall shape of a polypeptide resulting from interactions between the side chains (R-groups) of the various amino acids. A hydrophobic interaction : as a polypeptide folds into its functional shape, amino acids with hydrophobic (nonpolar) side. Meanwhile, hydrogen bonds between polar side chains and ionic bonds between positively and negatively charged side chains help stablilze tertiary structure. These are all weak interactions in the aqueous cellular environment, but their cumulative effect helps give the protein a unique shape.