Biochemistry Exam 1 PDF

Exam 1 1)​ What are the four most abundant elements in a human body a)​ C, N, O, H i)​ They make up a majority of biomolecules and can form carbohydrates, proteins lipids and nucleic acids 2)​ Which of the following developed during the evoluti...

Exam 1 1)​ What are the four most abundant elements in a human body a)​ C, N, O, H i)​ They make up a majority of biomolecules and can form carbohydrates, proteins lipids and nucleic acids 2)​ Which of the following developed during the evolution of eukaryotic cells from prokaryotic cells a)​ Nuclear membranes i)​ Prokaryotes lack membrane bound organelles 3)​ For a reaction with delta H = 23kj/mol and delta S= 22 j/kmol at 2 Celcius, the reaction is a)​ Nonspontaneous i)​ When delta G is positive than the reaction is nonspontaneous 4)​ The strongest noncovalent interactions are a)​ Ionic interactions i)​ Ionic interaction when in between oppositely charged particles are stronger than hydrogen bonds or van der waals forces 5)​ How many atoms in one urea molecule can function as hydrogen bond acceptors a)​ 3 i)​ Urea has 1 oxygen and 2 nitrogen atoms that can all take a hydrogen bond 6)​ Which of the following is the best explanations for the hydrophobic effect a)​ It is an entropic effect, caused by the desire of water molecules to increase their entropy by excluding hydrophobic groups, which they must otherwise surround with highly ordered structures i)​ Water molecules surrounding nonpolar molecules form structures shells. Excluding nonpolar groups reduces ordering and increases system entropy 7)​ The capacity of a buffer to resist changes in pH upon addition of protons or hydroxide ions depends on a)​ All of the above i)​ The pka of the weak acid in the buffer , the ph of the buffer, the total concentration of the weak acid and its conjugate base in the buffer (1)​ Buffers resist pH changes due to their weak acid/base pairs pKa, buffer pH and overall concentration 8)​ Nucleic acids are composed of nucleotides that are linked by phosphodiester a)​ Phosphodiester bonds link nucleotides creating sugar phosphate backbone of DNA and RNA 9)​ DNA separated at the replication fork is stabilized by SSB a)​ Single stranded DNA binding proteins prevent separated DNA strand from reannealing during replication 10)​Termination of replication fork movement in E.Coli involves the binding of Tus protein at a Ter site a)​ Tus binds ter sites in E.Coli to stop the replication fork 11)​The RNA segment to which DNA residues are added during the replication is the primer a)​ A short RNA primer provides a starting point for DNA synthesis by DNA polymerase 12)​Transfer RNA molecules are involved in translation a)​ Transfer RNA delivers specific amino acids to ribosomes during translation 13)​A double stranded DNA fragment contains 12% adenine residues. Calculate the percentage cytosine residues a)​ 38% i)​ If a is 12% and t is 12% then c and g make up 76% so each is 38% 14)​It is impossible for RNA to store genetic information, because a)​ RNA can store genetic information i)​ RNA as seen in retroviruses is capable of storing and transmitting genetic information 15)​Which of the following is not a requirement of genetic material a)​ The material must perform a read only function to minimize damaging changes in structure i)​ Genetic material must mutate replicate and direct protein synthesis- not act as a read only system 16)​In B-DNA a)​ The major groove is wide and deep i)​ The major groove in B-DNA allows binding of proteins that regulate transcription and replication 17)​Pol 1 synthesizes new DNA with very high fidelity due to its a)​ 3’ to 5’ exonuclease activity i)​ Its 3’ to 5’ exonuclease, activity proofreads and removes mismatched nucleotides 18)​Which of the following states about DNA polymerase 3 is TRUE a)​ DNA polymerase 3 has a greater turnover rate than pol 1 b)​ Pol3 is the primary replicase of E.Coli c)​ Pol3 does not contain 5’ to 3’ exonuclease activity i)​ All are true (1)​ Highly efficient and lacks 5’ to 3’ exonuclease activity and is the main enzyme for replication 19)​Which of the following statements about the fidelity of replication is FALSE a)​ Cells viability is removed when DNA point mutation are incorporated i)​ While mutations can sometimes disrupt viability, cells have mechanisms to tolerate or repair minor mutations 20)​A new DNA polymerase exhibitas: high processivity, low fidelity and ability to replace RNA and DNA, which of the following is probably true a)​ It has 5’ to 3’ exonuclease activity i)​ The enzymes exonuclease activity indicates it can remove RNA primers or damaged DNA  21)​Use the following diagram to complete the sentences below: ____ is the enzyme which catalyzes phosphodiester bond formation on both strands. Processivity of DNA pol is increased when associated with ___. DNA unwinding is accomplished by _____ a)​ A,D,B i)​ DNA ligase (A) forms bonds, the clamp loader (d) enhances DNA pol processivity and helicase (b) unwinds the DNA 22)​A prokaryotic replisome typically contains 2 molecules of DNA pol 3, but only one molecule of DNA pol 1. Why a)​ DNA Pol 1 replaces the RNA primers with DNA , Which really only needs to be done repetitively on one strand, while both strand are worked on by the DNA pol 3’s i)​ DNA Pol1 replaces RNA primers with DNA, which primarily occurs on the lagging strand due to Okazaki fragments Exam 2 1)​ Insertions or deletion of one or 2 nucleotides can cause a)​ Frameshift Mutations i)​ Insertions or deletions of one or two nucleotides shift the reading, altering the entire downstream protein sequence 2)​ In prokaryotic transcription the _____ factor base sequences in the _____ which facilitates RNA polymerase binding and initiates RNA synthesis a)​ Sigma; promoter i)​ Sigma factor recognizes the promoter helping RNA polymerase bind and initiate transcription 3)​ Which of the following is not a feature of tRNA structure a)​ Terminal phosphate arm i)​ Not a structural feature 4)​ The correct amino acid is covalently attached to a tRNA by the corresponding ____ which is specific for each a)​ Aminoacyl-tRNA synthetase; amino acid i)​ This enzyme covalently link the correct amino acid to its corresponding tRNA 5)​ In E. Coli base pairing between an mRNA’s ____ and the 3” end of the 16S rRNA permits the ribosome to select the proper initiation codon a)​ Start codon i)​ The start codon pairs with the 16S rRNA at the shine dalgarno sequence in prokaryotic translation 6)​ During elongation which site of the ribosome binds the new incoming amino acid-tRNA a)​ A SIte i)​ This site binds incoming aminoacyl-tRNA during elongation 7)​ Polypeptide Synthesis a)​ Proceeds from the N-terminus to the C-terminus i)​ Protein are synthesized from the N-terminus to teh C-terminus 8)​ What happens when a stop codon is reached by a ribosome  a)​ A release factor binds to the codon and is used to release the growing peptide from the P site tRNA i)​ When the ribosome reaches a stop codon, release factors bind freeing the synthesized protein 9)​ The steps involved in elongation of the newly synthesized protein are order as follows a)​ AA-tRNA binding, peptide bond formation, translocation, tRNA release i)​ The sequence is the binding of aminoacyl-tRNA, peptide bond formation, translocation and tRNA release 10)​The E.Coli’s ribosome’s 30S subunit binds to mRNA a)​ Teh small ribosomal subunit recognizes and bind mRNA in prokaryotes 11)​All tRNAs have the L shape a)​ All tRNAs adopt this shape, wich is critical dor proper ribosome positioning 12)​The elongation factor EF-G facilitates translocation of the tRNA’s in the ribosome a)​ EF-G promotes translocation of tRNAs,moving them to new ribosomal sites 13)​The DNA strand that serves as a template during transcription is known as the antisense or noncoding strand a)​ Teh antisense strand serves as the template for mRNA synthesis 14)​Which o the restriction enzymes listed in the table below produces blunt end fragments a)​ AluI ( AG - CT) i)​ Alul produces blunt ends by cutting both DNA strands at the same position 15)​In molecular cloning, transformed organisms must be identified. One common method for accomplishing this involves the inclusion of ____ in the plasmid a)​ An antibiotic resistance gene i)​ Antibiotic resistance genes help identify successfully transformed cells 16)​Which of the following conclusions about the human genome is false a)​ Most of the proteins found in humans are unique to vertebrates i)​ Most human protein are conserved across the species, they are not unique to vertebrates 17)​In burger to perform PCR, which of the following describes the reagents that must be included in the ration mixture a)​ DNA fragment, primers flanking the region of interest, dNTPs, DNA polymerase i)​ Teh reaction need DNA, primers, dNTP’s and a thermostable DNA polymerase 18)​The formation of a dipeptide from two amino acids involves a)​ Loss of water i)​ Condensation between 2 amino acids releases water 19)​In two homologous proteins which residue is most likely to replace a Glu residue as a conservative substitution a)​ ASP i)​ Aspartic acid can replace glutamic acid ue to similar properties 20)​Which of the representations describes the oligopeptide shown below a)​ Tyr-Ala-Ser  21)​Ribosomes use L amino acids to synthesize proteins. These amino acids are called L because a)​ They have a configuration of groups around the C-alpha that can be related to the configuration of groups around the asymmetric carbon in L-glyceraldehyde i)​ These amino acids are optically active and correlate with L-glyceraldehyde configuration 22)​The quantitation due to the absorbance at 280 nm (UV region) is due to the large absorbity of the ____ amino acids a)​ Aromatic i)​ Aromatic acid strongly absorb at 280nm 23)​Which of the physical characteristics is not commonly used in protein separation a)​ Stereochemistry i)​ Stereochemistry is not used in typical protein separation methods 24)​The two peptides shown in the diagram below ar linked through a)​ A disulfide bond i)​ These covalent bonds link cysteine residues in protein 25)​SDS-page separates proteins primarily due to differences in a)​ Mass i)​ Proteins are separated by mass as SDS gives them uniform charges 26)​Which linkage best describes the covalent bond between an amino acid and its cognate tRNA a)​ Carboxyl group of AA linked to 3’OH of tRNA i)​ The amino acid is covalently attached tp the 3’OH of teh tRNA Exam 3 1)​ Which of the following is not true for the alpha helix a)​ Glycine is the amino acid that most frequently appears in alpha helices i)​ Glycine rarely appears in helices due to inflexibility disturbing the structure 2)​ Which of the following does not describe the beta sheet a)​ Parallel beta sheet are most stable than antiparallel sheets i)​ Antiparallel sheets are more stable die to optimal hydrogen bonding 3)​ Which of the following would not alter the functional characteristics of alpha keratin a)​ Blocking the biosynthesis of 4-hydroxyproline i)​ Blocking 4-hydroxyproline synthesis does not affect keratin as it is not collagen related 4)​ The first step in the folding of disordered polypeptides into ordered functional protein is the formation of ___ a)​ 2nd degree structure i)​ Secondary structure formation is the first step in protein folding 5)​ Non covalent forces that stabilizes protein structure included all of the following except a)​ Disulfide bridges i)​ Disulfide bonds are covalent 6)​ Protein can denature due to change  a)​ pH, temp and ionic strength i)​ Changes in pH, temp or ionic structure all disrupt protein structure 7)​ Molecular chaperones bind to unfolded or partially folded polypeptide chains in order to accomplish which of the following a)​ Facilitate native folding in order to ensure that the protein is not damaged by heat denaturation i)​ These assist folding and protect protiens from aggregation during stress 8)​ Protein dynamics is a field of study that examines the movements within a protein, Which type of protein structure determination would be most useful to study this type of change a)​ NMR i)​ Nmr captures changes in proteins conformation over time 9)​ Humoral immunity is mediated by soluble molecules. Which cell type produces the soluble molecules that carry out the humoral immunity a)​ B cells ​ i)​ B Cells produce antibodies for humoral immune responses 10)​The requirement for glycine every 3rd amino acid is essential for the triplet helix formation of collagen a)​ Glycine every third residue enables tight packing in the helix 11)​If an enzyme catalyzed reaction has low rate at low pH and high rate at higher pH, this implies that a group on either the enzyme or the substrate must be deprotonated a)​ Inidates a functional group must be deprotonated at a high pH for activity 12)​Ona transition state diagram for a multistep reaction, the step with the greatest delta g is the rate determining step a)​ The highest delta g peak represents the rate determining step 13)​For efficient nucleophilic catalysis, a group such as the sulfhydryl on a cysteine residue must be able to form a good leaving group, in addition to being a good nucleophile a)​ Efficient catalysis requires a group that is both a good nucleophile and a leaving group 14)​DIPF, the nerve gas, covalently binds to and this inactivates acetylcholinesterase a)​ DIPF irreversibly inhibits acetylcholinesterase by covalently binding 15)​Oxyanion hole helps the catalysis of a serine protease by stabilizing the transition state a)​ Stabilize transition states in serine protease reactions 16)​How many antigen binding site are present on an IgG molecule a)​ 2 i)​ IgG molecules only have 2 antigen binding sites 17)​Which of the following is True about enzymes a)​ Enzymes typically catalyze reactions at much higher rates than chemical catalyst, Enzymes are often very specific for their substrates , Enzymes activities can often be regulated , enzymes typically act under milder conditions of temperature and pH than chemical catalysts i)​ Enzymes are specific, efficient and operate under mild conditions 18)​Which of the following is true regarding cofactors a)​ Cofactor is a broad term used for all enzyme helpers  i)​ Cofactors include metal and organic molecules aiding enzyme function 19)​____ metals are the most common metallic enzyme cofactors a)​ Transition i)​ Transition metals are commonly used 20)​Proton transfer from an acid, lowering the free energy of a reactions transition state is characteristic of a)​ General acid catalysis i)​ Acid donates protons which stabilizes the transition state 21)​Which of the following amino acid residues would not provide a side chain for acid base catalysis at physiological pH a)​ Leucine i)​ Leucine lacks a functional group for acid base catalysis 22)​Proximity effects a)​ Lower the energy of activation i)​ Reactants are brought together reducing activation energy 23)​Which of these amino acid groups would not make a good nucleophile catalyst a)​ Methyl i)​ Methyl group are poor nucleophiles due to their lack of lone pairs 24)​In the lysozyme reaction the D ring in NAM is tin the ____ conformation providing a contribution of catalytic energy via the _____distortion a)​ Half chair: strain i)​ The strained half chair conformation contributes to catalytic energy 25)​Which of following is correct a)​ If an enzyme catalyzed reaction requires a group with a low pK to be deprotonated and a group with a higher pK to be protonated, the pH vs. rate curve will have a peak in the middle of the two pK values , transition state analogs often bind the enzyme tighter than substrate analogs do. i)​ Transition state analogs bind more tightly than substrate analogs Chapter 8 1)​ Glycosaminoglycans a)​ Linear polysaccharides with repeating disaccharide units composed of a uronic acid and a hexosamine b)​ They are located in extracellular matrices especially in connective tissues such as cartilage tendons skin and blood vessel walls c)​ They are structured in alternating uronic acid and hexosamine residues, they are linear chains that do not branch d)​ The properties they have is; highing viscous and elastic that form hydrated gels, they are essential to provide a structural support lubrication and shock absorption for tissues 2)​ Hyaluronate ( Hyaluronic Acid) a)​ They are composed of beta 1 to 3 linked d glucuronate and N-acetyl D glucosamine, they are disaccharides that are linked by beta 1 to 4 bonds, the chain lengths range from 250- 25,000 repeating units b)​ They can expand up to 1,000 times in the dry state due to the binding with water and cations c)​ They provide viscosity that varies between different shear states i)​ Low shear from tangled masses that increases the resistance to flow ii)​ High shear molecules align with the flow and reduces resistance 3)​ Sulfated Glycosaminoglycans a)​ Heparin contains about 2.5 sulfate groups per disaccharide unit, making it the most highly charged polymer in mammalian tissues b)​ They are found in mast cells more particularly in arterial walls c)​ They function as a anticoagulant and prevents blood clots from forming at unwanted locations, it is widely used in medical setting to prevent clotting disorders d)​ Heparan sulfate is similar to heparin but with fewer sulfates and more n-acetyl groups e)​ Heparan sulfate is located on cell surfaces and extracellular spaces in blood vessel and in the brain f)​ They bind growth factors and their receptors, which promotes cell proliferation and differentiation, but also plays a role in wound healing and development 4)​ Plant polysaccharides - pectin a)​ Composed of alpha 1 to 4 linked galacturonate resides that are interspersed with rhamnose  b)​ They are modified with methyl or acetyl group and cross linked with calcium ions c)​ They are integral to plant cell walls and they function as a structural component in plants providing rigidity, this is similar to the role of glycosaminoglycans in animals 5)​ Bacterial polysaccharides - biofilms a)​ They are a semi solid extracellular matrix secreted by bacteria, they are composed of hydrated polysaccharides such as poly-D-glucuronate, poly N acetylglucosamine, cellulose like molecules and acetylated glycans b)​ They provide resistance to washing, desiccation and antibiotics, they form a protective layer against environmental threats 6)​ Glycoproteins a)​ They are proteins that are covalently attached to carbohydrate chains, the carbohydrate attaches enzymatically which is driven by post protein synthesis. They have a high variability in carbohydrate composition b)​ They are found in enzymes, transport protein receptors hormones and structural proteins, and they are key in cell-cell communication and structural integrity 7)​ Proteoglycans a)​ They are proteins that covalently and non-covalently attached to glycosaminoglycans and a they exhibit a bottlebrush like molecular architecture, they have a pretty high molecular mass that reach millions of daltoons b)​ They function by forming hydrated gels with high resilience , and in cartilage proteoglycans can fill spaces between the collagen fibrils to resist compression 8)​ Bacterial cell walls- peptidoglycan a)​ They are compared on alternating beta 1 to 4 linked N -acetylglucosamine and N-acetylmuramic acid, they are also cross linked by peptide side chains b)​ They provide rigidity allowing bacteria to survive in hypotonic environments, they also contribute to bacterial virulence, They are gram positive that have multiple peptidoglycan layer while gram negative bacteria have a single layer but have an additional outer membrane c)​ In peptidoglycan Specific antibiotics i)​ Penicillin inhibits bacterial enzymes that can cross link peptidoglycan strands ii)​ Subactam inhibits beta lactamase to combat bacterial resistance iii)​ Vancomycin binds and inhibits transpeptidation in bacterial cell wall synthesis 9)​ Glycosylation in proteins a)​ N linked glycosylation involved N acetylglucosamine linked to Asn in the sequence Asn–ser/thr, where X is any amino acid except pro b)​ O'Linked glycosylation occurs at Ser/Thr residues often with galactose or other sugars, they re added post transitionaly in stepwise manner c)​ The roles of glycosylation include defining protein structure and function, mediating protein recognition and cell cell communication and influencing protein folding and stability 10)​Carbohydrate recognition in cells  a)​ Lectins are carbohydrates binding proteins that mediate cell cell interactions b)​ Selectins are specialized lectin on leukocytes that bind to endothelial cells and facilitates immune responses c)​ Antigenic determinants are considered ABO blood group that are specifically oligosaccharides on cell surfaces 11)​Carbohydrates do not have a catalytic ability a)​ They do not self replicate b)​ They are more heterogeneous than other biological molecules c)​ The major functions of carbohydrates are; they ere energy sources, provide structure to the can use macromolecular recognition 12)​Monosaccharides are aldoses or ketoses ( aldehyde or ketone ) a)​ They contain at least 3 carbon atoms 13)​Aldoses have a chain that they follow a)​ Aldotriose → Aldotetroses → aldopentoses → aldohexoses i)​ Aldotetroses are epimers 14)​D-Glucose a)​ Has four chiral centers, with 16 possible stereoisomers b)​ Stereo assignment is according to Fischer conventions i)​ Asymmetric center farthest from carbonyl has the same absolute configuration as D-glyceraldehyde c)​ Epimers only differ by the configuration on one of the Carbon atoms 15)​Ketoses a)​ Has one less chiral center than the isomeric aldoses 16)​Aldehydes and ketones can form hemiacetals and hemiketals 17)​Cyclic sugar have two anomeric forms a)​ Anomeric carbon i)​ The carbonyl in the cyclic sugar b)​ Anomers i)​ The pair of stereoisomers that differ in configuration at the anomeric carbon c)​ The alpha and beta anomers are in different configuration and switching between them requires the breaking of bonds d)​ They have a slow equilibrium with each other with alpha being at 36.4% vs the beta ast 63.6% 18)​Sugar can adopt different conformations a)​ Five and six membered rings are the most favored b)​ Chair conformation is the most favored of the 6 membered rings c)​ Bulky group can be either equatorial or axial, however with ac informations shift the bonds do not break or experience breakage \ 19)​Sugars can be modified a)​ Sugar undergo reactions that are typical of aldehydes and ketones i)​ The oxidation of an aldehyde → aldonic acid ii)​ Oxidation of primary alcohol of aldoses → uronic acid iii)​ A reduction of a carbonyl → alditols ( polyhydroxy alcohols)  iv)​ Reduction of alcohol → deoxy sugars v)​ Amine substitution of alcohol → amino sugars (1)​ Important constituent of glycoproteins and glycolipids (2)​ N-acetylneuraminic acid and derivatives → sialic acids 20)​Pectins are the plant version if shock absorbers a)​ Methyl or acetyl groups can be added to pectin while other polysaccharide chains are attached to the galacturonate 21)​Bacterial biofilm is often a mixture 22)​Proteoglycan a)​ Protein and glycosaminoglycans in the extracellular matrix aggregate covalently and noncovalently to form a diverse a diverse group of macromolecules known as proteoglycans 23)​Peptidoglycan form a bacterial cell wall a)​ Lysozyme destroys bacterial cell walls and occurs widely in the cells and secretion of vertebrates 24)​Oligosaccharides may determine glycoprotein structure, function and recognition a)​ Glycosylation may or may not affect the function of a particular protein 25)​All cells are coated with glycoconjugates - glycoprotein and glycolipids 26)​Glycosidic bonds link the anomeric carbon to other compounds 27)​Polysaccharides (glycans) a)​ Monosaccharides are linked by glycosidic bonds i)​ Homopolysaccharides - consists of one type of monosaccharide ii)​ Heteropolysaccharides - consist of more than one type b)​ They can branch c)​ Can be cleaved by exoglycosidases and endoglycosidases 28)​Disaccharides - lactose a)​ Is a reducing sugar b)​ Occurs only in milk 29)​Sucrose a)​ The most abundant b)​ Major form in which carbohydrates are transported in plants c)​ Common table sugar d)​ Non reducing sugar 30)​Structural polysaccharides - cellulose a)​ Primary component of plant cell well → rigidity b)​ Cellulose accounts for over half of the carbon in the biosphere c)​ About 10^15kg of cellulose is estimated to be synthesized and degraded annually d)​ A linear polymer of up to 15,000 D-glucose residues linked by beta 1 to 4 glycosidic bonds 31)​Structure of cellulose fibers a)​ Sheets stack vertically staggered by half the length of a glucose unit b)​ Cellulose fibers are embedded in and crosslinked by a matrix containing other polysaccharides and lignin  32)​Breakdown of cellulose a)​ Vertebrates do not possess an enzyme capable of hydrolyzing the beta 1 to 4 linkages of cellulose b)​ Our symbiotic microorganisms in the digestive tract do c)​ Slow process due to its tight structure d)​ Cows chew their cud to help break down cellulose 33)​Chitin a)​ Is the homopolymer of beta 1 to 4 linked N-acetyl -D0 glucosamine b)​ Principle component of the exoskeletons of invertebrates and cell walls of most fungi and many algae c)​ Almost as abundant as cellulose 34)​Starch a)​ The principal energy reserve for plants b)​ A mixture of glycan polymers that are made of glucose c)​ Storing the glucose as a form of starch reduces the osmotic pressure d)​ Deposited in the chloroplasts of plant cells as insoluble granules e)​ Composed of alpha amylose and amylopectin 35)​Digestion of starch a)​ Main carb in the human diet b)​ Starts in the mouth by saliva (amylase) that can hydrolyze alpha 1 to 4 glycosidic bonds c)​ In the small intestine i)​ Pancreatic amylase cleaves the carbs into small fragments ii)​ Alpha glucosidase cleaves one glucose at a time iii)​ The debranching enzyme cleaves alpha 1 to 6 branches 36)​Glycogen a)​ Glycogen is the storage polysaccharide in animals b)​ Present in all cells but more common in skeletal muscle and the liver c)​ Stay in form of cytoplasmic granules d)​ Structure is similar to amylopectin, inly more highly branch every 8-14 units e)​ Degraded by glycogen phosphorylase f)​ Branching is many concurrent degradation to produce glucose quickly g)​ Alpa 1 to 6 cleaved by glycogen debranching enzyme Chapter 9 1)​ Introduction to lipids a)​ Lipids are diverse group of hydrophobic or amphiphilic molecules, including fats, oils and certain vitamins, primarily composed of hydrocarbons b)​ They are insoluble in water but soluble in organic solvents c)​ Serve as essential components of biological membranes, energy storage molecules and signaling mediators d)​ Lipids form bilayers which are critical for compartmentalization e)​ Hydrocarbons are a dense energy source f)​ Lipids participate in intra and intercellular signaling 2)​ Fatty acids a)​ Carboxylic acids with long hydrocarbon chains b)​ Saturated or unsaturated ( no double bonds or with double bonds) c)​ Saturated fatty acids i)​ Straight chains that are packed tightly and have higher melting points ii)​ Found in animal fats and solid at room temp d)​ Unsaturated fatty acids i)​ Have cis double bonds ii)​ Cannot pack tightly and lowers melting point iii)​ Found in plant oils and liquid at room temp e)​ Polyunsaturated fatty acids i)​ Have double bonds at regular intervals ii)​ Fatty acids are typically synthesized in even numbers, originating from acetyl-CoA 3)​ Triacylglycerols a)​ Fatty acid triester of glycerol i)​ Non polar and water insoluble b)​ Primary form of energy storage in animals i)​ Contain more energy per gram than carbohydrates due to their highly reduced state c)​ Stored in anhydrous form which unlike glycogen which binds to water i)​ Fats provide 6 times the energy per unit weight compared to glycogen d)​ Specialized cells i)​ Adipocytes store large amounts of triacylglycerols 4)​ Membrane lipids a)​ Glycerophospholipids i)​ Glycerol backbone with 2 fatty acid tails and a phosphate group esterified to a polar head group ii)​ Amphiphilic - hydrophilic head and hydrophobic tail b)​ Major structural component of cellular membranes i)​ The specific head group define functionality c)​ Sphingolipids i)​ Derived from sphingosine a c18 amino acid ii)​ Categories such as sphingomyelins,cerebrosides, gangliosides d)​ Abundant in neuronal membranes especially myelin i)​ Participate in cell recognition adhesion and signaling e)​ Plasmalogens i)​ A subclass of glycerophospholipids with an ether linked alkene at the C1 position ii)​ Found in the heart and neuronal tissues iii)​ Antioxidant properties 5)​ Steroids and cholesterol a)​ Steroids are derived from a four ring structure called cyclopentanoperhydrophenanthrene  b)​ Cholesterol is the most abundant steroid in animals i)​ Found in plasma membranes ii)​ Precursor for steroid hormones c)​ Synthesized from cholesterol​ i)​ Glucocorticoids ii)​ Mineralocorticoids iii)​ Androgen and estrogen 6)​ Vitamin D and Other isoprenoids a)​ Vitamin D is derived from cholesterol and activated by hydroxylation in the liver and kidney i)​ Regulates calcium homeostasis and bone mineralization ii)​ Deficiency can lead to rickets and osteomalacia b)​ Other isoprenoids i)​ Vitamin A ii)​ Vitamin E iii)​ Vitamin K 7)​ Lipid bilayers a)​ Formed by amphiphilic lipids due to the hydrophobic effect b)​ Two layers with hydrophobic tails inside and hydrophilic heads on teh outside c)​ The fluidity of lipids depends on the composition and temp i)​ Saturated fatty acids decrease fluidity and unsaturated fatty acids and cholesterol increase it d)​ Thick is about a 30A hydrophobic core e)​ Micelles vs bilayers i)​ Micelles form from lipids with one fatty acid tail while bilayers from from lipids with two tails 8)​ Membrane proteins a)​ Integral proteins span the bilayer interacting with the hydrophobic core b)​ Peripheral protein associate with the membrane surface via ionic interaction or binding to lipids c)​ Lipid linked protein covalently attach to lipids d)​ Functions include catalysis transport and signaling e)​ Lateral diffusion occurs within the bilayer 9)​ Lipid rafts a)​ Microdynamic enriched with cholesterol, sphingolipids and specific proteins b)​ They are platform for signaling and trafficking 10)​Vesicle transport and membrane trafficking a)​ Lipids and protein synthesized in the ER are transported to teh golgi and then to other organelles b)​ Transport mechanisms i)​ Coated vesicles (1)​ COPI returns escaper ER proteins to the ER (2)​ COPII transports from ER to the golgi  (3)​ Clathrin mediates endocytosis and golgi to plasma membrane transport c)​ Snare protein i)​ Mediate vesicle fusion with target membranes ii)​ Rsnares and Qsnared interact to drive fusion 11)​Viral membrane fusion a)​ Viruses such as influenza use membrane fusion to enter host cells i)​ Triggered by specific environmental cues b)​ Influenza hemagglutinin undergoes a conformational change at low pH exposing a fusion peptide 12)​Membrane Dynamic and Organization a)​ Asymmetry i)​ Lipid composition differs between the inner and outer leaflets of the bilayer and is maintained by the flippases and translocases b)​ Fluid mosaic model i)​ Membrane proteins and lipid can move laterally unless restricted by the cytoskeleton Chapter 9 1)​ Sphingolipids a)​ Occur chiefly in the cell membranes of the brain and nervous tissue b)​ Participate in tissue development, cell recognition and adhesion, act as receptors for toxins c)​ The head group attaches to the backbone via either a phosphate or a carbohydrate group d)​ Cerebrosides are a ceramide with a single sugar head group i)​ No phosphate group so it is nonionic 2)​ Gangliosides play significant roles both physiologically and medically a)​ The carbohydrate heads can function as signaling receptors for some pituitary glycoprotein hormones b)​ The can function as receptors for certain bacterial protein toxins c)​ Cell to cell communication needs gangliosides to perform their roll 3)​ Plants contain little cholesterol but synthesize other sterols a)​ Yeast and fungi also synthesize sterols b)​ Prokaryotes contain little to no sterol c)​ In mammals cholesterol is the metabolic precursor of steroid hormones 4)​ Steroids hormones a)​ Glucocorticoids and mineralocorticoids are synthesized in the cortex which is the outer layer of the adrenal gland b)​ Both androgen and estrogens are synthesized by testes and ovaries and to an lesser extent by the adrenal gland c)​ Steroids hormones are water insoluble and are transported through the blood by binding to proteins d)​ Addison's disease and cushing syndrome are condition that occur with adrenal system 5)​ Vitamin D compounds are sterol derivatives a)​ Vitamin D compounds are actually hormones 6)​ Liposomes is a suspension of phospholipids a)​ Stable but can be purified by dialysis gel filtration or a centrifuge b)​ Model of biological membrane c)​ Vehicle for drug delivery 7)​ The fluidity of a bilayer is temperature dependent a)​ Transitions temp like the melting point of fatty acids, increases with teh chain length and degree of saturation b)​ Cholesterol decreases membrane fluidity and broadens the temp range of phase transitions 1)​ Catalysis → transport → signaling a)​ Biological membranes differ in their protein components and protein/lipid ratio b)​ Myelinated membranes are 19% of proteins, mitochondria inner membranes are 76% of protein, plasma membrane of eukaryotes is about 50% of proteins 2)​ Integral proteins are asymmetrically oriented 3)​ To penetrate lipid bilayer, protein has to a)​ Expose hydrophobic side chains b)​ Hide polar backbones c)​ All known transmembrane domains consists of either alpha helices or beta sheets 4)​ All alpha helical transmembrane protein a)​ All helical bundle b)​ Binds retinal c)​ Light driven d)​ Generate proton gradient across membrane e)​ Powers ATP hydrolysis 5)​ Transmembrane protein can contain beta barrels 6)​ Lipid linked proteins a)​ Can anchor to thDe bilayer i)​ Prenylated protein ii)​ Fatty acylated proteins iii)​ Glycosylphosphatidylinositol-linked proteins 7)​ Peripheral membrane proteins associate loosely with membranes a)​ Peripheral proteins do not insert into lipid bilayer b)​ Bind to certain lipid head groups or integral proteins c)​ Behave like soluble proteins once purified 8)​ The membrane skeleton a)​ Helps define cell shape i)​ A membrane bag of hemoglobin ii)​ Biconcave disk-like shape iii)​ The lipid membrane can roll like “the tread of a tractor “ iv)​ Shape remains regardless of the content 9)​ Spectrin is a major component of erythrocyte membrane a)​ A loosely intertwined alpha beta dimer that further associates to a head to head b)​ Each polypeptide an alpha 280 and beta 246, consists of repeating 106 residue segments c)​ 100,00 tetramers per cell, accounts for 75% of the erythrocyte membrane, each cross linked at both ends by attachments to the cytoskeleton proteins d)​ Underlines the erythrocyte plasma membrane 10)​Membrane lipid sare distributed asymmetrically 11)​Gates and fences model rationalizes the different degrees of mobility of integral proteins 12)​Membrane lipid orientation determined by lipid synthesis and redistribution 13)​Two transport mechanisms a)​ Transmembrane and secretory proteins are carried as cargo of the membranous vesicle that bud dorm one cisternae and fuse with the next in the cis to trans direction b)​ They are also carried as a passenger in the golgi compartments during cisternal progression or maturation c)​ Mature protein are sorted at the translate-golgi network and sent to other cellular location 14)​Lumen is equivalent to extracellular a)​ ™ orientation is maintained b)​ COPI carry out both the anterograde and retrograde transport of protein between successive golgi compartments and also return esca[ed ER resident protein from the golgi back to the ER c)​ COPII transports proteins from the ER to the Golgi d)​ Clathrin Coats is a vesicle with polyhedral framework that transport TM , PI linked and sacred proteins from golgi to the plasma membrane 15)​ER residents proteins a)​ Most soluble ER-resident proteins contain specific C-terminal sequences b)​ They are like secretory proteins and lysosomal proteins which readily leave the ER via COPII coated vesicles, but the ER resident proteins are retrieved from the GOLgi and returned to the ER in COPI vesicles 16)​Vesicle fusion is mediated by specialized proteins a)​ Both lipids and proteins are transferred by vesicle fusion b)​ Neurotransmitters are also secreted this way c)​ Due to this repulsion, fusion between the vesicle and the target membrane is not spontaneous. d)​ Snare proteins mediate vesicle fusion 17)​Tetanus and botulinum toxins cleave Snares a)​ Tetanus and botulism are both caused by anaerobic bacteria belonging to the clostridium family b)​ Both bacteria produce extremely potent protein neurotoxins c)​ All toxins are first produced as single peptides which are then cleaved from the heavy chain and the light chain (heavy chain binds neurons and the light chain cleaves SNAREs) 18)​Membrane fusion in viral infection a)​ Virus mediated membrane fusion occurs in thee stages i)​ Host cell recognition ii)​ Activation of the viral membrane iii)​ Fusion of the viral membrane with a host cell membrane 19)​Membrane fusion of the influenza A virus Chapter 8 Glycosaminoglycans -​ Are linear polysaccharides composed of repeating disaccharide units, each consisting of uronic acid and hexosamine -​ They have alternating uronic acid and hexosamine residues and are linear, and they are NOT branched -​ They are highly viscous and elastic, forming hydrated gels due to their ability to bind water and cation -​ They are essential for providing structural support, lubrication and shock absorption in cartilage, tendons, skin and blood vessels -​ They provide structural integrity to tissues and important in joining for movement with no friction -​ They also help with shock absorption by resisting compressive forces Hyaluronate (Hyaluronic Acid) -​ They are made of repeating beta 1 to 3 linked D-Glucuronate and N-Acetyl -D -glucosamine disaccharide units -​ The disaccharides are linked by beta 1 to 4 bonds -​ The chains length can vary from 250 - 25,000 repeating units -​ This acid is unique for how it binds to water and expands up to 1,000 times in its dry state contributing to the viscosity of tissues -​ The viscosity of hyaluronate changes with shear stress -​ Low shear forms tangled masses and increases the resistance to flow -​ High shear align molecules with the flow and reduces resistance Sulfated Glycosaminoglycans (Heparin) -​ Heparin is highly sulfated with about 2.5 sulfate group per disaccharide unit, which makes it one of the most highly charged polymers in mammals -​ It is found in mast cells usually in arterial walls -​ They act as a anticoagulant, which prevents blood clots from forming in unusual and unwanted locations -​ Widely used in hospitals to prevent clotting issues -​ Heparan sulfate has fewer sulfates and more N-acetyl groups -​ They are usually found on cell surfaces and in the extracellular matric of the brain and blood vessels -​ They function to bind to growth factors and receptors, promoting cell proliferation, differentiation, wound healing and development Plant polysaccharides- Pectin  -​ Pectin consists of alpha 1-4 linked galacturonate residues intertwined with rhamnose -​ It is modified with methyl or acetyl groups and is crosslinked with calcium ions -​ Pectin is a major component of plant cell walls and provides structural rigidity and serves as a function similar to glycosaminoglycans in animal -​ Bacterial polysaccharides -​ Biofilms are extracellular matrices secreted by bacteria, composed on hydrated polysaccharides like poly-D-glucuronate, poly-N-acetylglucosamine and cellulose-like molecules -​ Biofilms provide protection against desiccation, antibiotics and environmental threats. -​ Biofilms make bacteria more resistant to external stresses like washing Proteoglycans​ -​ Proteoglycans are proteins covalently attaches to glycosaminoglycans and they have a bottle brush like molecular architecture with glycosaminoglycans extending from the central protein core -​ They function by forming hydrated gels that give resilience to tissues like cartilages where they help resist compression. -​ They fills places between the collagen fibers and provide structural integrity Bacterial cell walls (peptidoglycan) -​ They consist of alternating beta 1-4 linked N-acetylglucosamine and N-acetylmuramic acid -​ They provide rigidity to bacterial cell walls and allow bacteria to live in hypotonic environments -​ It also contributed to bacterial virulence -​ Penicillin inhibits enzymes that crosslink peptidoglycan strands -​ Vacomycin binds and inhibits transpeptidation in bacterial cell wall synthesis Glycosylation in Proteins -​ N-linked glycosylation involves the attachment of N-acetylglucosamine to asparagine in the sequence of ASN-X-Ser/Thr where x is any amino acid except proline -​ O-Linked glycosylation occurs at ser/thr residues, which often involves galactose or other sugars that are added stepwise and post translationally -​ Glycosylation plays a role in protein structure, function , recognition , cell-cell communication and protein folding/ stability Carbohydrate Recognition -​ Lectin are carbohydrate binding protein that medicate cell-cel interactions -​ Selectins are specialized lectins on leukocytes that bind to endothelial cells, and facilitates immune responses -​ ABO blood groups are examples of antigenic determinants which are specific oligosaccharides on cell surfaces Chapter 9: Lipids -​ Lipids are hydrophobic or amphiphilic and generally composed of hydrocarbons  -​They are insoluble in water but soluble in organic solvents -​Types of lipids include -​ Fatty acids : carboxylic acids with long hydrocarbon chains that can be saturated ( no double bonds) or unsaturated ( with double bonds) -​ Triacylglycerols : fatty acid triesters of glycerol, acting as the primary energy storage molecules in animals -​ Phospholipids: Major components of membranes and consists of a glycerol backbone, two fatty acid tails and a polar head group -​ Sphingolipids: derived from sphingosine and plays roles in cell recognition, adhesion and signaling. They are found primarily in neural tissues -​ Fatty acids consist of saturated fat that has straight chains that are packed tightly and has a higher melting point, found in animal fats and are solid at room temp. Unsaturated fatty acids contain cis double bonds that prevent tight packing lowering their melting points. They are found in plant oils and are liquid at room temp -​ Triacylglycerols are the primary energy storage form in animals that contain more energy per gram that carbohydrates due to their highly reduced state -​ Cholesterol are the most abundant steroid in animals that are found in plasma membranes and r a precursor for steroid hormones. They are essential for maintaining fluidity -​ Steroids hormones include glucocorticoids, mineralocorticoids , androgens and estrogens. All which are synthesized from cholesterol and regulate a variety of different physiological processes Membranes -​ Include the phospholipid bilayer which is formed by amphiphilic lipids, with hydrophobic tails that are facing inward and hydrophilic heads facing outward. Their fluidity depends on the lipid composition and temperature. -​ Integral membrane proteins span the bilayer and are often involved in catalysis, transport or signaling. -​ Lipid rafts are synthesized in the ER and transported to the golgi and then to other organelles or the plasma membrane. -​ Membrane proteins and lipid can move laterally unless restricted by the cytoskeleton or other structural elements.