2.5 Organic Molecules Flashcards
What do proteins do?
most of the cell’s work
- catalysts that accelerate the rates of chemical reactions (called enzymes)
- structural components necessary for cell shape and movement
What do nucleic acids do?
encode and transmit genetic information in their nucleotide sequence
What do carbohydrates do?
provide a source of energy for metabolism and make up the cell wall in bacteria, plants, and algae
What do lipids do?
make up cell membranes, store energy, and act as signaling molecules
What are polymers?
complex molecules made up of repeated simpler units connected by covalent bonds
What is the polymer of amino acids?
proteins
What is the polymer of nucleotides?
nucleic acids
What is the polymer of simple sugars?
carbohydrates
How are lipids defined?
by a property, rather than by their chemical structure
What do lipid membranes that define cell boundaries consist of?
fatty acids bonded to other organic molecules
What do functional groups do?
add chemical character to carbon chains
What are the simple repeating units of polymers based on?
a nonpolar core of carbon atoms
What are functional groups?
groups of one or more atoms that have particular chemical properties on their own regardless of what tjeu are attached to
What are the functional groups that are frequently encountered in biological molecules? (8)
amine (=NH3) amino (-NH2) carboxyl (-COOH) hydroxyl (-OH) ketone (=O) phosphate (-O-PO3H2) sulfhydryl (-SH) methyl (-CH3)
Functional groups containing which atoms are polar?
N, O, P, and S atoms in these groups are more electronegative than the carbon atoms so
functional groups containing these atoms are polar
exception: methyl is nonpolar
What does aqueous mean?
able to disperse in solution throughout the cell
Other information about functional groups.
- because many functional groups are polar, molecules that contain these groups (molecules that otherwise would be nonpolar) become polar and therefore soluble in the cell’s aqueous environment
- because functional groups are polar, they are reactive
What takes place between functional groups?
reactions joining simpler molecules into polymers
What is the general structure of amino acids?
each contain a central carbon atom (alpha carbon) that is covalently linked to 4 groups:
- amino group (-NH2)
- carboxyl group (-COOH)
- hydrogen atom (H)
- R group (or side chain) that differs from one amino acid to the next
What is the identity of each amino acid determined by?
structure and composition of the R group/side chain
What is the pH commonly found in a cell?
7.4
What happens at the pH (7.4) commonly found in a cell?
amino and carboxyl groups are ionized (charged) owing to interactions with the surrounding medium
- amino group gains a proton
- carboxyl loses a proton
*figure 2.17 textbook
What is a peptide bond?
carbon atom in carboxyl group of one amino acid joins the nitrogen atom in the amino group of the next by covalent linkage
What does the formation of a peptide bond involve?
the loss of water
- carbon atom of carboxyl group must release an oxygen atom
- nitrogen atom of the amino group must release two hydrogen atoms
Where does the loss of water occur?
- peptide bond formation
- linking of subunits to form polymers such as nucleic acids and complex carbohydrates
What are cellular proteins composed of?
combinations of 20 different amino acids, each of which can be classified according to the chemical properties of its R group
What does the particular sequence of amino acids determine?
how it folds into its 3D structure, which determines the protein’s function
What are nucleic acids?
informational molecules, which are large molecules that carry information in the sequence of nucleotides that make them up
What is DNA?
deoxyribonucleic acid: the genetic material in all organisms
- transmitted from parents to offspring
- contains the information needed to specify the amino acid sequence of all the proteins synthesized in an organism
What is RNA?
ribonucleic acid: key player in protein synthesis and the regulation of gene expression
What are nucleotides composed of?
5-carbon sugar
base (nitrogen-containing compound)
phosphate group (one or more)
*figure 2.18 textbook
What is the sugar in RNA and DNA?
RNA: ribose
DNA: deoxyribose
What is the difference between ribose and deoxyribose?
ribose has a hydroxyl (OH) group on the second atom (designated the 2 carbon)
deoxyribose has a hydrogen atom at this position
Why are the carbons in sugars numbered with primes (1’ / 2’ etc).
to distinguish them from carbons in the base (1 / 2 etc)
What are bases built from?
nitrogen-containing rings and are of two types: pyrimidine and purine
Describe the pyrimidine bases.
have a single ring and include cytosine (C), thymine (T), and uracil (U)
*figure 2.19 textbook
Describe the purine bases.
have a double-ring structure and include guanine (G) and adenine (A)
*figure 2.19 textbook
What are the bases of DNA? RNA?
DNA: A T G C
RNA: A U G C
What does the sequence of nucleotides determine?
the information in DNA and RNA molecules
What is a phosphodiester bond?
a bond that forms when a phosphate group in one nucleotide is covalently joined to the sugar unit in another nucleotide in each adjacent pair of nucleotides in DNA and RNA
they are relatively stable and form the backbone of a DNA strand
involves the loss of a water molecule
*figure 2.20 textbook
Describe the structure of DNA.
- two strands of nucleotides twist around each other in the form of a double helix
- sugar-phosphate backbones of the strands wrap like a ribbon around the outside of the double helix, and the complementary-paired bases point inwards
*figure 2.21 textbook
What does complementary base pairing result from?
hydrogen bonding between the bases
Why is DNA an efficient carrier of genetic information?
genetic info in DNA is contained in the sequence in which successive nucleotides occur along the molecule
successive nucleotides along a DNA strand can occur in any order, so a long molecule could contain any of an immense number of possible nucleotide sequences
What are carbohydrates?
organic molecules containing C, H, and O atoms (usually in the ratio 1:2:1) that provide a source of energy for metabolism and that forms the starting point for the synthesis of all other organic molecules
What are saccaharides?
aka sugar, the simplest carbohydrate molecule
Describe simple sugars.
linear, or more commonly, cyclic molecules containing 5 or 6 carbon atoms
Describe 6-carbon sugars.
- all have the same chemical formula, C6H12O6
- differ only in configuration (arrangement of atoms)
- ie. glucose, fructose, galactose
*figure 2.21 textbook
What is glucose?
product of photosynthesis
What is galactose?
found in dairy products
What is fructose?
a commercial sweetener
What is a monosaccharide?
another name for a simple sugar
What is a disaccharide?
two simple sugars linked together by a covalent bond
What is sucrose?
C12H22O11 aka table sugar
a disaccharide that combines one molecule each of glucose and fructose
What are polysaccharides?
polymers of simple sugars that provide long-term energy storage (starch and glycogen) or structural support (cellulose in plant cell walls)
What are complex carbohydrates?
long, branched chains of monosaccharides
Describe monosaccharides.
unbranched carbon chains with either an aldehyde (HC=O) or a ketone (C=O) group
What is an aldose?
monosaccharide with an aldehyde group
What is a ketoses?
monosaccharide with a ketone group
What do aldose and ketoses have in common?
in both types of monosaccharides, the other carbons each carry one hydroxyl (-OH) group and one hydrogen atom
when the linear structure of a monosaccharide is written with the aldehyde or ketone group at the top, the carbons are numbered from top to bottom
What form are almost all monosaccharides in cells?
ring form, rather than linear structures
How do monosaccharides form a ring?
one end of the chain bonds to another part of the chain, the carbon in the aldehyde or ketone group forms a covalent bond with the oxygen of a hydroxyl group carried by another carbon in the same molecule
When is cyclic glucose formed?
when the oxygen atom of the hydroxyl group on carbon 5 forms a covalent bond with carbon 1, which is part of an aldehyde group
cyclic structure is approximately flat, can be visualized as being perpendicular to the plane of the paper, with the covalent bonds indicated by thick lines in figure 2.23 textbook
What happens when the ring structure is formed?
- aldehyde oxygen becomes a hydroxyl group
- presence of polar hydroxyl groups through the sugar ring makes these molecules highly soluble in water
What are glycosidic bonds?
covalent bonds that attach one monosaccharide to another
- formation results in the loss of a water molecule
What is a glycosidic bond formed between?
carbon 1 of one monosaccharide and a hydroxyl group carried by a carbon atom in a different monosaccharide molecule
*figure 2.24 textbook
What is starch?
sugar storage molecule in plants composed completely of glucose molecules
What is pectin?
a component of the cell wall that contains up to 5 different types of monosaccharide
How are lipids different from proteins, nucleic acids, and carbohydrates?
instead of being defined by a chemical structure (made up of smaller repeating units with a defined structure), they share a particular property: they are all HYDROPHOBIC
Why are lipids a chemically diverse group of molecules?
because they share a property rather than a structure
Name some examples of lipids in this chemically diverse group of molecules.
- fats that make up part of our diet
- components of cell membranes
- signalling molecules
What is triacylglycerol?
What is it made up of?
lipid that is used for energy storage, it is the major component of animal fat and vegetable oil
3 fatty acids joined to glycerol
- carboxyl end of each fatty acid chain attaches to glycerol at one of the OH groups, releasing a water molecule
*figure 2.25 textbook
What is a fatty acid?
a long chain of carbon atoms attached to a carboxyl group (-COOH) at one end
*figure 2.25 textbook
What is glycerol made up of?
a 3-carbon molecule with OH groups attached to each carbon
*figure 2.25 textbook
How do fatty acids differ?
in length of their hydrocarbon chain (differ in the number of carbon atoms in the chain)
What is a hydrocarbon?
a molecule composed entirely of carbon and hydrogen atoms
Why do most fatty acids in cells contain an even number of carbon atoms?
because they are synthesized by the stepwise addition of 2-carbon units
What are saturated fatty acids?
fatty acids that do not contain double bonds
because there are no double bonds, the maximum number of hydrogen atoms is attached to each carbon atom, so all the carbon atoms are said to be “saturated” with hydrogen atoms
*figure 2.25 textbook
What are unsaturated fatty acids?
fatty acids that contain carbon-carbon double bonds
*figure 2.25 textbook
Compare the chains of saturated and unsaturated fatty acids.
saturated: straight
unsaturated: kink at each double bond
Triacylglycerols can contain different types of fatty acids attached to the glycerol backbone.
- hydrocarbon chains of fatty acids do not contain polar covalent bonds like those in a water molecule
- instead, their electrons are distributed uniformly over the whole molecule, so these molecules are uncharged
- as a consequence, triacylglycerols are all extremely hydrophobic and therefore form oil droplets inside the cell
Why are triacylglycerols an efficient form of energy storage?
by excluding water molecules, a large number can be packed into a small volume
Although fatty acid molecules are uncharged, what leads them to regions of slight positive or negative charges?
- the constant motion of electrons
- these charges, in turn, either attract or repel electrons in neighbouring molecules, setting up areas of positive and negative charge in those molecules as well
- van der Waals forces
*figure 2.26 textbook
What are van der Waals forces?
temporarily polarized molecules weakly bind to one another because of the attraction of opposite charges
When do van der Waals forces come into play?
only when atoms are sufficiently close one another and they are weaker than hydrogen bonds
What do many van der Waals forces do?
many forces acting together help to stabilize molecules
What do melting points of fatty acids depend on?
because of van der Waals forces, they depend on their length and level of saturation
What happens as the length of hydrocarbon chains increases?
- number of van der Waals interactions between the chains also increases
- melting temperature increases because more energy is needed to break the greater number of van der Waals interactions
*figure 2.26 textbook
What do kinks introduced by double bonds do?
reduce the tightness of the molecular packing, and therefore, the n umber of intermolecular interactions
as a result, melting temperature is lower, and unsaturated fatty acids have a lower melting point than a saturated fatty acid of the same length
What are animal fats (ie. butter) composed of?
triacylglycerols with saturated fatty acids, they are solid at room temperature
What are plant fats and fish oils composed of?
triacylglycerols with unsaturated fatty acids, they are liquid at room temperature
What are steroids?
type of lipid
ie. cholesterol
What is the structure of cholesterol?
like other steroids, cholesterol has a core composed of 20 carbon atoms bonded to form four fused rings, and it is hydrophobic
*figure 2.27 textbook
What is cholesterol?
a steroid (type of lipid) that is a component of animal cell membranes and serves as a precursor for the synthesis of steroid hormones such as estrogen and testosterone
What are phospholipids?
another type lipid
the major component of the cell membrane
