| What is cystiene? and what is its role? | cysteine is an aa with S side chain responsible for disulfide bonds (2 cycteine and close enough) |
| Can lipids be called macromolecules? | NO |
| Can macromoleules be polymerized from different molecules? give an example | Yes, nucleic acids are composed of sugar-nitrogenous bases and phosphate. |
| Do proportions of various classes vary? | yes they vary among cell types and species |
| Give some donors of H-bonds | OH , NH2 |
| Give some acceptors of H-bonds | C_--O , --O--, --N-- |
| List some roles done by (Fe, Ca) | Fe: oxygen transportation through Hb for oxidation reduction catalyzed by cytochromes
Ca: intracellular signaling, muscle contractions, (myosin-actin) release of nuerotransmitters. |
| give examples on proteins transporting electrons | proteins of respiratory system in the mitochonrion and photosynthesis chain in chloroplast |
| Give examples of proteins transporting ions and moleules | pumps and channels in plasma membrane. |
| Give examples of proteins that transport macromolecules. | cytoskeleton and pore proteins. |
| What is the only aa that doesn't have a chrial carbon? | glycin |
| Give examples of side chains of: polar, non polar, acidic and basic aa. | non-polar (ethyl, methyl...)
polar (NH2, OH, CO)
acidic (COO-)
Basic (NH3+) |
| Describe the nucleophilic attack | electrons of nitrogen of the N-terminus react with the carbon of the carboxyl group (C-terminus) leading to the elimination of water. |
| What are the torsion angles and between what molecules? | angles between back bone and extended chemical groups (aa side chains, Calpha-H, N-H, C_--O) and covalent bonds (Calpha-CO, CO-NH, Calpha-NH |
| How do helix shaped secondary proteins differ among each other? | number of residues per turn and helix patch |
| Give an example about alpha helix bondage | H-bonds between CO of aa at position n and NH aa at position n+3 |
| where are random coiling proteins mainly found? | regions that link helices. |
| hWhat connects the triple helical shape of collagen? | Lysine |
| How are domains of a teriatry structure protein occuring? | by bringing distant aa together, each domain cosists of helices and/or sheets folded together |
| What causes protein denaturation? | environmental causes (High temperature, low pH) or chemical detergants. |
| What are the main four cites a protein has? | Binding cite, substrate site, catalytic cite and allosteric sites. |
| Talk about the allosteric sites. | They are binding sites for specific ligands such as aa, ions, monosaccharides. |
| How do we get reversible conformation structures? | Since the 3D conformation is not rigid, ligand binding could cause reversible conformation strcture, one active and one inactive, this property is called allosteric transition. Also they might change their conformation because of environmental change (phosphorylation (bondage and release of phosphate in aa)) |
| How can we classify proteins depending on their composition? | holoproteins (apoproteins) are proteins only made up of aa (whose hydrolysis results only in aa), that can be soluble or insoluble,
heteroproteins, where aa polymers are conjugated to other non protein molecules (lipoproteins, nucleoproteins or ribonucleoproteins, glycoproteins, hemoproteins (heme group (metal inside) Hb that transports gases and cytochromes that catalyze oxidation-reduction rxns. the metal ion present in the heme center is iron, and other ions such as copper occur in other hemoproteins) |
| How can we classify proteins according to their functions? | Structural proteins (determination of structure of cells and membrane, Actin, myosin and tublin)/ Regulatory proteins (control physiological processes and metabolism, Hormones (insulin and glucagon, growth hormones))/Contraction proteins (organism movement, cell movement and organelle movement, actin myosin, tubulin, dynein and kinesin who are also refered to as motor proteins)-Defense proteins (effective actors in the immune system, antibodies, T lymphocyte receptors, protein of complement.)/Transport proteins (transportation of entities ranging from electrons (cytochromes) to ions (Na+ pumps) and macromolecules and vesicles (dynein, kinesin)/Catalytic proteins (catalyze biochemical reactions anabolic and catabolic (enzymes such as trypsin amylase..) |
| can a protein have several functions? | yes |
| How can we classify proteins ddepending on their 3D structures? | fibrous proteins (keratine and collagen -insoluble in water- playing structural roles and mechanically strong)
globular proteins (albumin, globins and histones-water soluble, compact and spherical |
| What are cells? (cell doctrine) | Cells are the fundemental unit of all living beings. They are generated from pre-exsisting material. Cells and their products are called organisms. They are the basis of life continuity. Each have the role of maintaining its own life and an outer physiological role. |
| What are the atoms that cells consist of? | C,H,N & O 96%
K,Cl,Ca,Na,Mg 4%
Zn,Fe,Cu (trace elements) |
| How are the molecules inside the cells classified? | They are classified into Organic molecules and inorganic molecules. |
| Talk about the organic molecules | organic molecules AKA biomolecules are mainly amino acids, lipids, carbohydrates, nucleotides. e.g: vitamins
They can be polymerized forming macromolecules such as proteins and starch |
| What are the main inorganic molecules? | H2O & Mineral salts |
| Talk about the properties of H2O | most abundant, electrically neutral, can be found freely in the cell or interacting with organic molecules, slightly negatively charged which enables forming H-bonds and Ionic bonds (mediating solubilization of mineral salts) |
| Talk about mineral salts | NaCl, KCl, MgSO4...present in ionic form.
Hydrated entities (surrounded by H2O)
Their balance leads to: -pH equivalence -osmotic pressure
[ions] in cell != [ions] outside/ interstitial fluid.
They have physiological roles:
-membrane permeability
-cell division
-muscular contraction (Ca)
-intracellular signaling-nerve impulse generation and propagation- Enzymatic activities (Fe for Hb) |
| What is permeability? | The allowance of passive flow of molecules |
| How are organic compounds presented? | As molecules (amino acids, fatty acids, monosaccharides, nucleotides) and as macromolecules (proteins, lipids, polysaccharides such as starch, cellulose, glycogen, nucleic acids such as DNA, RNA...) |
| What are the main groups of organic molecules inn the cells? | Proteins, lipids, carbohydrates & nucleic acids. Vitamins can be considered as a separate group rarely found |
| Talk about vitamins as a group of biomolecules | Vitamins can sometimes be regarded as a separate group of biomolecules. They play a coenzymatic role. But they don't form a homogenous independent class. Vitamins A,B and D are lipid molecules, vitamin C is a carbohydrate molecule. |
| List two properties of protein molecules | Most abundant - Most diverse |
| Why are proteins so diverse? | Proteins are a series of amino acids that are synthesized based on genetic material, so proteins are at least as diverse as the genetic material carried by cells. In addition, proteins differ in the sequence of amino acids, where proteins are made of 10s and 100s of amino acids sequenced differently which lead to more diversity |
| How does this diversity affect the cell? | The huge diversity of proteins lead to the diversity in the function of these proteins, where proteins , structural and catalytic, are responsible for almost all functions that sustain cell's and organism's life. |
| Can DNA perform these roles? Give an example | DNA cannot perform the specific roles but they carry information needed for the synthesis of the functional proteins. Hb genes cannot transport oxygen however Hb proteins can. |
| List the functions of proteins | -cell structure-molecular identity (HLA, Blood group)- morphology of organisms (skin and eye color) -physiological processes as DNA replication, translation and transcription-storage and transportation of particles (electrons/mitochonderion-ions/pumps-macromolecules/cytoskeleton)- intercellular communication- hormones- immune system (antibodies)- cell cycle and mitosis- muscles- energy converter for movement- senses- can be used as energy source. |
| What atoms compose the amino acids | C,H,O,N, S only in two types |
| What are the main components of the amino acid? | Amino group, Carboxyl group, side chain, chiral C atom |
| How may aa molecules are there? | 20 |
| What kind of isomers are amino acids? | L-setreoisomer |
| What are the main common points between all aa? | Presence of amino and carboxyl groups. |
| What is the only different aa and how? | Proline is the different one, by having a covalent bond between side chain and amino group |
| Classify amino acids by sythesizing region | essential (through diet) and non-essential (through cells) |
| Classify amino acids by side chain | non-polar, polar, acidic, basic |
| What does hydrophobic mean? | Doesn't interact with water |
| Are amino acids ionizable? Are proteins? | aa are ionizable due to amino and carboxylic groups, but some proteins are soluble while others are not. |
| What are the factors that affect ionization of aa? | pH and dissociation constants. |
| What are zwitterions? | free aa that have both amino and carboxyl groups ionized. |
| Are the aa ionizable in polypeptide chains? | No, except the side chains |
| What are polypeptides? | linear unbranched chain of aa connected via covalent peptide bonds (between amino group and carboxylgroup) |
| How are peptide bonds formed? | The are catalyzed by ribosome, reaction between N-terminous and C-terminous of two separate aa leading to elimination of water. |
| What other words describe the peptide bond? | amide bond |
| What happens if a simple error happens during the formation of polypeptides? | It will affect the final 3D structure of the protein which will lead to it becoming inactive. |
| Why are polypeptides flexible? | Since the side chains rotate around the covalent bond between N-C-C which forms the backbone so three torsion angels are formed between the backbone and those side chains. |
| What limits the flexibility of polypeptides? | the size of the side chains |
| How many structures of proteins are there? | 4 max |
| Talk about the primary structure of proteins (3 topics) | unbranched linear chain of amino acids, made by traslation and transcription of genetic material. Alteration might lead to affection of the role of protein. Same for every protein of the same kind (f.i insulin protein has same polypeptide chain |
| List four kinds of secondary structures | alpha helix, beta pleated sheet, irregular, coiled |
| Is the secondary structure happening randomly? | Secondary structures occur specifically for each certain polypeptide chains, thus if an alteration happens the protein won't have the specific structure which will lead to the alteration of its functionality |
| How are the shapes made? | Through H-bonds between side chains, amino and carboxylic groups... |
| Talk about the supercoiling type of secondary structures | Presence of covalent bonds between side chains (collagen- triple helix /elastin- irregular) |
| Talk briefely about tertairy structure. | Folding structures back together leading to more and more bonds that cause the formation of domains that perform certain roles for example enzymes have a domain that binds to the sustrate and a domain the catalyzes the reaction wit it |
| Can denatured proteins refold? | If mild yes |
| What about quaternary stuctures? | some proteins need to bind to other polypeptides/subunits to become active. For instance hemogobin has 4 subunits. They are stabilized by weak or strong bonds using certain specifications (also called dimerisation (dimers)) |
| What is the other name for carbohydrates? | oses |
| What mainly are the functions of carbohydrates? | energetic and structural functions, as well as the role of determination of cell identity at the molecular level (sugars may give diverse blood groups) |
| What role does glucose have? | glucose provides energy for almost all body cells through oxidation reaction, in addition to a structural role in plant cell wall (monomer of cellulose) |
| What are the main criteria of classification of carbohydrates? | number of carbon atoms per molecule, type of functional group, cyclic shape, number of monomers. |
| What are monosaccharides? | simple oses, their general formula is CnH2nOn (n =3-->6) (although there might be more than 6 (heptoses contains seven C). There are more than 200 monosaccharides (most are D-stereoisomers) |
| Are carbohydrates as diverse as proteins? | No, since only a few monosaccharides can polymerize with each other , and polysaccharides are usually made up of a monotonous repetition of one or two monosaccharides (glycogen and starch are polymers of alpha-D-glucose; cellulose is a polymer of beta-D-glucose |
| How can we classify monosaccharides? | Based on the group other than hydroxyl that is present in it into two groups;
-aldoses (containing aldehyde)
-ketoses (containing ketone) |
| Name the two simplest monosaccharides and what is their molecular structure | glyceraldehyde (CHO-CHOH-CH2OH) and dihydroxyacetone (CH2OH-CO-CH2OH). (C3H6O2) they are also named trioses (3 carbon atoms) |
| When are the simplest monosaccharides syntesized? | when a cell oxidizes carbs, and to synthesize glucose or ketoses. |
| What are the main pentoses? | aldoses (ribose CHO-CHOH-CHOH-CHOH-CH2OH) and ketoses (ribulose) |
| What are the main hexoses? | glucose-mannose-galactose.. (aldose CHO-CHOH-CHOH-CHOH-CHOH-CH2OH) or ketoses (fructose) |
| When do oses become cyclic? | Oses with more than 4 carbon atoms may form a cyclic structure, which is more stable than the linear one since it has lower free energy. |
| What are the two types of cyclic oses? | six-member rings (pyranoses such as glucose) or five-member rings (furanoses such as ribose, fructose) thus we can classify monosaccharides into pentagonal or hexagonal cycles.. |
| What are the isomers that form in cyclic oses? | alpha (formed OH group from aldehyde/ketone is facing downwardly) and beta (OH facing upwardly) |
| can cyclic oses switch from alpha to beta cycles? | if there is equilibrium they can alternate but if a cyclic molecule is polymerized it can no longer switch (cellulose and glucose) |
| Give examples about monosacchradis modifications | -replacement of OH in pos.2 of glucose with amino group producing glucosamine (osamines) and an acetyl group may be added to the amino group (acetyl-glucosamine)
-replacement of hydroxyl group of galactose also with amino group (galactosamine)
-Oxidation of the CH2OH leading to formation of COOH (uronic acid) oxidation of glucose leads to formation of glucuronic acid (precursor of vitamin C).
-NANA (N-acetyl nueraminic acid) ;derived from mannose linked to lipids and proteins during their maturation in Golgi apparatues (glycosylation). |
| What is the covalent bond formed between monosaccharides to make dimers called? | glycosidic bond. |
| Give three examples of disaccharides. | saccharose (glucose and fructose) lactose (glucose and galactose) maltose (2 glucose) |
| How is the glycosidic bond formed? | covalently between C-1 and C-4 or C-6 of the monosaccharaides leading to formation of water |
| What are polysaccharides? | complex carbs composed of long branched or unbranched chain of monosaccharides (simple or modified). |
| What roles do polysaccharides play? | Physiological role (cells and tissues)
Structural roles (such as cellulose in plant and peptidoglycans in bacterial wall) determining cell shape and protecting it
energy reserve (glycogen in liver and muscles and starch in plants) |
| What are the classes of polysaccharides? | Homopolysaccharides and heteropolysaccharides. |
| What are homopolysaccharides? | polymers of the same monosaccharide (cellulose (beta glucose), starch and glycogen (alpha glucose) are all glucose but glycogen is branched and forms granules, starch is branched and forms helical arrangements and granules, cellulose is unbranched forming fibers. |
| Give an example of homopolysaccharides | Chitin (forms outer cover of invertebrates, is an unbranched polymer of N-acetylglucosamine) |
| What are heterosaccharides? | polymers of two different oses or modified ones such as osamines and uronic acids. |
| Give examples on heteropolysaccharides? | glycosaminoglycans (GAG) proteins forming proteoglycans) rich in glucosamine and galactosamines.
Hyaluronan is a polymer of N-acytelglucosamine and glucuronic acids
Chondroitin sulfate (in extracellular matrix)is a polymer of N-acetylgalactosamine and glucuronic acid)
keratane sulfate is made of D-Galactose and N-acetylglucosamine occurs in cartilage and cornea |
| How are lipids classified? | Saponifiable and non saponifiable. (those with fatty acids are saponifiable) |
| List the roles of lipids | structural role (forming all basic structures in membranes)
Energy reserve (triglycerides in plant seeds and adipose tissues animals)
communication between the cells (hormones -estrogen progeserone and testosterone)
intracellular cellular communication (phosphatidyl inositol, arachidonic acids) |
| What are lipids? | organic compounds that are all non-polar, non-soluble in water, highly soluble in non polar organic solvents (benzene). |
