| Term | Definition |
|---|
| transcription | How we get to protein: _______ of DNA to messenger RNA, translation of messenger RNA to polypeptide chains. |
| messenger | How we get to protein: transcription of DNA to _______ RNA, translation of _______ RNA to polypeptide chains. |
| translation | How we get to protein: transcription of DNA to messenger RNA, _______ of messenger RNA to polypeptide chains. |
| polypeptide | How we get to protein: transcription of DNA to messenger RNA, translation of messenger RNA to _______ chains. |
| peptide | The bond that is formed when a protein is made is called the _______ bond and it has some interesting features that will affect the structure of the forming protein strands. |
| pi-system | The peptide bond exists in a _______ resonance between three atoms, the carbonyl oxygen, the carbonyl carbon and the amide nitrogen. |
| oxygen | The peptide bond exists in a pi-system resonance between three atoms, the carbonyl _______, the carbonyl carbon and the amide nitrogen. |
| carbon | The peptide bond exists in a pi-system resonance between three atoms, the carbonyl oxygen, the carbonyl _______ and the amide nitrogen. |
| nitrogen | The peptide bond exists in a pi-system resonance between three atoms, the carbonyl oxygen, the carbonyl carbon and the amide _______. |
| planar | The resonance causes a peptide bond to be rigid and thus holds the amide group in a _______ conformation to the other atoms in the peptide. |
| secondary | The planar conformation of peptide bonds is essential to bonding in the _______ structures of proteins. |
| primary | The _______ structure: the amino acid sequence that makes up the protein or polypeptide |
| secondary | The _______ structure: or the way that this strand of amino acids orients itself in the protein structure: these are the alpha helix and beta strand structure that you may have heard about in earlier classes. |
| tertiary | The _______ structure of a protein is the way that the entire polypeptide folds to form a unit of protein, a monomer. Tertiary structures can be globular, fibrous or barrel proteins of one or more secondary structure types. |
| Quaternary | _______ structure of proteins is the orientation of multiple monomers to form a large protein. Proteins can have very complex quaternary structures. |
| unique | The primary structure of proteins is _______ for each protein. |
| amino | The primary structure is numbered from the _______ end of the polypeptide to the carboxyl end. |
| carboxyl | The primary structure is numbered from the amino end of the polypeptide to the _______ end. |
| acid aminos | An easy way to remember how the peptide chain runs is to remember that we call them amino acids, not _______. |
| disulfide | ribonuclease is a single chain, that folds in such a way that _______ bonds can form between the cysteines. |
| proximal | cysteines can form disulfide bonds when they are _______ to each other. |
| Within | _______ a species, specific proteins will have the exact same sequence of amino acids, but between species, there may be differences in the amino acids used in the sequence. |
| between | Within a species, specific proteins will have the exact same sequence of amino acids, but _______ species, there may be differences in the amino acids used in the sequence. |
| mitochondrial | Cytochrome C is a very common _______ protein found in animals, plants and fungi. |
| electron | Cytochrome C functions as part of the _______ transfer chain in energy production within the mitochondria. |
| 104 | Cytochrome C is a protein of _______ residues or amino acids. |
| interrelatedness | The number of mutations is a measure of the _______ of the species. |
| function | A protein can have many differences in amino acid sequence but still have the same _______ across species. |
| ATP | cytochrome Cs can transfer electrons along the mitochondrial membrane and help to make _______ through oxidative phosphorylation. |
| mutations | By studying the _______ within a protein, we can make assumptions about the evolutionary path that species has taken and derive relationships between species that may not be obvious from the gross morphology of the organisms. |
| phylogenetic | But one has to be careful when studying mutations, and many genes should be compared when defining _______ relationships. |
| fibrous | one of the three protein structures: the _______ protein, where monomers can interact to form long thin proteins, such as we see with collagen and myosin. |
| globular | One of three protein structure: Proteins can also be _______, and this class of protein structure is the most common with soluble proteins, that is, proteins that exist free in the cytosol or other biological fluids. |
| membrane | Finally we have _______-bound proteins like bacteriorhodopsin or the glucose transporter. These proteins will be integral to the membrane, that is, inserted into the membrane and can function to either transport other molecules across the membrane or receive signals from the extracellular matrix and transmit these into the cell. |
| beta | The primary sequence of proteins can form two major secondary structures: the _______ strand, which often forms into a super-secondary structure of sheets, thus called _______ sheets, and the alpha helix. |
| alpha | The primary sequence of proteins can form two major secondary structures: the beta strand, which often forms into a super-secondary structure of sheets, thus called beta sheets, and the _______ helix. |
| one | a beta strand is composed of _______ strand. |
| many | a beta sheet is composed of _______ strands. |
| bonds | Why does a primary sequence form a beta strand or an alpha helix? The folding of proteins into these two secondary structures depends on the freedom of movement of the _______ within the peptide chain. |
| rotate | In the peptide chain, only two of the three bonds within the amino acid can _______. |
| sterics | In the peptide chain, only two of the three bonds within the amino acid can rotate, and the freedom of rotation of these bonds is limited by the _______ of the side chain of the amino acid. |
| plane | Recall that due to the double bond character of the nitrogen-carbonyl carbon bond, this bond will not rotate and so we say there is an amide _______ within each residue. |
| phi | The _______ bond is between the nitrogen and alpha carbon. |
| psi | the _______ bond is between the alpha carbon and the carbonyl carbon. |
| right | in secondary structures: For the most part, alpha helices are going to be _______ handed, that is, as the helix extends from the N-terminus of the polypeptide to the C-terminus, the turn of the helix will be counterclockwise, or if you hold out your right hand with the thumb up, indicating the elongation axis of the helix, then your fingers curve in the direction of the helix. |
| hydrogen | Along the alpha helix, there is _______ bonding between the carbonyl oxygen of the backbone with the backbone nitrogen of the residue that is four positions ahead. |
| 3.6 | It takes _______ residues to make a single turn in an alpha helix, so you can see how the residues would be aligned to allow this hydrogen-bonding. |
| away | Because of the sterics involved in forming the alpha helix, the side chains, point out _______ from the axis of the helix. |
| dipole | The hydrogen-bonding between carbonyl and nitrogen along the peptide backbone creates a _______ moment in the helix, such that the N-terminus of the helix is partially positive, while the C-terminus is partially negative. |
| positive | The hydrogen-bonding between carbonyl and nitrogen along the peptide backbone creates a dipole moment in the helix, such that the N-terminus of the helix is partially _______, while the C-terminus is partially negative. |
| negative | The hydrogen-bonding between carbonyl and nitrogen along the peptide backbone creates a dipole moment in the helix, such that the N-terminus of the helix is partially positive, while the C-terminus is partially _______. |
| zwitterion | the _______ of the peptide, the C-terminus would be negative, the N-terminus positive. |
| substrate | In an alpha helix the charges are not formal, but a dipole, so that at a turn from a helix within the protein structure you will have an area of partial charge that can contribute to _______ binding. |
| enzymes | Many _______ exploit the dipoles of helices in their active sites to help arrange the substrate molecule for catalysis. |
| binding/orientation | The dipole moments of alpha helices involved in enzymatic activity may not be involved in the actual catalyzing event, but work in the _______ of the substrate. |
| hydrophobicity | The choice of amino acids making up an alpha helix determines its _______. |
| aliphatic | In some alpha helices, the side packing to the protein may be full of _______ residues, that is, greasy amino acids, while the side facing the bulk aqueous solvent may be hydrophilic or charged residues. |
| hydrophilic | In some alpha helices, the side packing to the protein may be full of aliphatic residues, that is, greasy amino acids, while the side facing the bulk aqueous solvent may be _______ or charged residues. |
| Amphipathic | _______ structures have both characteristics of water loving and water hating. |
| Beta | _______ strands are more elongated than alpha helices and can pack into the super secondary structure of _______ sheets. |
| same | There are two types of beta sheets: parallel beta sheets, where the beta strands run from N-C in the _______ direction, or anti-parallel, where they run opposite to each other. |
| opposite | There are two types of beta sheets: parallel beta sheets, where the beta strands run from N-C in the same direction, or anti-parallel, where they run _______ to each other. |
| hydrogen | In both types of beta strands, we see similar _______ bonding to that seen in the alpha helix, where the carbonyl oxygen of one strand bonds with the amide nitrogen of the backbone of an adjacent strand. |
| oxygen | In both types of beta strands, we see similar hydrogen bonding to that seen in the alpha helix, where the carbonyl _______ of one strand bonds with the amide nitrogen of the backbone of an adjacent strand. |
| nitrogen | In both types of beta strands, we see similar hydrogen bonding to that seen in the alpha helix, where the carbonyl oxygen of one strand bonds with the amide _______ of the backbone of an adjacent strand. |
| dipole | Beta strands and sheets do not have _______ moments associated with them. |
| Quaternary | _______ Structures are formed from the same subunits, or different subunits associating. |
| stabilize | Quaternary structure helps to _______ the protein structures, disulfide bonds will form between subunits as seen in the immunoglobulin structure. |
| disulfide | Quaternary structure helps to stabilize the protein structures, _______ bonds will form between subunits as seen in the immunoglobulin structure. |
| cooperative | There can be _______ substrate binding in quaternary structure, as seen with hemoglobin, as more oxygen is bound to the hemoglobin, the binding of subsequent oxygens is much easer. |
| oxygen | There can be cooperative substrate binding in quaternary structure, as seen with hemoglobin, as more _______ is bound to the hemoglobin, the binding of subsequent _______ is much easer |
| subdomains | Many active sites will be located at the cleft between two _______ in the hemoglobin protein. |
| Enzyme | _______ catalyze reactions that would normally occur but at very slow rates. Examples are amylase, the salivary _______ that breaks down starch, and glutamine synthetase, that gargantuan protein we talked about earlier that synthesizes glutamine. |
| Regulatory | _______ proteins are often hormones, like insulin that control other processes in the body, in insulin's case, regulation of glucose metabolism. |
| Transport | - _______ proteins transport other molecules either through the blood or lymph systems or across cell membranes. |
| Storage | _______ proteins can store other molecules or atoms for later use in the body, iron is stored in ferritin, for example. Storage proteins can also be degraded to release the nutrients stored within their primary structure: ovalbumin for example functions as a nitrogen store for the growing embryo. Casein, the most abundant protein in milk also functions as a nitrogen store, storing the nitrogen within the amino acids making up the protein. |
| Contractile and motile | _______proteins are capable of causing movement or moving themselves. Actin and myosin are the major _______ proteins in muscle cells. Tubulin forms the microtubule system of the cellular matrix and help to get things moving in cell division. |
| Structural | _______ proteins help to strengthen tissues and cells. Collagen is a major component of our skin and connective tissues. _______ proteins are often long fibrous polymers. |
| Protective | _______ proteins function in cell defense against infectious agents, as in the case of immunoglobulins and antibodies. Thrombin, fibrinogen and fibrin are all part of the blood clotting cascade that protects the organism from blood loss by forming fibrous layers of fibrin in tissue damage. |
| prosthetic | Many proteins have additional chemical groups associated with them other than amino acids. Groups that are critical to the protein's function are called _______ groups. Examples of _______ groups are seen in the heme containing proteins, hemoglobin and cytochrome P450. The heme assists in oxidation reactions within this class of proteins. |
| Glycoproteins | _______ have carbohydrate chains attached to the surface of the protein; the term for this is glycosylation. |
| Glycosylated | _______ proteins are often integral proteins in the cell surface, with the carbohydrates presented to the extracellular matrix. These carbohydrates function in cell recognition events. |
| integral | Glycosylated proteins are often _______ proteins in the cell surface, with the carbohydrates presented to the extracellular matrix. These carbohydrates function in cell recognition events. |
| Lipoproteins | _______ have conjugated lipids. In plasma, _______ function to transport the blood lipids within the body. These lipids are then used to build cell membranes. |
| high | In serum cholesterol screening, it is the lipoprotein that are being evaluated, HDL and LDL levels, each standing for: _______ density lipoprotein and low density lipoprotein respectively. |
| low | In serum cholesterol screening, it is the lipoprotein that are being evaluated, HDL and LDL levels, each standing for: high density lipoprotein and _______ density lipoprotein respectively. |
| Nucleoproteins | _______ transiently bind nucleic acids and nucleotides in the conference of the genetic code. Examples of _______ include the ribosome, which functions to translate RNA to protein is a member of this group. DNA polymerases also belong in this category. |
| Phosphoproteins | _______ contain phosphorylated tyrosines, threonines or serines. Many proteins that function in cell signaling will transiently be _______. The signal is turned on or turned off by the phosphorylation of the protein, depending on the protein, the signal may be on when phosphorylated or turned off when phosphorylated. Nothing is ever general. |
| Metalloproteins | _______ have mettles associated with them; often divalent metals such as iron, copper, magnesium, manganese. These metals will sometimes aid in the binding of the substrate in the enzyme, or the protein may function as a metal storage unit. These types of proteins occur throughout metabolism and we'll see a lot of them in the coming months. And yes, all hemoproteins are also metalloproteins. |
| Flavoproteins | _______ contain flavin, a tricyclic aromatic molecule that is further conjugated to other groups, as in the case of FMN, flavin mononucleotide and FAD, flavin adenosine dinucleotide. These proteins catalyze oxidation and reduction reactions within many metabolic processes. |
Combine with other sets
Share on Facebook
Share on MySpace