Term
| what are the 4 kinds of macromolecules? |
|
Definition
| carbohydrates, lipids, nucleic acids, proteins |
|
|
Term
| why are the macromolecules so large? |
|
Definition
| becuase they are a series of small molecules linked up my polymerization. They are all organic molecules and thus contain many C-H bonds |
|
|
Term
| what are functional groups? |
|
Definition
| small side groups of molecules that hang off of the large molecule and give it certain properties |
|
|
Term
| what is dehydration synthesis? |
|
Definition
| the process by which all of the macromolecules are formed. Two molecules are joined by the removal of a water molecule |
|
|
Term
| what is the process that is the reversal of dehydration synthesis? |
|
Definition
| Hydrolysis. An H20 group is added to split a molecule |
|
|
Term
|
Definition
| a macromolecule made up of CHO in a ratio of 1 C and 1 O for every 2 H (CH2O)n |
|
|
Term
| why are C-H bonds so important to carbohydrates? |
|
Definition
| because they release a lot of energy when oxidized so they are good for storing energy |
|
|
Term
| what is an example of one of the most common kinds of carbohydrates? |
|
Definition
|
|
Term
| what are the three classes of sugars? |
|
Definition
| monosaccharides, disaccharides and polysaccharides |
|
|
Term
| which sugars are important biologically? |
|
Definition
| ones that contain 3, 4, 5, and 6 carbons |
|
|
Term
| what is the most important sugar biologically? |
|
Definition
|
|
Term
| what are the structural characteristics of glucose? |
|
Definition
| 6c with CH2OH off 5th C, O in top right of ring, OH is up on 3C, down on all others. Glucose almost always forms a ring in water |
|
|
Term
| what is a structural isomer? |
|
Definition
| two molecules that have the same molecular formula, but are structurally different. i.e. O double bond on a different numbered carbon |
|
|
Term
|
Definition
| two molecules who have the same molecular formula and same structure, just in a different orientation, i.e. the OH and H are swapped around one carbon. *only possible on a chain with 4 or more carbons |
|
|
Term
| what are the two different isomers of carbohydrates that can exist and which ones are used in Bio and why? |
|
Definition
| D or L, only D (detro) is used in Bio because the enzymes only bind to the d shape |
|
|
Term
| what are the 3 most common kinds of 6 carbon sugars? |
|
Definition
| glucose, galactose and fructose |
|
|
Term
| which of the 6 c sugars are stereo isomers? |
|
Definition
|
|
Term
| what is the difference between ribose and deoxyribose? |
|
Definition
| both 5 c sugars, however, deoxyribose just has an H on C2 where ribose has an OH |
|
|
Term
| what are the 2 different shapes a glucose can form? |
|
Definition
| alpha or beta. alpha OH down on C1, beta OH up on C1 |
|
|
Term
| what shapes do the alpha and beta forms correspond to? |
|
Definition
|
|
Term
| what are the three most common disaccharides? |
|
Definition
maltose (2 glucose)
sucrose (1 glucose + 1 fructose)
lactose (1 glucose + 1 galactose) |
|
|
Term
| maltose is most common in what? |
|
Definition
|
|
Term
| sucrose is most common in what? |
|
Definition
| table sugar, cane sugar, easily digestible |
|
|
Term
|
Definition
| in breast milk and milk generally. although our gene to digest it gets turned off during childhood |
|
|
Term
| how are most disaccharides formed? |
|
Definition
| through a 1, 4 glycosidic linkage, essentially dehydration synthesis that results in an alpha or beta bond |
|
|
Term
|
Definition
| a chain of alpha glucose subunits linked by a glycosidic bond. Amylose is linked at C1, 4 and amylopectin is linked at C1, 6 |
|
|
Term
| what kind of starch is linked at C1, 4? |
|
Definition
|
|
Term
| what kind of starch is linked with alpha glycosidic linkages at C1, C6? |
|
Definition
|
|
Term
| in plants starch is always _______ |
|
Definition
| a mix of amylose and amylopectin |
|
|
Term
| what is cellulose aka dietary fiber? |
|
Definition
| chains of beta linked glucose that occurs in plants. humans cannot digest it, that's why we call it fiber. |
|
|
Term
| how are starches broken down? |
|
Definition
| by enzymes in our saliva that eat up the starch by breaking it down into maltose, however they can only do this to the branch points in a chain (when it becomes amylopection). At this point it gets passed to the intestine where the amylopectin will be digested |
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|
Term
|
Definition
| up to three fatty acid chains connected to a glycerol group |
|
|
Term
| what do we know about the number of carbons in the fatty acid tail of a lipid? |
|
Definition
| there is always an even number because it is formed of units of acetic acid which exist in 2's |
|
|
Term
| what happens when a lipid is placed in H20? |
|
Definition
| it forms a micelle. the hydrophobic non-polar tails face in and the heads face outwards. |
|
|
Term
| lipids are said to be amphipathic, what does this term mean? |
|
Definition
| that they have 2 sympathies, they can act as both polar and non polar because the head is polar and the tail is non polar |
|
|
Term
| When lipids form the fatty acid is _______ to the glycerol |
|
Definition
|
|
Term
| What is the difference between a saturated and unsaturated fat? |
|
Definition
| *in saturated fats the fatty acid chain is neutral, all of the carbons are linked to as many H’s as possible. The tails are straight and do not have bends. However, in unsaturated fats some of the carbons in the chains have double bonds which causes the tails to bend. This is usually the case in plant oils and why they are not solid at room temp, because they cannot pack flat. |
|
|
Term
| Which macromolecules are easiest to breakdown? Which are most energy dense? |
|
Definition
| *carbs are easiest to digest on a day to day level, however lipids are the most energy dense of the macromolecules, i.e. the most calories per gram. |
|
|
Term
| what are three kinds of lipids other than fats? |
|
Definition
| phospholipids, steroids, terpenes, waxes or prostoglandins |
|
|
Term
| what kind of structure do phospholipids form? |
|
Definition
| phospholipid bilayer, found in most cell membranes |
|
|
Term
| what happens to phospholipids in H20? |
|
Definition
| they form vesicles, basically a ring of a phospholipid bilayer where H20 is both on the inside and outside. |
|
|
Term
| what is the function of lipids? |
|
Definition
| "The main biological functions of lipids include energy storage, as structural components of cell membranes, and as important signaling molecules." |
|
|
Term
| what is the function of nucleic acids? |
|
Definition
| to store and transfer genetic information |
|
|
Term
| what are the 2 kind of nucleic acids? |
|
Definition
|
|
Term
| what are the major structural components of a nucleic acid? |
|
Definition
| phosphate group, sugar and nitrogenous base (ex. adenine) |
|
|
Term
| what is the monomer unit for a nucleic acid? |
|
Definition
|
|
Term
| what is the primary molecular difference between DNA and RNA? |
|
Definition
| DNA has an H on the 2' C of the sugar molecule, where RNA has an OH |
|
|
Term
|
Definition
| sugar + nitrogenous base (no phosphate) |
|
|
Term
| how do the sugar and phosphate group in a nucleotide link together? |
|
Definition
-through dehydration synthesis.
-the phosphate becomes esterified, loses Hs and becomes an Acid |
|
|
Term
| what are the 2 classes of nitrogenous bases? |
|
Definition
| purines and pyramidines. purines have 2 rings, pyramidines have only 1 |
|
|
Term
| what are the two purines? |
|
Definition
| adenine and guanine. "A" and "G" |
|
|
Term
| what are the three pyramidines? |
|
Definition
| Cytosine "C", Thymine "T" *DNA only, and Uracil "U" RNA only |
|
|
Term
| to elongate a nucleic acid, always add at the ___ end |
|
Definition
|
|
Term
| how are multiple nucleotides joined? |
|
Definition
| the OH group at the 3' C on the sugar synthesizes with the OH group on the phosphate of another nucleotide, H2O leaves. There are now 2 ester groups at the phosphate group |
|
|
Term
| which bond is stronger, AT or CG? |
|
Definition
| CG because it has 3 H bonds (AT has 2) |
|
|
Term
| what forms the backbone of DNA? |
|
Definition
|
|
Term
| where do most regulatory proteins bind to DNA? |
|
Definition
|
|
Term
| what is ATP? what is it used for? |
|
Definition
adenosine triphosphate
-nucleotide precursor that is used to make RNA* verify RNA not DNA*, it is an energy containing molecule |
|
|
Term
| what is a protein? what is its function |
|
Definition
polypeptide. (series of amino acids linked by peptide bonds)
-function: workhroses of the cell, hold things together and transport material around the cell |
|
|
Term
| what is the monomer for proteins? |
|
Definition
| amino acids (20 diff ones) |
|
|
Term
| what are the kinds of categories for amino acids? |
|
Definition
non-aromatics (non polar vs. polar, if charged, basic or acidic)
aromatics.
these properties are carried along to the proteins that result from these amino acids |
|
|
Term
| what isomers are all amino acids except glysine? |
|
Definition
|
|
Term
| what is the general structure of an amino acid? |
|
Definition
a central carbon that is attached to:
1. amino group
2. acid group
3. R group which determines its identity |
|
|
Term
|
Definition
| an ion with a double charge, ex. an amino acid which has a + on the amino group and - on the acid group |
|
|
Term
| what shape do the bond angles around the central C in an amino acid form? |
|
Definition
|
|
Term
| what are these examples of: glycine, lysine, tyrosine? |
|
Definition
|
|
Term
| what is the function of: proline? |
|
Definition
| adds a link to a chain. usually found at turns in structures |
|
|
Term
| what is the function of: methionine? |
|
Definition
R group has a sulfur.
it is ALWAYS the first amino acid in a polypeptide chain |
|
|
Term
| what is the function of: cysteine? |
|
Definition
| can form a disulfide bond to another cysteine. this bond is significant to the final shape of the protein |
|
|
Term
| what are some characteristics of a peptide bond? |
|
Definition
1.flexible but stiff right at the bond
2. e- density shared by all 4 members of the bond
3. link together amino acids in polypeptide chains |
|
|
Term
| how is a peptide bond formed? |
|
Definition
|
|
Term
| how many amino acids are in an average protein? |
|
Definition
|
|
Term
| what amino acid starts all polypeptide chains? |
|
Definition
|
|
Term
| how are polypeptide chains named? |
|
Definition
| numeral prefix for # of amino acids + peptide |
|
|
Term
| polypeptide chains must be added to from the ________? |
|
Definition
| terminus or carboxy group |
|
|
Term
| what is the primary structure of a protein? |
|
Definition
| the sequence of amino acids beginning with methionine |
|
|
Term
| what do we call a group of only a few peptides? |
|
Definition
|
|
Term
|
Definition
| always in the same way every time, and usually with the hydrophobic R groups facing the interior of the protein |
|
|
Term
| what 5 things determine the shape of a protein? |
|
Definition
1. H bonds
2. Disulfide bonds (cysteine)
3. Ionic bonds
4. inst. dipole/ van der waals forces
5. hydrophobic exclusion |
|
|
Term
| what are the two kinds of disulfide bonds that can form? |
|
Definition
interchain: between two chains
intrachain: between the same chain that is bent |
|
|
Term
| what can cause proteins to denature or change shape? |
|
Definition
-heat
-changes in pH
-detergent
-changes in ionic condition
-changes in the ReDox state |
|
|
Term
| what kinds of hydrogen bonds occur in proteins? |
|
Definition
1. between 2 peptide bonds
2. between a peptide bond and an R group
3. between 2 r groups |
|
|
Term
| what is the secondary level of protein structure: |
|
Definition
alpha helix or beta sheets
local structure, H-bonding |
|
|
Term
| What adds stability to an alpha helix in a protein structure? |
|
Definition
| H bonds between NH and CO every 4th residue |
|
|
Term
| what is the tertiary structure in proteins? |
|
Definition
| combination of beta sheets and alpha helixes |
|
|
Term
| what is the quaternary structure in proteins? |
|
Definition
| viewing the whole molecule, i.e. all of the tertiary structures combined, the final product |
|
|
Term
| what is a prosthetic group? |
|
Definition
| an extra thing a protein has to have for added function |
|
|
Term
| what is covalent modification? |
|
Definition
| a way for cells to control the activity of enzymes. i.e. that they are only turned "on" when the enzyme gains a phosphate group. |
|
|
Term
|
Definition
| A set or group of secondary structures in the sub region that commonly reoccur and effect the STRUCTURAL identity of the protein |
|
|
Term
| what is a protein domain? |
|
Definition
| functional sub-regions or tertiary structures that effect the functional identity i.e a "DNA binding domain" |
|
|
Term
| what are molecular chaperone proteins and what do they do? |
|
Definition
| they are proteins that function much like enzymes and facilitate the folding of other proteins without becoming part of the final product. they make sure proteins fold correctly and fix damaged proteins, help quaternary formation of multi subunit proteins |
|
|
Term
| what are the 2 classes of chaperone proteins? |
|
Definition
|
|
Term
| how do misfolded proteins effect other proteins? |
|
Definition
| the cause other proteins to change shape also |
|
|
Term
| what diseases are misfolded proteins associated with? |
|
Definition
| alzheimer's, mad cow disease |
|
|
Term
| what kinds of higher order structures do proteins form? |
|
Definition
|
|
Term
| which amino acids are non polar? |
|
Definition
| non aromatics whose R groups are hydrocarbon chains, |
|
|
Term
| which amino acids are polar uncharged? |
|
Definition
| non aromatics without a charge that have other functional groups than just CH on the R group |
|
|
Term
| which amino acids are basic? |
|
Definition
| non aromatics that have a + charge |
|
|
Term
| which amino acids are acidic? |
|
Definition
| non aromatics with a - charge |
|
|
Term
| what are the three tenets of cell theory? |
|
Definition
1. all organisms are made of cells
2. a cell is the smallest unit of life
3. cells arise only from other cells |
|
|
Term
| what is the most general form possible for a cell? |
|
Definition
| genetic material and cytoplasm surrounded by a plasma membrane |
|
|
Term
| what are the two kinds of cells? |
|
Definition
| prokaryotes and eukaryotes |
|
|
Term
| what are the three major differences between prokaryotes and eukaryotes? |
|
Definition
| prokaryotes do not have a nucleus, they don't have compartments or organelles, and they are 10 times smaller than eukaryotes |
|
|
Term
| what is the purpose of the flagellum in a prokaryotic cell? |
|
Definition
| -drives the cell forward (relatively stiff, spins on axis) |
|
|
Term
| what are the little arms that stick off of prokaryotic cells and what do they do? |
|
Definition
| pili, they help the cell attach to other things |
|
|
Term
| what are the three layers from inside to out of the prokaryotic cell? |
|
Definition
| the plasma membrane, peptidoglycan cell wall, and the capsule |
|
|
Term
| what are the three major differences between a plant an animal eukaryotic cells? |
|
Definition
| plants have a cellulose based cell wall, they have a large central vacuole and they have cytoplasts for photosynthesis |
|
|
Term
| what is the main advantage of eukaryotic cell compartments? |
|
Definition
| it allows the cell to distribute/isolate various functions without interference from the cytoplasm |
|
|
Term
| what is the nuclear lamina |
|
Definition
| a layer of fibrous material on the inside of the nuclear membrane |
|
|
Term
| what goes in and goes on in the nucleus? |
|
Definition
-proteins that make DNA and enzymes
-DNA makes copies of RNA that leave the nucleus
-lots of traffic at the nuclear pore that complex proteins have to regulate |
|
|
Term
| what is the nucleolus and what happens in it? |
|
Definition
-it is the area inside the nucleus where ribosomes are assumbled.
sort of a fibrous substructure, since technically there are no major substructures in the nucleus |
|
|
Term
|
Definition
| DNA and associated proteins in the nucleus |
|
|
Term
|
Definition
| the lighter chromatin which includes the active parts of the DNA |
|
|
Term
| what is the Heterochromatin? |
|
Definition
| the darker areas of the chromatin where the inactive parts of DNA are located. Scientests think that it appears darker because the inactive parts of DNA are compressed so there is a greater density in that area |
|
|
Term
| What happens to the parts of DNA that code for a different kind of cell? i.e. bone-coding DNA in a skin cell? |
|
Definition
|
|
Term
| what is the function of lysosomes? |
|
Definition
to digest cellular components, typically:
-damaged or old cells
-food that is brought into the cell |
|
|
Term
| how does a lysosome digest material? |
|
Definition
1. it begins as a primary lysosome with pH 7
2. it fuses with the cell it will digest, and dumps its enzymes into the cell
3. it turns on a protein pump that acidifies the cell to a pH of about 5 and turns the enzymes on. the cells are then digested or destroyed. |
|
|
Term
| what are the two kinds of endoplasmic reticulum? |
|
Definition
|
|
Term
| what are the main differences between smooth and rough er? |
|
Definition
rough er actually looks smooth and has ribosomes attached to it. this is where proteins that will be exported are synthesizd.
smooth er looks rough, no enzymes, synthesizes lipids and carbohydrates, has detoxifying activity |
|
|
Term
| True/ False: the ER lumen is contiguous with the cytoplasm? |
|
Definition
|
|
Term
| where are the proteins made that are not for export? |
|
Definition
| on free ribosomes in the cytoplasm |
|
|
Term
| how does the signalling hypothesis work? |
|
Definition
signal contained in DNA of protein that it will be exported.
signal section of amino acid is recognized by the signal recogniation particle (SRP)to ship out.
the SRP takes the protein to the smooth ER membrane where it will be shipped out. |
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