0 Flashcards
electronegativity
- Determines the distribution of electrons within a covalent bond
- Higher values indicate stronger attraction of electrons.
Oxygen = 3.5
Nitrogen = 3.0
Sulfur & Carbon = 2.5
Phosphorus & Hydrogen = 2.1 - Electrons in covalent bonds between atoms of equal
electronegativity have a greater potential energy than those between atoms with unequal electronegativity. - Covalent C — H bonds have greater potential energy than O — H or C — O bonds
nonpolar
A nonpolar covalent bond, where the atoms have similar electronegativities. Electrons are distributed equally (or more or less
equally) between atoms.
e. g. C-H (almost equal); O=O (equal)
polar
A polar covalent bond, where the atoms have dissimilar electronegativities. Electrons are distributed unequally between atoms.
e.g. H-O, C-O, H-N
surface tension
Surface tension is a measure of how hard it is to break the surface
of a liquid
– Water has an unusually high surface tension due to hydrogen bonding
between the molecules at the air-water interface and to the water below
H bonding
Hydrogen bonding is a special type of dipole-dipole attraction between molecules, not a covalent bond to a hydrogen atom. It results from the attractive force between a hydrogen atom covalently bonded to a very electronegative atom such as a N, O, or F atom and another very electronegative atom.
salts
Compounds formed by ionic bonds are called ionic compounds, or salts. Salts, such as sodium chloride (table salt), are often found in nature as crystals.
ionic bonds
§ Instead of sharing electrons, as in covalent bonds, sometimes atoms strip electrons from their bonding partners. § An example is the transfer of an electron from sodium to chlorine. § After the transfer of an electron, both atoms have charges. § A charged atom (or molecule) is called an ion.
Water: The Solvent of Life
Water is a versatile solvent due to its polarity.
- Even large polar molecules such as proteins can
dissolve in water if they have ionic and polar regions
hydration shell
When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell.
hydrophilic vs phobic
- A hydrophilic substance is one that has an affinity for water (e.g. polar or charged molecules like this protein or the ions Na+ and Cl-). - A hydrophobic substance is one that does not have an affinity for water (e.g. non-polar neutral molecules like lipids or oils).
H atoms in water molecules
§ Sometimes a hydrogen atom in a water molecule making a hydrogen bond with another water molecule shifts from one water molecule to the other.
§ The molecule with the extra proton is now a hydronium ion (H3O+), (it is often represented as simply H+).
§ The molecule that lost the proton is now a hydroxide ion (OH−).
acidity / alkalinity
- An acid is any substance that increases the H+
concentration of a solution.
A base is any substance that reduces the H+
concentration of a solution - acidic: more H+ than OH-; basic: vice versa
Variations in carbon skeletons
- With four valence electrons, carbon can form four
covalent bonds with a variety of atoms. - This ability makes large, complex molecules possible.
- Four ways that carbon skeletons can vary: length, branching, position of double bonds, presence of rings
- In molecules with multiple carbons, each carbon bonded to four other atoms forms a tetrahedral shape.
- However, when two carbon atoms are joined by a double bond, the other atoms joined to the carbons are
in the same plane as the carbons.
isomers
compounds with the
same molecular formula but different
structures and properties.
- Structural isomers have different
covalent arrangements of their
atoms.
- Cis-trans isomers differ in arrangement about a double bond. cis: 2 groups on same side; trans: 2 groups on opposite sides
- Enantiomers differ in spatial arrangement around an asymmetric
carbon, resulting in molecules that are mirror images
macromolecules and cellular function: 1) Fuels. 2) Energy stores. 3) Structural molecules. 4) chemical signals 5) Facilitation of chemical reactions. 6) Cellular (and thus organismal) movement. 7) Storage, transmission, and interpretation of genetic information.
- C L P
- C L P
- C L P
- L (steroids) P
- P (enzymes)
- P
- nucleic acids
importance of enantiomers
§ Enantiomers are important in the pharmaceutical industry.
§ Two enantiomers of a drug may have different effects.
§ Usually only one isomer is biologically active because only
that form can bind to specific molecules in an organism.
- ex: ibuprofen for pain and inflammation; albuterol for asthma
functional groups
- chemical groups that contribute to function by affecting shape of molecule or by being directly involved in chem rxns
- 7 groups most impt in biological processes: HCCASPM hydroxyl, carbonyl, carboxyl, amino,
sulfhydryl, phosphate, and methyl groups
hydroxyl
- -OH, HO-; O atom bonded to C skeleton
- alcohols, ex ethanol
- polar
- Can form hydrogen bonds with
water molecules, helping dissolve
organic compounds
carbonyl
- C=O
- Ketones if the carbonyl group is
within a carbon skeleton; Aldehydes if the carbonyl group is at the end of the carbon skeleton - acetone, propanol
• A ketone and an aldehyde may be
structural isomers with different properties.
• Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses and aldoses
carboxyl
- “hydroxyl + carbonyl”; C=O + OH; -COOH
- carboxylic/organic acids, ex acetic acid
• Acts as an acid; can donate an
H+ because the covalent bond
between oxygen and hydrogen
is so polar
• Found in cells in the ionized form
with a charge of 1 and called a
carboxylate ion.
amino
- (-NH2) consists of a nitrogen atom single-bonded to two hydrogen atoms and to the carbon skeleton.
- amines, ex glycine
• Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms)
• Found in cells in the ionized form with a charge of 1
sulfhydryl
- -SH; resembles HYDROXYL in shape; S is the one bonded to C skeleton
- thiols, ex cysteine
- Two sulfhydryl groups can
react, forming a covalent
bond. This “cross-linking”
helps stabilize protein
structure
phosphate
- -OPO3 2-; 1 O bonded to C skeleton, 1 O double-bonded to central P, 2 Os w/ 1- charge, 3 single bonds
- organic phosphates, ex glycerol phosphate
• Contributes negative charge to the
molecule of which it is a part (2
when at the end of a molecule; 1 when located internally
in a chain of phosphates).
• Molecules containing phosphate
groups have the potential to react
with water, releasing energy
methyl
- -CH3; 3 C-H single bonds
- methylated compounds, ex 5-methyl cytidine (component of DNA that has
been modified by addition of
a methyl group)
• Addition of a methyl group to
DNA, or to molecules bound
to DNA, affects the expression
of genes.
• Arrangement of methyl
groups in male and female sex
hormones affects their shape
and function
four classes of life’s organic molecules
– Carbohydrates (polysaccharides): (monomers: sugars or
monosaccharides).
– Lipids: (monomers: glycerol and fatty acids).
– Proteins: (monomers: amino acids).
– Nucleic acids: (monomers: sugars and nucleotide bases).
dehydration rxn
Monomers are connected by a reaction in which two molecules are covalently bonded to each other, with the loss of a
water molecule; this is known as a dehydration reaction. When a bond forms between two monomers,
each monomer contributes part of the water molecule that is
released during the reaction: One monomer provides a
hydroxyl group (—OH), while the other provides a hydrogen
(—H).
hydrolysis
- breaking down a polymer
- The bond between the monomers is broken by the addition of a water molecule, with the hydrogen from the water attaching to one
monomer and the hydroxyl group attaching to the adjacent
monomer. An example of hydrolysis working within our bodies is the process of digestion
carbohydrates: fuels
- Fuels: carbohydrates are a major source of energy for cells. Breaking down simple carbohydrates (sugars) releases energy in a form that cells can use for other processes. ex glucose
monosaccharides
Monosaccharides have molecular formulas that
are usually multiples of CH2O. Glucose (C6H12O6 ) is the most common monosaccharide
Monosaccharides are
classified by…
-the location of the carbonyl group (as aldose or ketose).
-the number of carbons in the carbon skeleton.
- trioses: 3-carbon (c3h6o3)
- pentoses: c5h10o5
- hexoses: c6h12o6
linear and ring structures
Although they are often drawn as linear skeletons, in aqueous solutions many sugars (e.g. glucose) form rings.
disaccharide
2 monosaccs linked by glycosidic linkage
sugar rxns
- dehydration rxn between 2 glucose molecules to make a maltose (1-4 glycosidic linkage)
- dehydration rxn btwn a glucose (6-sided ring) and fructose (5-sided ring) to make a sucrose (1-2 linkage)
carbs: energy stores
- Energy stores: energy can be stored in the form of complex carbohydrates (polysaccharides). These are broken down when required to sugars (e.g. glycogen (animals), starch (plants)).
carbs: structure
- Structure: some polysaccharides are used to maintain the structural integrity of cells. An important example of this is cellulose, used by plants in their cell walls.
lipids: fuel
- lipids are a very efficient sources of energy for cells.
Breaking down lipids can release twice as much energy as an
equivalent mass of carbohydrate. - However, they are broken down (metabolized) slowly and the
energy in the C-H bonds is transferred to other smaller molecules
for use in the cell.
lipids: energy stores
Energy stores: animals can store energy lipids in special cells
(adipocytes).
lipids: structural
- Are strongly hydrophobic because of the large numbers of non-polar
C-H bonds. (Recall: polar bonds needed to H-bond with water.) - Special types of lipids (phospholipids & steroids) are integral
components of cell membranes.
starch
- Plants store starch, a polymer of
glucose monomers, as granules within cellular structures
known as plastids, which include chloroplasts. - Most of the glucose monomers in starch are joined by
1–4 linkages; all glucose monomers are in alpha configuration
glycogen
Animals store a polysaccharide called glycogen, a polymer
of glucose that is like amylopectin but more extensively
branched. Humans and other vertebrates store
glycogen mainly in liver and muscle cells. Hydrolysis of glycogen in these cells releases glucose when the demand for sugar
increases.
alpha and beta glucose
When glucose forms a ring, the hydroxyl group attached to
the number 1 carbon is positioned either below or above the
plane of the ring. These two ring forms for glucose are called
alpha (α) and beta (β), respectively. (remember a and b are flipped)
cellulose
Organisms build strong materials from structural polysaccharides. For example, the polysaccharide called cellulose is a
major component of the tough walls that enclose plant cells. Humans cannot hydrolyze
cellulose.
- 1-4 linkage of beta glucose, making every glucose monomer “upside down” with respect
to its neighbors
- straight, never branched
amylose
- simplest form of starch
- unbranched, largely helical
- 1-4 linkage of alpha glucose monomers
microfibrils
Cellulose is never branched, and
some hydroxyl groups on its glucose monomers are free to
hydrogen-bond with the hydroxyls of other cellulose molecules lying parallel to it. In plant cell walls, parallel cellulose
molecules held together in this way are grouped into units
called microfibrils
- this adds strength to the fibers
amylopectin
- a more complex starch
- branched
- 1-4 linkage of alphas with 1-6 branches.
fats structure
- constructed from two kinds of smaller molecules: glycerol and fatty acids
- Glycerol is an alcohol; each of its
three carbons bears a hydroxyl group. - A fatty acid has a long carbon skeleton, usually 16 or 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 - In making a fat, three fatty acid molecules are each joined to glycerol by an ester linkage, a bond between a hydroxyl group and a carboxyl group. The resulting fatis also called a triacylglycerol (3 dehydration rxns)
fatty acid
- The fatty acids in a fat can be all the same or of two or three different kinds
- Fatty acids vary in length (number of carbons) and in the number and locations of double bonds.
saturated fatty acids
- Saturated fatty acids have the maximum number of hydrogen atoms possible (they are “saturated” with hydrogens) and have no double bonds.
- Most animal fats are saturated and are solid at room temperature.
- ex stearic acid
unsaturated fatty acids
- Unsaturated fatty acids have one or more double bonds. Cis double bond causes bending
- Plant fats and fish fats are usually unsaturated and are liquid at room temperature.
- ex oleic acid
phospholipid structure
- hydrophobic part: 2 fatty acid tails (w/ kind due to cis double bond)
- hydrophilic part: the head – choline + phosphate + glycerol
bilayers
When phospholipids are added to water, they self-assemble into double-layered structures called bilayers.
At the surface of a cell, phospholipids are also arranged in a bilayer, with the hydrophobic tails pointing toward the interior.
The existence of cells depends on phospholipids.
why’re fats hydrophobic
The relatively 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 hydrogenbond to one another and exclude the fats
steroids
- lipids characterized by a carbon skeleton
consisting of four fused rings (three rooms and a garage). - Cholesterol, a type of steroid, is
a component in animal cell
membranes and a precursor from
which other steroids are
synthesized.
sex hormones
- Female (estradiol) and male (testosterone) sex hormones are both derived from cholesterol.
- E: -OH (hydroxyl) single-bonded to one end
- T: O atom double-bonded to one end, 1 more methyl (CH3) group
enzymatic proteins
Function: Selective acceleration of
chemical reactions
Example: Digestive enzymes catalyze the
hydrolysis of bonds in food molecules.
defensive proteins
Function: Protection against disease
Example: Antibodies inactivate and help
destroy viruses and bacteria.
storage proteins
Function: Storage of amino acids Examples: - Casein, the protein of milk, is the major source of amino acids for baby mammals. - Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.
transport proteins
Function: Transport of substances
Examples: Hemoglobin, the iron-containing
protein of vertebrate blood, transports
oxygen from the lungs to other parts of the
body. Other proteins transport molecules
across membranes
hormonal proteins
- function: coordination of an organism’s activites
- ex: insulin, a hormone secreted by pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration
receptor proteins
- func: response of cell to chemical stimuli
- ex: receptors built into membrane of nerve cell detect signaling molecules released by other cells
contractile and motor proteins
- func: mvmnt
- ex: motor proteins are responsible for undulations of cilia and flagella. actin and myosin proteins are responsible for the contraction of muscles
structural proteins
- func: support
- ex: keratin is the protein of hair, horns, feathers, and other skin appendages. insects and spiders use silk fibers to make their cocoons and webs, respectively. collagen and elastin proteins provide a fibrous network in animal connective tissues
amino acids
- Amino acids are organic molecules with amino and
carboxyl groups. - Amino acids differ in their properties due to differing side
chains, called R groups. - structure: central carbon atom w/ 4 attachments: H atom, amino group, carboxyl group, R group
making a polypeptide chain
- Amino acids are linked by covalent bonds called peptide bonds. Bond formation is via a dehydration reaction.
- Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)
primary structure
- The primary structure of a protein is its unique sequence of amino acids.
- The primary structure is important for determining its overall structure and function.
The consequences of a single amino acid substitution
A slight change in primary structure can affect a protein’s structure and ability to function.
Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin.
2ndary structure
- Most proteins have segments of their polypeptide chains repeatedly coiled or folded in patterns that contribute to the protein’s overall shape. These coils and folds, collectively referred to as secondary structure, are the result of H bonds between the repeating constituents of the polypeptide backbone (not the
amino acid side chains). - Within the backbone, the O atoms
have a partial negative charge, and the H atoms attached to the N atoms have a partial positive charge; therefore, H bonds can form between these atoms. Individually, these hydrogen bonds are weak, but because they are repeated
many times over a relatively long region of the polypeptide chain,
they can support a particular shape for that part of the protein
2 main 2ndary structures
- alpha helix: a delicate coil held
together by hydrogen bonding between every fourth amino acid - beta pleated sheet: two or more strands of
the polypeptide chain lying side by side (called β strands) are
connected by hydrogen bonds between parts of the two parallel
polypeptide backbones
tertiary structure
Tertiary structure, the overall shape of a polypeptide, results from interactions between R groups, rather than interactions between backbone constituents.
Different types of bonds are found within a protein to allow complex (tertiary) folding.
- H bonds (btwn groups that have polar side chains)
- ionic (between positively and negatively charged side chains)
- hydrophobic interactions: As a polypeptide
folds into its functional shape, amino acids with hydrophobic
(nonpolar) side chains usually end up in clusters at the core of the
protein, out of contact with water. Thus, a “hydrophobic interaction” is actually caused by the exclusion of nonpolar substances by
water molecules. Once nonpolar amino acid side chains are close
together, van der Waals interactions help hold them together - These are all weak interactions in
the aqueous cellular environment, but their cumulative effect helps
give the protein a unique shape.
disulfide bridges
- contributes to tertiary structure
- Disulfide bridges form where two cysteine
monomers, which have sulfhydryl groups (¬SH) on their side
chains, are brought close together by the folding
of the protein. The sulfur of one cysteine bonds to the sulfur of the
second, and the disulfide bridge (¬S¬S¬) rivets parts of the protein together
quaternary structure
- Some proteins consist of two or more polypeptide chains aggregated
into one functional macromolecule. Quaternary structure is the
overall protein structure that results from the aggregation of these
polypeptide subunits. - Collagen is a fibrous protein consisting of three identical
polypeptides coiled like a rope. - Hemoglobin is a globular protein consisting of
four polypeptides: two alpha and two beta chains.
Environmental conditions can affect a protein’s structure and function
- In addition to primary structure, physical and chemical conditions can affect
structure. - Alterations in pH, salt concentration, temperature, or other environmental
factors can cause a protein to unravel. This loss of a protein’s native structure is called denaturation. - A denatured protein is biologically inactive.
- Sometimes renaturation can occur, sometimes it can’t
nucleic acids
— Forms the molecular the basis of inheritance; the
ability to pass on instructions for making proteins from
one generation to the next.
— Has been identified as a constituent of cells for over a
hundred years.
— Had been considered as a component of inheritance
since the 1940s (protein was the other candidate).
watson and crick
The structure of DNA was elucidated in 1953, and
spawned the explosion in molecular biology that
continues today.
nucleic acid structure
• Nucleic acids are polymers also called polynucleotides.
• Each polynucleotide is made of monomers called nucleotides.
- Adjacent nucleotides are joined by a phosphodiester linkage, which consists of
a phosphate group that links the sugars of two nucleotides.
nucleotide vs nucleoside
- nucleotide = nitrogenous base + pentose (5-carbon sugar) + one or more phosphate groups (In a polynucleotide, each monomer has only one phosphate group)
- The portion of a nucleotide without any phosphate groups is called a nucleoside; thus, nucleotide = nucleoside + phosphate
There are two families of nitrogenous bases
- Pyrimidines (cytosine, thymine, and uracil)
have a single six-membered ring. - Purines (adenine and guanine) have a six-membered ring fused to a five-membered
ring.
DNA structure
- DNA molecules are composed of two polynucleotides
spiraling around an imaginary axis, forming a double
helix. - backbone of sugar-phosphate units with nitrogenous
bases as appendages.
gene expression
- synthesis of mRNA in nucleus (DNA –> mRNA)
- movement of mRNA into cytoplasm via nuclear pore
- at ribosome, synthesis of protein using information carried on mRNA
