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Cell Chapter 3
| Term | Definition |
|---|---|
| contain carbon + hydrogen (hydrocarbons | organic molecules |
| living organisms | Where are organic molecules abundant? |
| large, complex organic molecules | macromolecules |
| 4 valence e-; can make 4 bonds so very reactive (H,O,N); lends to our ability to live in extreme conditions because C-C bonds are very short and are not broken by physical factors; diff types of compounds with different properties to help sustain life | carbon (alpha element) |
| a set of atoms that comes together that haven't fulfilled the octet rule; each brings in their own set of physical and chemical properties; ex. compounds with alcohol functional groups all ahve similar properties | functional group |
| one or more of the hydrogens bonded to the carbon skeleton of a hydrocarbon | chemical groups can replace... |
| by being directly involved in chemical reactions | How do functional groups affect molecular function? |
| Hydroxyl (OH), Carbonyl (CO), Carboxyl (COOH), Amino (NH2), Sulfhydryl (SH), Phosphate (PO4 ^2-), Methyl (CH3) | Names of functional groups and their formulas |
| compounds with an identical molecular formula and same number of elements but different structures and characteristics (physical and chemical properties) based off of bonding relationship or spatial organization; ex. C6H12O6 | isomer |
| structural and stereo | types of isomers |
| contain the same atoms but in different bonding relationships | structural isomers |
| identical bonding relationships, but the spatial positioning of the atoms differs in the two isomers | stereo isomers |
| geometric and enantiomers | sub-groups of stereo isomers |
| positioning around double bond or functional groups | geometric isomers |
| mirror image of another molecule | enantiomers |
| linear forms of glucose and fructose | example of structural isomers |
| alpha/beta glucose ring forms; cis/trans isomers | examples of geometric stereo isomers |
| linear form of glucose and fructose (even just 1) | examples of enantiomer stereo isomers |
| trans isomers | Are cis or trans isomers more stable? |
| starts as unsaturated fat, very bad for you because body can't break it down; ex. heat olive oil, starts as unsaturated fat then heat changes bonds from cis to trans and hydrogen introduced breaks double carbon bonds | trans-fat |
| an organic molecule called adenosine attached toa string of three phosphate groups; stores the potential to react with water, releasing energy for the cell; energy currency (like a dollar bill); nucleotide (ribonucleotide); core molecule is penta-sugar | ATP (adenosine triphosphate) |
| add phosphates | How do you form a nucleotide from a nucleoside? |
| form of electrostatic repulsion between negatively charged phosphate molecules | Where does ATP store its energy? |
| carbohydrates, proteins, nucleic acids, lipids | Four macromolecules |
| never any from nucleic acids; 1 gram of carbs/proteins = 4.3 cals; 1 gram lipids = 9.3 cals | energy of macromolecules |
| easy source of energy; provide structure through cartilage (dobby's ears) | Carbohydrate functions |
| long term energy source; best form of storing energy; hormones; prostaglandin mediates inflammation response | lipids function |
| 1- tools of gene instruction; 2- workhorse of the cell (structure of proteins determines function of cell); most important - capacity to catalyze | proteins function |
| DNA: storing information; RNA: gene expression (translation); also catalysis (ribozyme) | Nucleic acids function |
| often polymers; formed by dehydration synthesis and broken by hydrolytic cleavage (n-1 rule) | macromolecules |
| long molecule built by linking together small, similar subunits | polymers |
| removes OH and H (water) during synthesis of a new molecule; ex. Four monomers are put together to form a polymer, and it releases water | dehydration synthesis |
| hydrolysis breaks a covalent bond by adding OH and H (water) | hydrolytic cleavage |
| If I put together 500 molecules to make a polymer, I will lose 499 water molecules (n-1); If I have a polymer made of 500 monomers I need to put in 499 water molecules to break it | n-1 rule for dehydration synthesis and hydrolytic cleavage |
| hydrated carbon Cn(H2O)n; number of C-H are less than lipids so easier energy to break; C-H non-polar, C-O polar); transport energy through sugars (blood glucose in a blood test) | carbohydrates |
| classified based on number of carbon atoms they contain; building block of polysaccharides | monosaccharides |
| 3 carbons, glyceraldehyde (byproduct of glucose metabolism; helps to make lipids also) | trios monosaccharides |
| 4 carbons (cellulose, etc.) | tetrose monosaccharide |
| 5 carbons; ribose and deoxyribose (missing an oxygen at the second carbon) | pentose monosaccharides |
| 6 carbons (glucose, galactose, fructose) | hexose monosaccharides |
| carbs composed of two monosaccharides; glucose + fructose = sucrose (glycosidic bond); glucose + galactose = lactose; glucose + glucose = maltose (maltose forms starch) | disaccharides |
| many monosaccharides come together to form long polymers; structural component (cellulose and cartilage) and energy component (starch and glycogen | polysaccharides |
| Cellulose: formed by beta glucose; herbivores and termites don't have capacity to break down cellulose, but they have bacteria in their tummy that release cellulase to break it down | What is the structural component of polysaccharides in plants? |
| cartilage: long chains of polysaccharides connected by negatively charged disaccharides (attract water which forms a cement like hardy substance); presence of glycosaminoglycans; ex. crab shell | What is the structural component of polysaccharides in animals? |
| starch: rice (amylose pockets of glucose) vs. potatoes (amylopectin); water reaches amylopectin polar branches in 80% of potatoes so they boil faster | What is the energy component of polysaccharides in plants? |
| glycogen: very complicated branch for of energy storage for animals (how humans store polysaccharides) | What is the energy component of polysaccharides in animals? |
| made of C,H,O,N and small amounts of sulfur (cystine and methine); used for storage, structure, immunity (antigens/antibodies), enzymes | Proteins |
| monomer of proteins; common structure with variable R group that determines structure and function; R and H group flip to form isomers (except in glycine where R group is H); total 20 | Amino Acids |
| CH2, CH3 | Non-polar amino acids |
| OH, NH2 | polar uncharged amino acids |
| acids and bases | charged amino acids |
| aromatic carbon ring with single or double bonds | aromatic amino acids |
| methionine: if AUG start coder is not present in mRNA for translation, methionine can initiate; cysteine: HS group, can connect long chains of amino acids; proline: can break up long chain of amino acids | special-functioning amino acids |
| those that we don't make in our body and must be consumed through food (8/20) | essential amino acids |
| polymer of proteins; proteins are made of 1 or more polypeptides; formed by amino acids through dehydration synthesis or condensation reaction; broken by hydrolysis; the first amino acid in chain will have N+ terminal and last will have C- terminal | polypeptides |
| made of amino acids hooked end to end like a bracelet; twist and fold to activate; final shape determines function | Structure of a protein |
| have only 1 polypeptide (primary --> secondary --> tertiary) | Simple Proteins |
| have more than 1 polypeptide (primary--> secondary --> tertiary --> quaternary) | Multimeric (Complex Proteins) |
| DNA to RNA; part of gene expression | transcription |
| how the structures of the protein are formed; taking codes on mRNA and arranging amino acids based on sequence codes | translation |
| bacteria have collinearity between DNA and RNA strands because of lack of introns; Eukaryotes and Archaea first make an exact copy of pre-RNA and then they remove the introns and splice the exons together (collinearity is absent) | How is translation different in Bacteria vs. Eukaryotes and Archaea |
| peptide bonds; as mRNA is being translated into a string of amino acids, the first long string is primary structure; will never see this structure in a cell, but it is important because structure and function are determined by primary structure | Primary Structure |
| 1 changed amino acid can result in loss of structure and function of the protein; ex. one of Hb beta globin's converts glutamic acids (charged) to valine (non-polar) which causes sickle shape (loss of oxygenation and clots); anemia, reduced life (30 yrs) | Why is the primary structure important? |
| hydrogen bonds; when AA chain reaches certain length, first folding in a protein using H-bonds is the 2ndary structure | Secondary Structure |
| Alpha helices, beta pleated, motif | What are the different shapes in a secondary structure? |
| formed when hydrogen bonds arise from distant amino acids of a chain | Alpha helices |
| formed when hydrogen bonds arise from adjacent amino acids as they fold | beta pleated |
| turn, loop, randomly coiled structure, or supercoiled structure that connects two primary structures together soon after they are formed using hydrogen bonds but lacks the structural organization of alpha helices or beta pleated | motif |
| the strength of the protein; ex. black widow web is very strong (7x steel) | What does the secondary structure determine? |
| H-Bonds, Ionic/polar bonds/interactions, hydrophobic bonds, Van der Waals, disulfide bridges; folding that gives protein complex 3D shape; ex. hydrophobic exclusion pushes non-polar AA to the center of the protein | Tertiary Structure |
| Disulfide bridges found between amino acids containing sulfur (most commonly cysteine) | What is the only covalent bond present in tertiary structure? |
| H-Bonds, Ionic/Polar Bonds/Interactions, hydrophobic bonds, Van der Waals, VERY FEW disulfide bridges; only present in multimeric proteins; presence of Domains; | Quaternary structure |
| part of a protein that helps with the function of the proteins; has its own shape and its own sequence of amino acids and its particular function; usually formed when protein goes through its final folding, ultimate structure | Domain |
| Yes, if part of their function is identical; ex. Sucrase has glucose-binding and fructose-binding domains and maltase has two glucose-binding domains even though one breaks apart sucrose and one breaks apart maltose | Can a domain that is in one protein be seen in a totally different protein? |
| NOT COVALENT (don't want milky way to stick to tongue forever); Temporary forces of attraction: hydrogen, ionic/polar, hydrophobic, Van der Waals | What type of bonds exist between proteins? |
| Denaturation and Disassociation | What determines protein function? |
| unfolding of a protein; all bonds broken except peptide; all proteins can denature; if not renatured, risk of disease; ex. albumin in egg whites denatures with heat; ex. forehead proteins denature with fever, must renature or at risk for metabolic disease | Denaturation |
| polypeptides of a multimeric protein disengage; only multimeric proteins can dissociate; no disease involved; ex. alpha globins and beta globins in Hb drift apart | Dissociation |
| class of heat shock proteins that have the capacity to identify and bond to misfolded proteins | Chaperone Protein |
| HSP 70 binds with ATP which increases its affinity to bind with an unfolded protein and its domain opens; HSP 40 is the co-chaperone that brings in the misfolded protein and drops it in the domain; hydrolysis of ATP occurs and HSP protein's cap closes the | How does chaperone protein function pt. 1? |
| the misfolded protein very firmly inside (giving proper environment for refolding); the protein renatures; nucleotide exchange factor brings in more ATP so that the HSP 70 no longer has an affinity to bind with the renatured protein | How does chaperone protein function pt. 2? |
| the cap raises and the HSP 70 pushes the refolded protein out | How does chaperone protein function pt. 3? |
Created by:
MBarfield