Unit 1 chapter 2-3 studyguide

Electronegativity

atoms in a molecule attract shared bonding electrons to varying degrees, depending on the element. the attraction of a particular atom for the electrons of a covalent bond is called this. the more electronegative an atom is, the more strongly it pulls shared electrons toward itself.

define acid, base, and the pH scale

base: When a substance has more OH- ions than H+ ions. acid: When a substance has more H+ ions than OH- ions pH scale: The typical pH scale runs from 0 - 14. A pH of 7 is neutral, a pH < 7 is called acidic while pH > 7 is called basic.

properties of water great solvent

because its polar molecules are attracted to ions and polar substances that can form hydrogen bonds.

List the four major classes of macromolecules.

carbohydrates, lipids, proteins, and nucleic acids

functional groups carboxyl

carboxylic acid or organic acid, examples are acetic acid

explain how a change in the subunits of a polymer may lead to changes in structures or function of the macromolecule

carbs- they compose of linear chains of sugar monomers connected by covalent bonds protein- Proteins comprise linear chains of amino acids, connected by the formation of covalent bonds at the carboxyl terminus of the growing peptide chain. lipids- Differences in saturation determine the structure and function of lipids. Phospholipids contain polar regions that interact with other polar molecules, such as water, and with nonpolar regions that are often hydrophobic nucleic acid- Adenine nucleotides pair with thymine nucleotides via two hydrogen bonds. Cytosine nucleotides pair with guanine nucleotides by three hydrogen bonds

pH formula

ex: What is the pH of a water sample that has a hydrogen ion concentration of 4.0 x 10-5? pH = -log10 [H+] = -log10 [4.0 x 10-5] = ans What is the hydrogen ion concentration of a solution with a pH of 5.6? pH = -log10 [H+] 5.6 = -log10 [H+] [H+] = 10^5.6 = ans

intermolecular forces

forces of attraction between molecules

(ethene) ethylene space-filling model

(draw your own)

ethane space filling model

(draw your own)

what is the difference between a polypeptide and a protein?

A polypeptide is a linear chain of amino acids linked by peptide bonds. A protein is a macromolecule that consists of one or more polypeptides folded into a conformation specified by the linear sequence of amino acids.

Scientific Method

A series of steps followed to solve problems

roles of carbon

All living things are made of chemicals based primarily around this. Carbon is so essential to life, that the study of Organic Chemistry is based solely on carbon compounds. •Carbon skeletons" form the backbone of many organic molecules.•They vary in length and shape.All of the molecules featured here are "hydrocarbons

Polysaccharides

A plymer of of up to over a thousand monosaccharides, formed by dehydration synthesis reactions.

explain how carbon's electron configuration accounts for its ability to form large, complex, and diverse organic molecules (due to the number of bonds it can form)

A carbon atom has 4 valence electrons, and has a strong tendency to form covalent bonds with other atoms in order to complete its octet. In an organic compound, a carbon atom could be bonded to as many as 4 other carbon atoms. Carbon atoms also readily form double bonds (in which 4 electrons are shared between 2 atoms) and triple bonds (in which 6 electrons are shared).

dehydration reaction

A chemical reaction in which molecules combine by releasing water. Monomers form larger molecules by dehydration reactions.

draw diagrams to illustrate dehydration synthesis and hydrolysis reactions. what role do these reactions play in forming or digesting organic compounds?

A dehydration reaction occurs when two monomers bond together through the loss of a water molecule. Dehydration reactions' role is to create polymers from monomers while hydrolysis' role is to split polymers into monomers.Dehydration = building up. Hydrolysis = breaking down.

Disaccharides

A double sugar, consisting of two monosaccharides joined by dehydration synthesis.

hydrolysis

Breaking down complex molecules by the chemical addition of water. Polymers can disassemble dehydration reactions by the reverse process, hydrolysis.

ethene (ethylene) molecular formula

C2H4

Ethane molecular formula

C2H6

examples of carbohydrates, lipids, proteins, and nucleic acids

CARBS: monosaccharides: glucose, fructose disaccharides: lactose, sucrose polysaccharides: cellulose, starch, glycogen, chitin LIPIDS: triaclyglycerols (fats or oils- 3 fatty acids + glycerol), fats, steroids, phospholipids (2 fatty acids + glycerol), cholesterol PROTEINS: enzymes, structural components, storage proteins, transport proteins, hormones, receptor proteins, motor proteins, defensive proteins NUCLEIC ACIDS: DNA: - sugar = deoxyribose - nitrogenous bases = CGAT - usually double-stranded RNA - sugar = ribose - nitrogenous bases = CGAU - usually single-stranded

Methane molecular formula

CH4

polymer

Chain-like molecules, consisting of many similar or identical building blocks linked by covalent bonds.

explain how water's cohesion and adhesion contribute to the movement of water from the roots to the leaves of a tree

Cohesion -> The binding together of like molecules, often by hydrogen bonds. Adhesion -> The attraction between different types of molecules.Adhesion makes the water stick to the tree and cohesion makes it travel up the roots.

distinguish between DNA and RNA (compare and contrast characteristics of each).

DNA: - sugar = deoxyribose - nitrogenous bases = CGAT - usually double-stranded RNA - sugar = ribose - nitrogenous bases = CGAU - usually single-stranded

list the major components of a nucleotide, and describe how these monomers are linked to form a nucleic acid

Pentose sugar, a phosphate group, and a nitrogenous base. The phosphate group of one nucleotide bonds with the pentose sugar of another nucleotide to form nucleic acids.

list and describe the 4 major components of an amino acid. draw a picture of the basic structure of an amino acid. (you do not need to memorize all 20 but you should know the basic structure, including the 4 main components of all amino acids!)

H (a hydrogen atom) NH2 (an amino acid functional group) COOH (a carboxyl functional group) a distinctive R group.

describe the basic structure of a hydrocarbon and explain why these molecules are hydrophobic.

Hydrocarbons consists of only carbon and hydrogen. The nonpolar C-H bonds in hydrocarbon chains account for their hydrophobic properties

Scientific method steps

Identify a question, research, form a hypothesis, experiment, collect and analyze data, conclusion, publish

using the bicarbonate buffer system in the body as an example, explain how buffers work. explain the importance of buffers in biological systems

It minimizes change in the pH when an acid or base is added. Bicarbonate acts as a pH regulator in blood. If hydrogen concentration in blood rises, the reaction proceeds to the left with HCO3 removing hydrogen ions from solution and forms H2CO3.

monomer

Make up polymers: connected by covalent bonds.

name the major functional groups found in organic molecules.

Methyl, hydroxyl, carbonyl, amino, carboxyl, sulfhydryl, phosphate

macromolecules

Molecules composed of thousands of atoms: the four main classes being carbohydrates, lipids, proteins, and nucleic acids (ALL OF THESE ARE POLYMERS). the MONOMERS that make up all of these are monosaccharides, fatty acids and glycerol, amino acids, and nucleotides.

distinguish between monomers and polymers

Monomers are the small molecules that make up a Polymer. A Polymer is a long chain consisting of monomers that are connected by covalent bonds.

emergent properties

New properties that arise through interactions among smaller parts that alone do not exhibit these properties. ex- a smaller part might be a cell. the cell by itself does not exhibit the same properties, vs multiple cells that are put together to form a multicellular organism! to elaborate: a cell by itself cannot form tissue. but if multiple cells come together, they can act and form tissue.

explain how the properties of water that result from its polarity and hydrogen bonding affect its biological function

Polarity makes water a good solvent, gives it the ability to stick to itself (cohesion), stick to other substances (adhesion), and have surface tension (due to hydrogen bonding Living systems depend on properties of water that result from its polarity and hydrogen bonding. The hydrogen bonds between water molecules result in cohesion, adhesion, and surface tension

explain the difference between energy storage polysaccharides and structural support polysaccharides and give 2 important examples of each

Polysaccharides that function as energy storage are starch and glycogen. starch serves as energy storage in plants. Starch consists of amylose and amylopectin Amylose and amylopectin are formed from condensation of a-glucose joined at a-1,4-glycosidic bonds Polysaccharides that function as structural support are cellulose and chitin. Cellulose serves as structural support in plants. Cellulose are the main components of cell wall. Chitin forms exoskeleton of arthropods and cell walls of fungi

explain how hydrogen bonding, van der waals interactions, hydrophobic interactions, and disulfide bridges a role in protein structure TERTIARY

TERTIARY STRUCTURE: one type of interaction that contributes to tertiary is called hydrophobic interaction. as a polypeptide folds into its functional shape, amino acids with nonpolar side chains end up in clusters at the core of the protein, out of contact with water. Once nonpolar amino acid chains are close together, van der waals interactions help hold them together. meanwhile, hydrogen bonds between polar side chains and ionic bonds between postively and negatively charged side chains also help stabilize teritary structure. covalent bonds called disulfide bridges help further reinforce the shape. they form where 2 cysteine monomers (-SH) are brought closer together by the folding of the protein.

describe the properties of the monomers and the type of bonds that connect the monomers in biological macromolecules

The monomers combine with each other using covalent bonds to form larger molecules known as polymers.

Monosaccharides

The simplest carbohydrate, active alone or serving as a monomer for disaccharides and polysaccharides. Also known as simple sugars, the molecular formulas or monosaccharides are generally some multiple of CH2O.

what is the result of a wrong amino acid sequence in a polypeptide? give a biological example of this

The tRNA would carry the wrong amino acid, and it would be incorporated into the growing peptide. Small changes in the amino acid sequence of a protein can cause devastating genetic diseases such as Huntington's disease or sickle cell anemia.

describe the composition of macromolecules required by living organisms

These macromolecules are proteins, nucleic acids (DNA and RNA), lipids (fats) and carbohydrates.

list 5 characteristics of water that are emergent properties resulting from hydrogen bonding

Water Has a Neutral pH. Water Expands When It Freezes Water Is a Good Solvent Water Maintains a Relatively Constant Temperature. Water is Cohesive and Adhesive.

with the use of a diagram or diagrams, explain why water molecules are a. polar b. capable of hydrogen bonding with four neighboring water molecules

Water molecules are polar because the electrons of the polar covalent bond spend more time by the oxygen than the hydrogen. They are also unevenly distributed. Polarity allows water molecules to form hydrogen bonds with each other

buffers

a buffer is a substance that minimizes changes in the concentrations of H+ and OH- in a solution. It does so by accepting hydrogen ions from the solution when they are in excess and donating hydrogen ions to the solution when they have been depleted.

what is the standard error of the mean? how is this represented on a graph? how is the significant difference between data sets shown by SEM bars?

a measure of how far or how precise your sample mean is likely to be true/accurate. You get this by adding and subtracting the standard deviation from the average. If you're comparing 2 data sets, the SEM bars can prove if both histograms are statistically similar or different. If the SEM bars are "overlapping", then there's not much of a difference in data, both are accurately similar.

single bond and double bond

a single bond is a pair of shared electrons. a double bond is 2 atoms share 2 electrons.

explain the following observations by referring to the properties of water: a. coastal areas have milder climates than adjacent inland areas b. ocean temperatures fluctuate much less than air temperatures on land c. insects like water striders can walk on the surface of a pond without breaking the surface d. if you slightly overfill a water glass, the water will form a convex surface above the top of the glass e. if you place a paper towel so that it touches spilled water, the towel will draw in the water f. ice floats on water g. humans sweat and dogs pant to cool themselves on hot days

a. Water has a higher heat capacity b. water has a higher specific c. surface tension d. The cohesive property of water e. adhesion f. Water expands as it changes from a liquid to a solid, becoming less dense rather than more dense g. High specific heat Water absorbs latent heat in order to evaporate, and this absorption of heat causes a cooling for sweating humans and panting dogs.

properties of water adhesion and cohesion

ad: the clinging of one substance to the OTHER co: water molecules stay close to each other as a result of hydrogen bonding.

functional groups hydroxyl

alcohol, -OH. example: ethanol.

functional groups amino

amine. examples are glycine. (in ionized form, it is N+ and has 3 H's)

macromolecules lipid- what are they?

are a diverse group of hydrophobic molecules

distinguish between hydrophobic and hydrophilic substances

hydrophobic substances do not have an infinity for water. hydrophilic substances have an infinity for water

covalent bonds non polar

in a covalent bond between 2 atoms of the same element, the electrons are shared equally because the two atoms have the same electronegativity-the tug-of-war is at a standoff.

ionic bonds

in some cases, 2 atoms are so unequal in their attraction for valence that the more electronegative atom strips an electron completely away from its partner. the two resulting oppositely charged atoms are called ions. a cation is positively charged, an anion is negatively charged. because of their opposite charges, cations and anions attract each other, hence why this is called an ionic bond.

properties of water high specific heat

it is difficult to change the temperature of water (water can hold TONS of heat). This is why it has a high specific heat, because it takes longer for water to get hot! definition: the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1-degree Celcius heat is absorbed when hydrogen bonds break and is released when hydrogen bonds form. this helps keep temperatures relatively steady, within limits that permit life

functional groups carbonyl

ketone and aldehyde, C=O. examples are acetone and propanal

describe the structural differences and similarities between DNA and RNA

length: DNA is a much longer polymer than RNA. structure: DNA consists of 2 strands arranged in a double helix. RNA only has one strand.

define mean, range and standard deviation

mean: The average. This is calculated by dividing the number and the sum of your data once it's rearranged from smallest to largest. range: The difference between the lowest and highest values. standard deviation: Measures the spread or variation of a graph's average in a bell curve.

functional groups methyl group

methylated compound. examples are 5-methylcytosine, a component of DNA that has been modified by addition of a methyl group

macromolecule nucleic acid

nucleic acids store, transmit, and help express hereditary information, they are made from nucleotides!

macromolecule nucleotide

nucleotides are composed of 3 parts: a nitrogen-containing (nitrogenous) base, a five-carbon sugar (a pentose), and one to three phosphate groups.

van der waals interactions

occur between transiently positive and negative regions of molecules.

functional groups phosphate

organic phosphate. examples are glycerol phosphate

properties of water pH

pure water is on the neutral pH scale. this means that H+ = OH-. if theres more H+, its more acidic, if theres more OH-, its more basic. The pH of a solution is defined as the negative logarithm (base 10) of the hydrogen ion concentration. ex: H+ is

distinguish between saturated and unsaturated fatty acids

saturated fat: at room temperature, the molecules, such as the fat in butter, are packed closely together, forming a solid. the structure - each hydrocarbon chain is represented as a zigzag where each bend represents a carbon atom and hydrogens aren't shown unsaturated fat: at room temp, the molecules, such as olive oil, cannot pack together closely enough to solidify because of the kinks in some of their fatty acid hydrocarbon chains.

macromolecules carbohydrate- what are they?

serve as fuel and building material

macromolecules nucleic acid/nucleotide- what are they

store, transmit, and help express hereditary information

covalent bonds polar

when an atom is bonded to a more electronegative atom, the electrons of the bond are not shared equally. An example is a hydrogen trying to bond with oxygen. Because oxygen has more valence electrons and has a stronger electronegativity, the shared electrons are pulled more towards oxygen. oxygen then has a negative greek letter charge, while the hydrogen has a positive greek letter charge. electrons of a polar covalent bond are pulled closer to the more electronegative atom, such as the oxygen in H2O

what does it mean for a protein to become denatured? list several conditions under which proteins may be denatured

the irreversible process in which the native structure of a protein is disrupted. what this means is: Loss of 3D shape, loss of biological function and changes the characteristics of food. E.g. adding alcohol to milk denaturing agents include: Heat, alcohol, Acid, enzyme, mechanical energy and salts.

covalent bonds

the sharing of a pair of valence electrons by two atoms. valance electrons are electrons on the outermost shell. it determines the behavior of an atom, it can make them react or unreact with other atoms depending on if their outermost shell is completed or not.

macromolecules amino acid/protein- what are they

they include a diversity of structures, resulting in a wide range of functions

functional groups sulfhydryl

thiol, -SH or -HS. examples are cysteine

draw the basic structure of a fat (triglyceride), a phospholipid, and a steroid. give the function of each type of lipid and some examples of each

triglyceride: 3 fatty acids covalently bonded to three carbon alcohol, glycerol molecule. phospholipid: 75% of membrane lipids.Structural foundation of cell membrane. Fatty acid "tail" are hydrophobic, Phosphate head is hydrophilic. steroid: made of cholestrol. Cholestrol is the "parent" steroid from which the other steriods are synthesized

distinguish between primary, secondary, tertiary, and quaternary structures of proteins.

van der waals interactions occur between transiently positive and negative regions of molecules. primary: a sequence of amino acids. secondary: coils and folds that result of hydrogen bonds between the repeating constituents of the polypeptide backbone tertiary: the overall shape of a polypeptide resulting from interactions between the side chains of the various amino acids quaternary: the overall protein structure that results from the aggregation of these polypeptide subuntis.

isomers

variation in the architecture of organic molecules can be seen in isomers, compounds that have the same number of atoms of the same elements but different structures and hence different properties. They have the same molecular formula but different structures and properties example: pentante and methylbutane have the same molecular formula C5H12 but they are branched differently!

properties of water density of ice

water is one of the few substances that is less dense (as a solid) than as a liquid. that's why ice floats on liquid water. the ability for ice to float due to its lower density is an important factor in the suitability of the environment for life. if ice sank, then eventually all ponds, lakes, and even oceans would freeze solid, making life as we know it impossible on earth.

what is a peptide bond? explain how this is formed, and show where the peptide bond is in a diagram of a polypeptide (draw one)

what it is: The chemical bond that forms between the carboxyl group of one amino acid and the amine group of another amino acid. Formed by dehydration synthesis.

hydrogen bonds

when hydrogen 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 nearby. the noncovalent attraction between a hydrogen and an electronegative atom is called this. in living cells, the electronegative partners are usually oxygen or nitrogen atoms. it is an attraction between a hydrogen atom carrying a partial positive charge and an electronegative atom.

explain how hydrogen bonding, van der waals interactions, hydrophobic interactions, and disulfide bridges a role in protein structure SECONDARY

within the backbone, the oxygen atoms have a partial negative charge, and the hydrogen atoms attached to the nitrogens have a partial positive charge. therefore, hydrogen bonds can form between these atoms.