biology 1 midterm 2

electronegativity

(EN) refers to an atom's tendency to pull electrons in a covalent bond towards its own nucleus. -In biology, covalent bonds with electronegativity (EN) differences less than 0.5 are generally NOT considered to be significantly polar. -From left to right, the electronegativity increases while it decreases as you move down a group of elements.

disulfide bonds

(disulfide bridges) are covalent bonds that can form between two separate cysteine side chains in the same amino acid chain or different chains

Equilibrium & Energy key points

-A reaction mixture that is not already at equilibrium will show a spontaneous tendency to move there. Energy (so-called "free energy") is released as a reaction moves towards equilibrium. -Cells can use energy that is released to drive cellular processes

Acid Strength

-Acids differ in their relative tendencies to release protons and increase H3O+ concentrations in water. For stronger acids, the position of equilibrium lies farther to the right. -The larger the Ka for an acid, the stronger the acid. -The smaller the Ka, the weaker the acid Ka = [A-]eq[H3O+]eq/[HA]eq

Key Points About Equilibria

-At equilibrium, the overall (net) concentrations of reactants and products remain constant over time. -At equilibrium, the rate at which reactants are converted to products equals the rate at which products are converted to reactants. -The position of the equilibrium does not depend on the composition of the starting mixture.

Acid/Base Equilibria

-Equilbrium mixtures of acids can be described by the acid dissociation constant, or Ka. The Ka is derived from the equilibrium constant, Keq. "HA" represents a generic acid, with "A" standing for "acid,", and "H" the acidic hydrogen(s). 1. If Ka is far bigger than 1, H3O+ and A− are present in excess over protonated acid (HA) at equilibrium. 2. If Ka is far less than 1, HA is present in excess over H3O+ and deprotonated acid (A−) at equilibrium.

Molecules Do Not Exist In Isolation

-Molecules can interact with other nearby molecules through non-covalent interactions. For instance, water molecules can feel forces of attraction or repulsion towards other nearby water molecules -Water molecules interact with each other in space, but no new covalent bonds are formed. -Energy is required in order to break any kind of non-covalent bond. The stronger the bond, the more energy needed to break it.

You Must Learn How To Correctly Number The Carbon Atoms In Glucose & Ribose Rings

-Oxygen is reference point -Carbon on the outside of the ring is the highest numbered carbon -First carbon atom is next to the oxygen atom, but is not connected to the outside carbon

Proteins fold into unique 3D structures

-Protein polymers will not remain as linear chains in aqueous solutions. Rather, they will fold into the energetically most favorable structure. -The folded structure seeks to minimize exposure of nonpolar amino acid side chains to surrounding water, while maximizing exposure of polar and charged groups to surrounding water. Nonpolar side chains are largely buried in a protein's interior; another example of the hydrophobic effect 1. hydrophobic side chains tend to pack in the interior 2. hydrophilic and electrically charged side chains tend to be exposed on the protein surface 3. charges, either full or partial, tend to orient themselves around opposite charges (tend to be stabilized); charge stabilization refers to the fact that opposite charges can stabilize each other -unfolded conformation = not functional -folded conformation = active form (native/form found in the body) -energy of maintaining the unfolded conformation increases compared to the energy of maintaining the folded conformation unfolded ⇌ folded

The Sugars of DNA and RNA

-RNA has ribose -DNA has deoxyribose -The two pentoses differ only at the carbon-2 position. Ribose has a hydroxyl group, whereas deoxyribose does not. Both have a hydroxyl group at carbon-3.

Polarity in Covalent Bonds

-The sharing of electrons in a covalent bond is not always equal. Atoms differ in their intrinsic tendencies to pull shared electrons towards their nuclei. -In a polar covalent bond, the electrons in a bond spend more time around the more electronegative atom. This results in partial charges (but not formal charges).

Trans Fats

-Unsaturated fatty acids containing trans-double bonds do not form strong kinks. While only found in limited amounts in nature, they can be made during food processing. -Trans fat consumption has been correlated with a significant risk of coronary heart disease. They are soon to be banned in all US states.

Triglycerides

-a major subclass of lipids -They include fats and oils; contain different chemical properties -Consist of: One glycerol molecule and Three fatty acids, which contain a long nonpolar hydrocarbon chain and a shorter polar end Chemical differences between fats and oils: -*Fats are solid at room temperature* -*Oils are liquid at room temperature*

Polar Bonds

-affect solubility in water -Because water is quite polar, any molecule with polar covalent bonds is able to interact well with water. The more polar bonds there are, the more soluble the molecule is. -polar molecules readily form hydrogen bonds with water and dissolve

Why is the equilibrium mixture for a reversible reaction energetically most favorable?

-because total entropy is maximized at this state. -The precise mixture simply depends on the nature of reactants and products.

What Causes Branching?

-because you can form glycosidic bonds in more than one position -enzymes are present that can form these bonds in some organisms and not others

Catalysts

-cannot make a reaction that is non-spontaneous become spontaneous -they do not alter the equilibrium mixture (Keq) of a reaction. -rather, they speed up the rate at which a reaction reaches equilibrium

Phospholipids

-contain two fatty acids together with a phosphate group bound to glycerol. The phosphate group is negatively charged inside cells, making that part of the molecule very hydrophilic (polar). -Phospholipids constitute a major lipid component of biological membranes -Structure: polar & electrically charged hydrophilic heads, which contrast with the nonpolar hydrophobic tails -In Water, Phospholipids Form Bilayers

van der Waals interactions

-hydrophobic interactions -Non-polar molecules can experience temporary, weak forces of attraction with regions in other non-polar molecules due to random electron movement & displacement -Can sum up over larger surfaces -temporary displacements of electrons -transient excess of electrons in one area (one side) -> induces a transient shortage of electrons in a neighboring region of another molecule on the other side - occurs at many different places

phospholipid bilayer

-in an aqueous environment, phospholipids spontaneously assemble to form a phospholipid bilayer. -The nonpolar hydrophobic "tails" pack together and the phosphate-containing "heads" face outward, where they interact with water. All biological membranes are composed of phospholipid bilayers.

Base pairing

-is specific, as are the numbers of hydrogen bonds that are formed -Adenine (A) always pairs with Thymine (T) to form TWO H-bonds -Cytosine (C) always pairs with Guanine (G) to form THREE H-bonds

gel electrophoresis with proteins

-longer chain moves slower than the shorter chain -if we apply an electric field, we pull these electrically charged proteins -low molecular weight moves faster (has fewer amino acids) -high molecular weight moves slower (more amino acids)

pH

-measures the total concentration of H+ (or H3O+) present in a solution. Unlike the pKa, it is a property of a solution, NOT of an acid or acidic group. -use when talking about a *solution*, not an acid pH = -log10[H3O+] -By definition, a solution whose pH = 7.0 is said to be at "neutral" pH.

Fatty acids

-they are amphipathic; they have a hydrophilic end (COOH group) and a longer hydrophobic "tail."

starches

-type of polysaccharide -branched polymers of glucose (hexose), made in plants. Plants use them to store energy, while some animals (including humans) obtain energy by consuming them. -branching limits the number of hydrogen bonds that can form in starch molecules, making starch less compact than cellulose -form 1,4 glycosidic bonds -form 1,6 glycosidic bonds in addition to 1,4-bonds

cellulose

-type of polysaccharide -most common polymer on earth -unbranched polymer of glucose (hexose) (linear) -Important structural material, especially in plants! -parallel cellulose molecules form hydrogen bonds, resulting in thin fibrils -form 1,4 glycosidic bonds -do NOT form 1,6 glycosidic bonds in addition to 1,4-bonds.

Glycogen

-type of polysaccharide -stored in the liver -highly branched polymer of glucose (hexose); major energy storage molecule in mammals. -the high amount of branching makes its solid deposits more compact than starch -form 1,4 glycosidic bonds -form 1,6 glycosidic bonds in addition to 1,4-bonds

Determining Formal Charges In Atoms

1. All lone pair electrons are assigned to the atom they belong to 2. For each covalent bond, one electron is assigned to each bonding partner. 3. Formal charge is determined by comparing the total number of electrons (including inner shell) to the number of protons in the atom of interest.

Nucleotide Basics

1. Bases are ALWAYS connected to the 1' carbon of the sugar. 2. Phosphate(s) is ALWAYS connected to the 5' carbon of the pentose ring.

What are some "telltale" signs that characterize cyclic monosaccharides? How would you describe them chemically?

1. Can form hydrogen bonds 2. Hydrophillic (soluble in water) - lots of OH bonds; water can interact with these parts of the molecule 3. Small molecules; have less than 100 atoms 4. Polar. They have polar-covalent bonds

Nonpolar Aggregation Does Two Things:

1. It maximizes the number of favorable H-bonds that can form between adjacent water molecules. 2. It reduces the number of waters that must become "ordered" to form favorable H-bonds. -reduces the number of ordered waters per nonpolar molecule -ordering is not favorable; minimize number of ordering spontaneously

Four levels of protein structure

1. Primary 2. Secondary 3. Tertiary 4. Quaternary

Major functions of carbohydrates

1. Source of stored energy inside of many organisms. 2. Structural molecules that give many organisms their shapes. Cellulose in plants is an example. 3. Recognition molecules inside and on the surfaces of cells. Blood groups in humans are an example. Blood group depends on a polymer of carbohydrates on the surface of your red blood cell.

Two Chemically Distinct Ends of DNA and RNA

1. The 5' end has one or more "free" phosphate groups exposed (not bound to another sugar's 3' hydroxyl group). 2. The 3' end has a "free" (exposed, unbound) 3' hydroxyl group.

determine the net charge on an atom in a molecule

1. assign all lone pairs to the atom that has them 2. divide valence electrons in each covalent bond equally between both atoms that form the bond. 3. Add inner shell electrons 4. Compare total number of electrons to the total number of protons. number of valence electrons (group #) - number of electrons in lone pairs - ½(number of electrons in bonding pairs)

Limited Capacity of Electron Shells

1st shell = 2 2nd shell =8 3rd shell = 18

how many groups do amino acids have that can donate and accept protons?

2

glucose

6-carbon sugar -a hexose -largely present as ring (cyclic) structures.

phosphodiester bonds

A bond formed between adjacent nucleotides which consists of a phosphate group that links the sugars of two nucleotides -Pyrophosphate is released each time a phosphodiester bond is formed. Along with the subsequent conversion of pyrophosphate into two phosphates, this contributes to increases in total entropy -Pyrophosphate breaks into 2 identical phosphates

ribose

A five-carbon sugar (a pentose) common type of biological monosaccharides -largely present as ring (cyclic) structures.

Phosphate Group

A functional group consisting of a phosphorus atom covalently bonded to four oxygen atoms -Universally found in many small and large biological molecules. Notice that phosphorous forms 5 bonds. -Acidic -Enters into condensation reactions by giving up -OH. When bonded to another phosphate, hydrolysis releases much energy

amphipathic

A molecule that has both a hydrophilic region and a hydrophobic region.

Numbering of Carbons in Ribose

A prime (') symbol is used to distinguish the carbon atoms in the sugar ring from carbon atoms in the bases. For instance, carbon 1 in the sugar ring is referred to as the 1' carbon, pronounced "one-prime carbon." -You do not need to know the carbon positions in the bases.

condensation reaction

A reaction in which two molecules become covalently bonded to each other through the loss of a small molecule, usually water; also called dehydration reaction. -two monomers; a new covalent bond forms between them; in the process of doing this, prior bonds have to be broken -for every molecule that is formed, there is one molecule of H2O that is released

Hydrogen bonds

A specific type of non-covalent interaction -interaction depends on the distance and the orientation of the H+ -water molecules can orient their hydrogen atoms relative to oxygen lone pairs on adjacent water molecules. These interactions are strongest in ice, weakest in water vapor. -specifically occurs between: 1. a lone pair on either N or O atoms 2. a partially positive hydrogen atom bonded to a different N or F or O atom -this H is pulled towards the above lone pair -2 parts: H-bond "donor" (can also be the N-H group) and H bond "acceptor" (the lone pair on the oxygen)

The Carboxyl Group

Acidic. Ionizes in living tissues to form -COO- and H+ -enters into condensation reactions by giving up -OH -some carboxylic acids are important in energy-releasing reactions

Purine Bases

Adenine and Guanine -Two fused rings

The Hydroxyl Group

All monosaccharides have several hydroxyl groups (-OH), a common functional group also contained in many other biological molecules. -Properties: polar. hydrogen bonds with water help to dissolve molecules. Enables linkage to other molecules by condensation.

electrically charged side chains

All of these side chains have functional groups that can donate/accept protons

Lone Pair Electrons

Any valence electrons not involved in covalent bonding are present as pairs of non-bonded electrons

up to how many H-bonds can a single water molecule form at the same time?

At most four: two through having its hydrogens interacting with unshared electron pairs on other water molecules, and two by having its unshared electron pairs interacting with hydrogens on other water molecules. (Each water molecule has two hydrogens and two unshared electron pairs.) Because of this balance, all the molecules in a sample of water can theoretically form 4 hydrogen bonds. In actual fact, the bonds are constantly breaking and reforming, so at any given instant the average number of hydrogen bonds per molecule in liquid water is less than 4, but more than 3. This still amounts to very strong intermolecular bonding, which accounts for water's high boiling and freezing points, plus surface tension and other properties.

Formation of Carbon Dioxide (CO2)

Atoms can also fill their outer shells by forming double bonds or triple bonds with other atoms. In the case of CO2, carbon forms two double bonds with two oxygen atoms.

stacked arrangement of bases

Bases Are "Stacked" In the Double Helix -The top and bottom surfaces of bases are actually hydrophobic, which promotes stacked arrangement -they stack together spontaneously because the space between the bases excludes water and it is released (minimizes the ordering of water); gain in entropy of releasing thousands of water molecules is greater than the ordering entropy; hydrophobic effect Complementary DNA strands (unbound) ⇌ Double Helix formation -Keq > 1 because double helix is more ordered; entropy goes down; order is going up, disorder is going down -tells us that even though entropy is going down, something is going up - releasing water molecules

DNA melting points

Because three hydrogen bonds form between guanine/cytosine base pairs and two hydrogen bonds form between adenine/thymine base pairs, more energy is required to denature the former. DNA with a greater number of guanine/cytosine base pairs denatures at a higher temperature than adenine/thymine base pairs.

What end are amino acids added to?

C-terminus

monosaccharides

Carbohydrate monomers; These include the simple sugars, such as glucose, ribose. -Monomers are linked together covalently to form polymers called polysaccharides. -important polysaccharides: glycogen, cellulose

Pyrimidines

Cytosine, Thymine, Uracil -Only one ring

Forming and Breaking Disulfide Bonds

Disulfide bonds are formed in so-called oxidation reactions. They are broken in a process called reduction. Both processes happen inside of cells or can be done in the lab with chemicals. -occurs between cysteine that are further away

Alpha helices

Folding of the protein backbone in the form of a helix, stabilized by H-bonds between backbone C=O and N-H groups. R2C=O ---- H-NR2

Beta sheets

Folding of the protein backbone in the form of two or more adjacent beta strands, stabilized by H-bonds between backbone C=O and N-H groups. One b-sheet consists of two or more b-strands

Nonpolar side chains

Glycine (g), alanine (a), valine (v), lecuine (L), isoleucine (I), phenylalanine (F), tryptophan (W), proline (P), methionine (M) -These side chains mostly contain nonpolar covalent bonds.

equilibrium mixture

If we let a reversible reaction proceed until there is no further NET change in reactants and products, a stable mixture of reactants and products is achieved.

Complementary Base Pairing in RNA

In RNA, uracil (U) replaces thymine and always pairs with adenine. Guanine (G) pairs with Cytosine (C) in RNA the same as in DNA. -Adenine (A) always pairs with Uracil (U) to form TWO H-bonds. -Cytosine (C) always pairs with Guanine (G) to form THREE H-bonds

Distinguishing Polar vs. Nonpolar Covalent Bonds

In biology, covalent bonds with electronegativity (EN) differences less than 0.5 are generally NOT considered to be significantly polar. -Hydrogen is least electronegative -Oxygen is most electronegative

DNA Structure In Cells

In cells, DNA typically forms a double helix structure. Two separate DNA strands containing many monomers form a double-stranded helix. Both strands are oriented antiparallel to each other (see below). -The bases in one strand are complementary to bases in the other strand. Complementary bases interact through Hydrogen bonding -Four bases occur in DNA: A, C, G and T

DNA Function

In cells, the main function of DNA is to encode information for hereditary traits. Information is encoded by the sequence of nucleotides.

secondary structure of protein

Locally folded, continuous sub-regions in the entire protein chain. There are two main types: 1) Alpha (a) helix 2) Beta (b) sheet. A b sheet consists of two or more aligned b strands. Both structures are stabilized by hydrogen bonds between backbone C=O and N-H groups. -Side Chains Do Not Determine Secondary Structures -Side chains project outwards of a helix (see below), and above and below the plane of a beta strand. They do not interact to form secondary structures.

non-covalent interactions

Molecules can interact with other nearby molecules through non-covalent interactions. For instance, water molecules can feel forces of attraction or repulsion towards other nearby water molecules. -Water molecules interact with each other in space, but no new covalent bonds are formed

Acids

Molecules capable of "donating," or releasing, one or more H+ ions (protons) to another molecule or atom when dissolved in water

Bases

Molecules or atoms that covalently bind to (accept) protons donated by acids

Amino Acids

Monomers Of Proteins -All share a common general structure: A central carbon atom (the alpha carbon) is connected to: an amino group (-NH3+ or -NH2) • a carboxyl group (-COOH or -COO-) • a hydrogen atom • a side chain (R-group)

Formation of Water (H2O)

Oxygen needs two bonds to fill its valence shell, hydrogen needs one. Within each covalent bond, the two electrons are shared by O and H (even though one originated from O, and the other from H).

What are the bonds between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another called?

Phosphodiester bonds

Phosphorous and Sulfur

Phosphorous and Sulfur are in the third row of the periodic table, and the octet rule does not apply perfectly. Simply know the typical number or covalent bonds formed by both in biological molecules. P = 5 bonds formed by electrically neutral atom S = 2 bonds formed by electrically neutral atom

Keq >> 1

Products are present in excess over reactants at equilibrium.

Keq << 1

Reactants are present in excess over products at equilibrium.

α-carbon in an amino acid

The carbon atom next to the carboxyl group

Entropy Changes

The change in total entropy, is the key determinant for whether reactions proceed spontaneously and release energy. Total entropy takes into account the entropy changes of the system and the entropy changes of the surroundings △STotal = △SSys + △SSurr -Involve System & Surroundings -*System:* The molecules or atoms involved in the reaction of interest. It must be defined. -*Surroundings:* Everything else.

Keq = 1

The equilibrium mixture contains roughly equal concentrations of reactants and products.

primary structure of protein

The linear sequence of amino acids (aka "residues") in a polymer chain. -stabilized by peptide bonds

2nd law of thermodynamics

The principle whereby every energy transfer or transformation increases the entropy of the universe. Ordered forms of energy are at least partly converted to heat, and in spontaneous reactions, the free energy of the system also decreases. -It is about the quality of energy; as energy is transferred or transformed, more and more of it is wasted -the change in total entropy must always be positive.

Why Is Equilibrium Favorable?

The second law of thermodynamics states the following: -In any reaction that proceeds spontaneously, there is always an increase in total entropy. -The equilibrium state achieves the maximum amount of total entropy (total randomness or disorder) for a given reaction mixture. -entropy is favored

The Hydrophobic Effect

The tendency for nonpolar molecules to spontaneously aggregate in water minimizes the total number of water molecules that become ordered around nonpolar regions. This principle drives the assembly of phospholipid bilayers.

polar but electrically neutral (uncharged) side chains

These side chains have one or more polar covalent bonds (can you identify them?), but they are not formally charged.

Types of Polysaccharides

Three main types we'll consider: 1) *Cellulose* - unbranched polymer of glucose. Important structural material, especially in plants! 2) *Starches* - branched polymers of glucose, made in plants. Plants use them to store energy, while some animals (including humans) obtain energy by consuming them. 3) *Glycogen* - highly branched polymer of glucose; major energy storage molecule in mammals. -All have the same monomers

Water decreases the strength of attraction somewhat. Why is that?

Two oppositely charged, hydrated ions can experience ionic interactions (in this case attraction).

melting points of unsaturated vs saturated fatty acids

Unsaturated fatty acids have lower melting points than saturated fatty acids of the same length -The geometry of the double bond is almost always a cis configuration in natural fatty acids. These molecules do not "stack" very well. The intermolecular interactions are much weaker than saturated molecules. As a result, the melting points are much lower for unsaturated fatty acids. -Stacked trans fats are extremely stable and have much higher melting point than the corresponding cis unsaturated fat. -Monounsaturated fats have a higher melting point than polyunsaturated

Writing Conventions

When writing the sequence of only one strand of DNA or RNA, the 5' end of the strand is typically written on the left. This is a standard convention. 5'-CCATGG-3'

Molecular Structure

Within molecules, covalent bonds and lone pair electrons are oriented relative to each other in order to maximize the distance between them and minimize electrostatic repulsion. Like charges repel. -Electrostatic repulsion between covalent bonds affects molecular structure. Ex: methane

when pH > pKa...?

[A-] > [HA]

when pH < pKa...?

[HA] > [A-]

chitin

a carbohydrate polymer found in many organisms such as insects and fungi -it is a chain of modified glucose molecules -have 1,4 glycosidic bonds

Lipids

a large group of molecules composed largely of hydrocarbons (chains of C and H atoms). They are very nonpolar and therefore insoluble in water. -base the definition on solubility; not on structure *Major Functions:* 1. Store energy - humans would retain lots of water if they used carbohydrates to store energy 2. They form cell membranes 3. Fat in animal bodies serves as thermal insulation

Polymers

are macromolecules made up of many repeating subunits called monomers. Make it your goal to recognize the monomers of polysaccharides, nucleic acids and proteins. -it is implied that the monomers are ALWAYS linked together using covalent bonds

Formal charges

are net electrical charges that occur when there is an imbalance of electrons and protons in an atom or molecule. -number of valence electrons (group #) - number of electrons in lone pairs - ½(number of electrons in bonding pairs)

pKa of carboxyl group

around 2; depronated form will dominate if pH is greater than 2

pKa of amine group

around 9 depronated form will dominate if pH is greater than 10

Nucleic acids

biological polymers specialized for storage, transmission, and use of genetic information. -There are two main groups: DNA = deoxyribonucleic acid RNA = ribonucleic acid

cis configuration

both hydrogen atoms are on the same side of the carbon-carbon double bond -Fatty acid chains containing cis double bonds can show significant kinks (bends) in the chain. This is because double bonds cannot rotate freely.

five nitrogenous bases of RNA and DNA

can be classified as either purines or pyrimidines. You need to know which bases belong to which group, but no need to memorize any base structures.

Four Major Types of Macromolecules

carbohydrates, lipids, proteins, nucleic acids

Glycosidic Bonds

carbons on adjacent sugar units are bonded to the same oxygen atom like links in a chain -Monosaccharides are linked together by glycosidic bonds. These are covalent bonds. -a type of covalent bond that joins a carbohydrate molecule to another group, which may or may not be another carbohydrate. -what is the glycosidic bond that links the monomers? --> 1,4 -Glycosidic bonds are named according to the positions of the carbon atoms involved in linking adjacent monomers.

What are the bonds between monosaccharides called?

glycosidic bonds

trans configuration

hydrogen atoms are on opposite sides. -Cis Double Bonds Cause Kinks, but Trans Double Bonds Do NOT Cause Significant Kinks.

Synthesis of a triglyceride

involves three condensation reactions. Because only three fatty acids can be added to each glycerol molecule, triglycerides are not considered true "polymers." -largely hydrophobic

RNA Structure

is often (though not always) single-stranded, but strands are folded into unique 3-D structures by hydrogen bonding of bases within the same strand. -Because folded RNA can take on many different structures, it fulfills many more roles inside of cells than does DNA. -Different structures = different functions -the base Uracil (U) replaces Thymine (T). Adenine forms two H-bonds with Uracil, just like with Thymine.

equilibrium constant, Keq

is used to describe the composition of the equilibrium mixture for a reaction. [ ] Square brackets denote concentrations (in moles/liter)

Hydrophobic

molecules dissolve poorly in water. Instead, they aggregate together (think of pouring oil into water) -very weak interactions, and therefore cannot dissolve -nonpolar molecules aggregate in water which helps maximize the number of hydrogen bonds water molecules can form with other water molecules

Hydrophilic

molecules dissolve readily in water

saturated fatty acid

no carbon-carbon double bonds, all carbons are saturated with H -they are packed together tightly and therefore mostly solid at room temperature -Animal fats tend to have saturated fatty acids

Ionic Interactions

often occur between formally charged atoms that are part of larger molecules. The distance between the formally charged atoms determines how strong the interaction is -In living organisms, ions are typically surrounded by water (hydrated) but can still experience ionic attraction or repulsion if close enough.

unsaturated fatty acid

one or more carbon-carbon double bonds -monounsaturated = 1 DB -polyunsaturated = more than 1 DB -Plant oils tend to have one or more cis-unsaturated fatty acids. These cause chain kinks that prevent tight packing and make oils mostly liquid at room temperature. -The presence of carbon to carbon double bonds in the oil molecules distorts the long fatty acid chains and the molecule's shape. As a result the molecules cannot pack closely together.

cysteine

only amino acid with a Sulfhydryl (-SH) Group in Its Side Chain

pka

pKa = -log10(Ka) Ex: If the Ka = 1.0 x 10-3, what is the pKa? -Take the negative of the exponent on 10 pKa of 10-3 = -(-3) = +3

Henderson-Hasselbalch equation

pKa = pH + log10 [HA]/[A-] -If [HA] = [A-], then log10[HA]/[A-] = 0, then pKa = pH -*difference in 10s* -for every one change, it is a 10 difference

What are the bonds between amino acids called?

peptide bonds

reversible reactions

proceed in both the forward and reverse directions -Stacked arrows indicate that the reaction proceeds in both directions to a significant degree. -If we let a reversible reaction proceed until there is no further NET change in reactants and products, a stable mixture of reactants and products is achieved. This is the equilibrium mixture.

quaternary structure of a protein

protein structure is a protein consisting of more than one folded amino acid chain -Two or more separate polypeptide chains (subunits) assemble to form a larger structure. There are many different quaternary structures (many don't have unique names). -Each subunit is an independently folded protein polymer -stabilized by hydrogen bonds, disulfide bridges, van Der Waals interactions, ionic bonds

tertiary structure of protein

protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3D structure -Entire polypeptide chain is bent and folded upon itself. Side chains play a prominent role here -stabilized by hydrogen bonds, disulfide bridges, van Der Waals interactions, ionic bonds

denaturation

refers to the disruption of the natively folded structure of a protein. Heat, chemicals, pH changes, etc. can disrupt weaker bonding interactions in a protein and destroy secondary, tertiary and quaternary structures. folded -> unfolded

Monomers

repeating subunits used to build substances -linked together covalently by condensation reactions. They are removed by hydrolysis reactions -does not need to be one atom; it is almost always composed of several atoms -Key point: *ONE water is released / needed for each bond formed / broken*

protein backbone

shows the fold of the main chain without all the side chains.

hydrolysis reaction

splitting of a chemical bond by the addition of water, with the H+ going to one molecule and the OH- going to the other

Nucleotides are ALWAYS added to what end?

the 3′ end of a growing strand, NOT the 5' end. Strands extend in a 5' to 3' direction

Nucleotides

the Monomers of Nucleic Acids -are linked by *covalent* phosphodiester bonds. Linkage ALWAYS occurs between a 5' phosphate group of one nucleotide and the 3' hydroxyl group of another's sugar. -Nucleic acid monomers consists of three parts: 1. a 5-carbon sugar 2. a nitrogen-containing base 3. three phosphate groups

hydration shell

the sphere of water molecules around a dissolved ion -very ordered

What is the strongest type of non covalent interaction between adjacent triglycerides?

van der Waals interactions -ionic bonds are not possible -hydrogen bonds are not a likely option because there are no Hydrogen atoms connected to O or N, so you cannot form hydrogen bonds