Module 2 Unit 1 Flashcards
1
Q
What macromolecules do all organisms contain?
A
Carbohydrates, proteins, lipids, nucleic acids
2
Q
The core of these macromolecules is________?
A
carbon
– Carbon must flow from the atmosphere to photosynthesizers to organisms
3
Q
What are monomers and polymers?
A
- A polymer is a long molecule consisting of many similar or identical building blocks linked by covalent bond
- The repeating units that serve as the building blocks of a polymer are smaller molecules called monomers
- The monomers used to make these polymers are the same across different species
4
Q
What is a dehydration reaction?
A
- The reaction connecting monomers with the formation/loss of a water molecule
- 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)
- a covalent bond is formed between the monomers
5
Q
What is hydrolysis?
A
- a process that is essentially the reverse of the dehydration reaction (how polymers are disassembled by monomers)
- The bond between monomers is broken by the addition of a water molecule, with a hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other
ex. digestion in our bodies; the bulk of the organic material in our food is in the form of polymers that are much too large to enter our cells so enzymes attack these polymers to speed up hydrolysis and the released monomers are then absorbed into the bloodstream for distribution to various cells; those cells can then use dehydration reactions to assemble the monomers into new, different polymers that can perform specific functions required by the cell
- The bond between monomers is broken by the addition of a water molecule, with a hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other
6
Q
Are dehydration and hydrolysis reactions only for polymers?
A
False, can also be involved in the formation and breakdown of molecules that are not polymers, such as some lipids
7
Q
What is the difference between polymers and macromolecules?#
A
- When all the subunits (monomers) are of the same type the macromolecules are called polymers
- When the subunits (monomers) are of different types they are simply referred to as macromolecule
8
Q
What are the different types of monomers?#
A
sugars, amino acids, fatty acids, and nucleotides
9
Q
What are carbohydrates?
A
- comprised of Carbon, Hydrogen & Oxygen in a 1:2:1 ratio
- The simplest carbohydrates are the monosaccharides, or simple sugars
- polymers called polysaccharides, composed of many monomers called monosaccharides
- major source of energy (stored in the arrangements of the electrons in the bonds) and structural support in both plants and animals
10
Q
What is the structure monosaccharides and how are they classified?
A
- generally have molecular formulas that are some multiple of the unit CH2O
- Depending on the location of the carbonyl group, a sugar is either an aldose or a ketose (glucose, C6H12O6, is an aldose and fructose is a ketose)
- Another criterion for classifying sugars is the size of the carbon skeleton which ranges from 3 - 7 carbons long; trisoses are 3 carbons long and hexoses are 6 carbons long
- Monosaccharides don’t just differ in terms of the size of the skeleton or location of carbonyl group, but they also differ in terms of the spatial arrangements around the asymmetric carbon (a carbon that is attached to four different types of atoms or groups of atoms); for example glucose and galactose differ in the spatial arrangement of the hydroxyl group attached to the asymmetric carbon
11
Q
What is the difference between and aldose and a ketose?**
A
- In an aldehyde, the carbonyl group is bonded to at least 1 hydrogen atom and located at the end of the parent chain of the molecule
- A ketone is an organic compound whose molecules have a carbonyl group bonded to 2 carbon atoms in the carbon chain
12
Q
What happens to glucose in aqueous solutions?
A
– In aqueous solutions, glucose molecules, as well as most other five- and six-carbon sugars, form rings, because they are the most stable form of these sugars under physiological conditions
13
Q
What are disaccharide?
A
- consists of two covalently bonded monosaccharides joined by a dehydration reaction called a glycosidic bond (because it is carbohydrates, we describe the linkage as a glycosidic bond)
- Plants generally transport carbohydrates from leaves to roots and other nonphotosynthetic organs in the form of sucrose
- Lactose (a disaccharide) intolerance is a common condition in humans who lack lactase, the enzyme that breaks down lactose
- The sugar is instead broken down by intestinal bacteria, causing formation of gas and subsequent cramping
14
Q
What are polysaccharides?
A
- are macromolecules (polymers) with a few hundred to a few thousand monosaccharides joined by glycosidic linkages
- can function storage molecules (starch, glycogen) or structural compounds (cellulose, chitin)
15
Q
How is the architecture and function of polysaccharides determined?
A
– determined by its sugar monomers and by the positions of its glycosidic linkages
16
Q
What are storage polysaccharides?
A
- Plants store starch, a polymer of glucose monomers
- Most of the glucose monomers in starch are joined by amylose (polypeptide) 1–4 linkages (number 1 carbon to number 4 carbon) which is a straight branch; Amylopectin, a more complex starch, is a branched polymer with 1–6 linkages at the branch points (both alpha glucose monomers)
- Because glucose is a major cellular fuel, starch represents stored energy; the sugar (glucose) can later be withdrawn from this carbohydrate “bank” by hydrolysis
- Animals store a polysaccharide called glycogen, a polymer of glucose with either alpha glucose C-1,4 or C-1,6 linkages
- Hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases. (The extensively branched structure of glycogen fits its function: More free ends are available for hydrolysis)
- This stored fuel cannot sustain an animal for long and must be replenished by eating (why low-carb diets cause weakness and fatigue)
17
Q
What are structural polysaccharides?
A
– the polysaccharide called cellulose is a major component of the tough walls that enclose plant cells
– Like starch, cellulose is a polymer of glucose, with 1–4 glycosidic linkages, but the glycosidic linkages in these two polymers differ; starch is made up of 1,4 linkage of alpha glucose monomers while cellulose is made up of 1,4 linkages of beta glucose molecules (the difference between alpha and beta glucose is the hydroxyl group attached to the number 1 carbon is positioned either below or above the plane of the ring)
– humans and most other animals don’t have the enzymes to break down beta 1,4 linkages (cellulose), however does abrade the walls of the digestive tract to stimulate the secretion of mucus which aids in the smooth passage of food
– Certain starch molecules are largely helical, fitting their function of efficiently storing glucose units. Conversely, a cellulose molecule is straight so some hydroxyl groups are free to hydrogen bond with other hydroxyls of other cellulose molecules lying parallel to it, which forms microfibrils in plant cell walls)
– Another important structural polysaccharide is chitin, the carbohydrate used by arthropods (insects, spiders, crustaceans, and related animals) to build their exoskeletons; Chitin is similar to cellulose, with β
linkages, except that the glucose monomer of chitin has a nitrogen-containing attachment
18
Q
What are lipids?
A
- No monomer or structural unit common to all lipids (not a true polymer and not big enough to be considered macromolecules)
- they are grouped with each other because they share one important trait: They mix poorly, if at all, with water
- Consist mainly of carbon and hydrogen atoms linked by nonpolar covalent bonds, also a smaller amount of Oxygen and phosphorus
- are important in long-term energy storage (contain twice as much energy as carbphydrates)
19
Q
What are the different types of lipids?
A
– fats, phospholipids, steroids
20
Q
What are fats?
A
- Most common form of lipid
- A gram of fat stores more than twice as much energy as a gram of a polysaccharide, such as starch
- A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids (Glycerol is an alcohol; each of its three carbons bears a hydroxyl group; fatty acids are chain of hydrocarbons terminating in a carboxyl group
- A glycerol molecule attached to only one fatty acid is called a monoglyceride, but in making a fat, three fatty acid molecules are each joined to glycerol by an ester linkage, a bond formed by a dehydration reaction between a hydroxyl group in the glycerol and a carboxyl group in the fatty acid (The fatty acids in a fat can all be the same, or they can be of two or three different kinds)
21
Q
What’s the difference between saturated and unsaturated fatty acids?
A
- saturated fatty acids are fats with the maximum number of hydrogens attached to the carbon (no double bonds so all 4 hydrogens are able to bond to the carbon)
- unsaturated fats are fatty acids containing one or more double bonds which are usually cis double bonds that causes bends in the hydrocarbon chain where they occur (this prevents the fatty acids from packing together tightly and solidifying at room temperature while saturated fatty acids lacks double bonds which allows them to pack together tightly); unsaturated fatty acids are usually liquid at room temperatures (oils) while saturated fats are solid at room temperature (butter, animal fats)
22
Q
What are trans fats?
A
- Hydrogenated vegetable oils are unsaturated fats that have been converted to saturated fats by adding hydrogen (eliminating the double bond)
- The process of hydrogenating vegetable oils produces not only saturated fats but also unsaturated fats with trans double bonds
- during the process of hydrogenation, the hydrogens on the same side of the double bond (cis) change to opposite sides of the double bond (trans) which gets rid of the bend/kink making it straight so it can pack tightly together creating trans fat
23
Q
Where do you store fat?
A
- Humans and other mammals stock their long-term food reserves in adipose cells which swell and shrink as fat is deposited and withdrawn from storage
- In addition to storing energy, adipose tissue also cushions such vital organs as the kidneys, and a layer of fat beneath the skin insulates the body (subcutaneous layer)
24
Q
What are phospholipids?
A
- a phospholipid is similar to a fat molecule but has only two fatty acids attached to glycerol
- The third hydroxyl group of glycerol is joined to a phosphate group (P attached to four O), which has a negative electrical charge in the cell
- Typically, an additional small charged or polar molecule is also linked to the phosphate group (ex. choline)
- The hydrocarbon tails are hydrophobic and are excluded from water. However, the phosphate group and its attachments form a hydrophilic head that has an affinity for water
- When phospholipids are added to water, they self-assemble into double-layered structures called “bilayers,” shielding their hydrophobic portions from water (phospholipid bilayer which forms the cell membrane)
25
What are steroids?
- - Lipids in which the carbon skeleton contains four fused rings
- - Different steroids are distinguished by the particular chemical groups attached to this ensemble of rings
- - Cholesterol, a type of steroid, is a common component of animal cell membranes and is also the precursor from which other steroids, such as the vertebrate sex hormones, are synthesized
26
What are proteins?
- - Amino acid monomers are linked together by a dehydration synthesis: joining carboxyl group of one amino acid to the amino group of the next amino acid, and creating a peptide bond.
- - a polymer of amino acids are called polypeptides, and a protein is a biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific three-dime
- - Each specific polypeptide has a unique linear sequence of amino acids
- - The term polypeptide is not synonymous with the term protein; A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape
- - Chemical reactions are enabled by proteins (enzymes)
- - Also form scaffolding/structural support (connective tissue, hair, etc)
27
What are amino acids?
- - An amino acid is an organic molecule with an amino group, a carboxyl group, a hydrogen atom and a variable group symbolized by R
- - At the centre of the amino acid is an asymmetric carbon atom called the alpha ( α ) carbon
- - The R group may be a simple H atom or may be a carbon skeleton with various functional groups attached that bestows different chemical properties on each amino acid which affects protein structure and thus function
- - The R group differs with each amino acid
28
How are amino acids grouped?
- - amino acids are grouped 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
- - Electrically charged side chains: Acidic amino acids are those with side chains that are generally negative in charge due to the presence of a carboxyl group, which is usually dissociated (ionized) at cellular pH (realizes H atom meaning it is acidic); Basic amino acids have amino groups in their side chains that are generally positive in charge
- - Because they are charged, acidic and basic side chains are also hydrophilic
29
What are essential amino acids?
-- A number of these amino acids can be generated by our cells, however some cannot and are referred to as ‘essential amino acids’ which must be taken in by food
30
What is the polypeptide backbone?
- - The polypeptide has a repetitive backbone to which the amino acid side chains are attached
- - one end of the polypeptide chain has a free amino group (N-terminus), while the opposite end has a free carboxyl group (C-terminus)
31
How are proteins folded/shaped?
- - When a cell synthesizes a polypeptide, the chain may fold spontaneously, assuming the functional structure for that protein
- - This is driven by different parts of the chain and the chemical and electrical activities of those R groups (which in turn depends on the sequence and type of amino acids)
- - Many proteins are roughly spherical (globular proteins), while others are shaped like long fibres (fibrous proteins).
- - the function of a protein depends on its ability to recognize and bind to some other molecule (an antibody (a protein in the body) and the particular foreign substance on a flu virus that the antibody binds to and marks for destruction)
32
What is the primary structure of a protein?
- - The primary structure of a protein is its unique amino acid sequence (like the order of letters in a very long word)
- - A change in this sequence may affect the protein’s ability to function (affect its shape)
- - the precise primary structure of a protein is determined by the inherited genetic information (1 codon codes for 1 amino acid and genes are made up of different codons)
- - the primary structure dictates the secondary and tertiary structure
33
What is the secondary structure of a protein?
- - Protein secondary structure results from the formation of H- bonds between repeating constituents of the polypeptide backbone (not the amino acid R group side chains).
- - Within the backbone, the oxygen atoms have a partial negative charge, and the hydrogen atoms attached to the nitrogens have a partial positive charge
- - Results in the formation of coils and folds within the chain; the alpha-helix and beta-sheet
- - the a-helix is a delicate coil held together by hydrogen bonding between every fourth amino acid
- - beta-pleated sheet is when two or more segments of the polypeptide chain lay side by side and connected by hydrogen bonds between parts of the parallel segment
- - Most proteins contain both motifs as part of a larger structure (contains regions of a-helix and regions of b-pleated)
34
What is the tertiary structure of a protein?
- - while the secondary structure involve interactions between the backbone constituents, tertiary structure is the overall final shape of a polypeptide resulting from interactions between the side chains (R groups) of the various amino acids
- - One type of interaction that contributes to the tertiary structure is called a hydrophobic interaction; as a polypeptide folds into its functional shape, amino acids with hydrophobic (non-polar side) chains usually end up in clusters at the core of the protein, out of contact with water and Van Der Waals interactions help hold them together. Meanwhile, hydrogen bonds between polar side chains and ionic bonds between positively and negatively charged side chains also help stabilize tertiary structure
- - The other type of interaction that contributes to the tertiary structure is called a disulphide bridge; form when two cysteine monomers, which have a sulfhydryl group (SH) on their side chains, are brought close together by the folding of the protein. The sulphur of one cysteine bonds to the sulphur of the second and the disulphide bride (-S-S-) brings part of the protein together
35
What is the quaternary structure of a protein?
-- Sometimes, two or more folded polypeptides associate in order to form one functional protein – this is referred to as quaternary structure
36
How does denaturation occur?
- - Environmental conditions can disrupt bond formation and result in denatured or misfolded proteins (pH levels, temperature, salt concentration, etc) because the weak chemical bonds and interactions within a protein may be destroyed causing the protein to unravel (hydrogen bonds, ionic bonds, disulphide bridges)
- - Most proteins become denatured if they are transferred from an aqueous environment to a nonpolar solvent, such as ether or chloroform; the polypeptide chain refolds so that its hydrophobic regions face outward toward the solvent
- - Denaturation can also result from excessive heat, which agitates the polypeptide chain enough to overpower the weak interactions that stabilize the structure
- - When a protein in a test-tube solution has been denatured by heat or chemicals, it can sometimes return to its functional shape when the denaturing agent is removed
37
What are nucleic acids?
- - are polymers (polynucleotides) made of monomers called nucleotides
- - The two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), enable living organisms to reproduce their complex components from one generation to the next
- - DNA provides directions for its own replication and so is copied and passed on to subsequent generations so that they may do the same
38
How does gene expression work?
- - DNA does not build proteins directly - it works through another nucleic acid intermediary: ribonucleic acid (RNA).
- - DNA is transcribed into RNA --> this transcribed RNA is then translated into protein --> proteins go on to control the activities of the cell
- - Each gene along a DNA molecule directs synthesis of a type of RNA called messenger RNA (mRNA). The mRNA molecule interacts with the cell’s protein-synthesizing machinery (ribosomes) to direct production of a polypeptide, which folds into all or part of a protein
39
What does a nucleotide consist of?
- - composed of three parts: a nitrogen-containing (nitrogenous) base, a five-carbon sugar (a ribose), and one or more phosphate groups
- - In a polynucleotide, each nucleotide (monomer) has only one phosphate group but the portion of a nucleotide without any phosphate groups is called a nucleoside
- - In DNA the sugar attached to the nitrogenous base is deoxyribose; in RNA it is ribose; The only difference between these two sugars is that deoxyribose lacks an oxygen atom on the second carbon in the ring
- - To complete the construction of a nucleotide, we attach a phosphate group to the 5′ carbon of the sugar and a hydroxyl to the 3' carbon of the sugar
40
What are nitrogenous bases made up of?
- - Each nitrogenous base has one or two rings that include nitrogen atoms (called bases because the nitrogen atoms take up H+)
- - There are two families of nitrogenous bases: pyrimidines and purines; A pyrimidine has one six-membered ring of carbon and nitrogen atoms (cytosine, thymine, uracil); Purines are larger, with a six-membered ring fused to a five-membered ring (adenine, guanine)
- - The specific pyrimidines and purines differ in the chemical groups attached to the rings
41
How are nucleotides bonded together to form nucleotide polymers?
- -Nucleotides are joined together, sugar to phosphate, into a polynucleotide backbone by dehydration synthesis, generating a covalent linkage referred to as a phosphodiester bond (nitrogenous bases are not part of the backbone)
- - The two free ends of the polymer are distinctly different from each other; one end has a phosphate attached to a 5′ carbon, and the other end has a hydroxyl group on a 3′ carbon
42
How is DNA/RNA structured?
- - DNA molecules have two polynucleotides, or “strands,” that wind around forming a double helix
- - The two sugar-phosphate backbones run in opposite 5’ → 3’ directions from each other; this arrangement is referred to as antiparallel
- - The two strands are held together by hydrogen bonds between the paired bases
- - in DNA, Adenine (A) in one strand always pairs with thymine (T) in the other, and guanine (G) always pairs with cytosine (C) - in other words, a purine nitrogenous base always pairs with its complementary pyrimidine base
- - -- The linear order of bases in a gene specifies the amino acid sequence—the primary structure—of a protein
- - RNA molecules, by contrast, exist as single strands. Complementary base pairing can occur, however, between regions of two RNA molecules or even between two stretches of nucleotides in the same RNA molecule
- - base pairing within an RNA molecule allows it to take on the particular three-dimensional shape necessary for its function (a tRNAs functional shape results from base pairing between nucleotides)
- - Note that in RNA, adenine (A) pairs with uracil (U); thymine (T) is not present in RNA
