Exam 2 BIOCHEM
Dextran
, found in yeast and bacteria, is composed of a-1-6 linkages of D-glucose, with branched chains (1-2, 1-3 or 1-4 linkages between glucose units). It forms a component of dental plaque (from bacteria).
what are the features of a carb that allows it to function the way it does
- 1 or more asymmetric centers, ability to form ring/linear structure, form polymers through glycosidic bonds, hydrogen bonding ability
- How are the subclasses sphingomyelins and glycosphingolipids (cerebrosides and gangliosides) defined?
- Cerebrosides (glycolipid): ceramide plus monosaccharide: galactocerebroside is an important component of the brain, sulfogalactocerebroside is found in myelin - Gangliosideds (glycolipid): globoside plus one or more sialic acid residues: found mainly in ganglions.
what does it mean to be saturated vs unstatured
- Saturated means no double bond, unsaturated has.
what is the purpose of superhelical forms
- yield compact shape - result in unwinding of dna helix 2 enzymes work to maintain supercoiling in dna
what are the two types of N-glycosylation
-glcNac, L-fructose, NANA present - contain mainly mannose
Understand and describe the phase transition and the characteristics associated with it.
1. Transitions are endothermic 2. Phospholipids have distinctive TM. The longer the chain the higher the TM. It decreases with unsaturation. 3. Pure bilayers transition over a narrow temperature range and are all or nothing in structure (gel or crystal.) 4. Biological membranes also have this phase transition, but due to their complexity and heterogeneity (lateral phase separation), the transition occurs over a much broader temperature range. 5. The volume of the cell or vesicle increases with the phase change. 6. The presence of ions or other solutes affects the phase change.
how many stereoisomers of heptulose? how many d vs l
16, 8d 8l it has 4 chiral centers 8 names
what are the 2 motifs of o links
1: leukosialin 2: LDL receptor, decay accelerating factors
how many epimers of d glucose, a-d- glucose?
2 and 3
how many stereoisomers are available
2^n n=chiral centers
only ____ sugars form rings
5-7 C 6 atoms: pyranose, 5 atoms: furanose
1 turn of helix has ___ glucose units
6
fructose forms either
6C pyranose ring, by rxn of C2 keto group with OH on c6 or 5C furanose ring by rxn of c2 keto group with OH on C5
What is the general structure of a glycerophospholipid?
A glycerophospholipid is made of one polar head region constructed from an amino alcohol and a phosphate group, and two non-polar tails that are fatty acids.
How are nucleotides made from nucleosides?
A nucleoside consists of a nitrogen base and a ribose or deoxyribose sugar. It can be converted to a nucleotide by adding a phosphate to the 5-OH of the sugar component.
define bile acids (steriods)
Act as detergents secreted by the gallbladder that help solubilize lipids in diet (Ex. chloric and deoxycholic acid)
Calcium ions travel through the cell membrane into the cell, using an integral protein. There is a higher concentration of calcium in the cell.
Active transport is a process that uses a transport protein and energy in the form of ATP to transport molecules against their concentration gradient. Since molecules are moving against their concentration gradient in the scenario, we know it must be active transport
what are the msot abundant aa found in histones and why
All histones have a high percentage of arginine, lysine, and positively charge aa that give them a net positive charge. Positive charges attract the phosphate backbone of dna
What part of the structure of all phospholipids is considered the polar region?
All phospholipids have a polar region made of an amino alcohol attached to a phosphate group.
define androgen (steriod)
Androgens - Mediate development of sexual characteristics and function (e.g. testosterone, estradiol)
Why aren't lipids soluble in water?
Because they are predominantly hydrocarbons, hydrophobic.
What are the two sugars found in the nucleosides used to make DNA and RNA?
Both of the sugars found in nucleic acids are pentoses. Ribose is found in RNA, and 2´-deoxyribose is found in DNA.
which structures is a 20:2 (Delta4, 9) FA
CH3(CH2)9CH=CH(CH2)3CH=CH(CH2)2COOH
what is the difference between a channel and carrier protein
Channel proteins: provide corridors that allow a specific molecule or ion to cross the membrane. Carrier proteins: undergo a subtle change in shape that translocate the solute binding site across the membrane. Most passive transport proteins are solute specific. simple diffusion and passive transport by membrane transport proteins (facilitated diffusion) occur spontaneously. Active transport requires an input of metabolic energy. Only carrier proteins can carry out active transport =, both carrier proteins and channel proteins mediate facilitated diffusion. Transport by carrier proteins can be either active or passice, whereas transport by channel proteins is always passive
what is chromatin
Chromatin: chromosome material which does not stain strongly except during cell division, it represents the major genes and is involved in transcription. Comprises the most active portion of the genome.
Oxygen molecules travel through the cell membrane into the cell, passing between the phospholipids. There is a higher concentration of oxygen outside the cell.
Diffusion is a passive process that does not require energy. Molecules that diffuse are also small and hydrophobic enough to pass through the phospholipid bilayer without the assistance of channel proteins.
osmosis
Diffusion of water across a differentially permeable membrane. Water moves from a high concentration to a low one. Down the concentration gradient
lipid nomenclature, delta x
Each double bond is indicated by a ∆x, where the double bond is located on the xth carbon-carbon bond, counting from the carboxylic end ▪ Each double bond is preceded by a cis- or trans- prefix
what is endocytosis
Endocytosis is the opposite. Brings things into the cell. The plasma membrane sinks inward, pinches off and forms a vesicle, vesicle often merges with golgi for processing and sorting of its contents.
describe glycogen
Energy Storage, . . It is highly branched with \alphaα-1-6 branches. It is hydrolyzed by \alphaα- and \betaβ-amylases to yield glucose and maltose (glucose-\alphaα-1-4-glucose disaccharide). It can also be hydrolyzed by glycogen phosphorylase (in liver and muscle) to release glucose-1-phosphate.
what is starch and its function
Energy storage, it is a glucan with 2 polysaccharide forms.
what are open chain saponifiable lipids
FA, TG, phospholipids, sphingolipids, waxes
what are the factors that affect diffusion
Factors affecting diffusion rate: steepness of concentration gradient... steeper gradient, faster diffusion, molecular size: smaller molecules, faster diffusion, temperature: higher temperature, faster diffusion
how does the distinction between saturated and unsaturated affect packing structure and flexibility
Fatty acids are very flexible with free rotation of their single bond. They are generally found in a trans (zig-zag)conformation. This formation allows for closed packing between the molecules. When double bonds are added this adds cis "kinks" to the chains that prevent this close packing and the fatty acids become more fluid.
describe flippases and floppases
Flippases and floppases Are ATP dependent moving phospholipids to the inner and outer side of the membrane respectively.
omega reference , lipid nomenclature
Indicates the number of carbons, the number of double bonds, and the position of the double bond closest to the omega carbon
What is the difference between integral and peripheral proteins?
Integral proteins extend through the lipid bilayer, and peripheral proteins are just on the surface of the inside or outside of the cell.
what are lipid signaling events
Involve lipid messengers which can bind to receptors and mediate certain processes lipid signalling is normally a response to some inner or outer stimulus leading to the release of lipids moieties
What is an anomeric Carbon and its relationship to "reducing sugars"?
Isomers that vary only in the orientation of this new carbon stereocenter are called anomers. Sugars with free anomeric carbons act as reducing agents and as they are oxidized become sugar acids. These sugars are called reducing sugar
Why is cholesterol known as a sterol?
It contains a hydroxyl group on carbon 3.
what is euchromatin
It contains the most active genes. Undergoes the normal process of condensation and decondensation in the cell cycle.
Describe supercoiling
It is an additional level of twisting When the strain Of over rotating or under rotating cannot be compensated by the turning of the ends of the double Helix which is the case of the DNA circular that is there are no free ends some viral chromosomes are in the form of simple circles and readily undergo supercoiling
when does supercoiling occur
It occurs only if two polynucleotide strands of the DNA double helix are unable to rotate about each other freely.
describe lactose
Lactose is comprised of a galactose linked to glucose via a \betaβ-1-4 glycosidic bond. "Milk sugar" - it is the principle carbohydrate of milk. Must be broken down into galactose and glucose by the enzyme lactase.
Which statement is true about lecithins and cephalins?
Lecithins always have choline as their amino alcohol group and cephalins have either an ethanolamine or a serine as their amino alcohol group.
what is heterochromatin
Less transcribed chromatin Remains in a highly condensed state throughout the cell cycle, even during interphase. Activity of genes is modified or suppressed.
what is a linking number
Linking Number (L) - This is the basic parameter used to characterize supercoiling. It is the number of times the two DNA strands are intertwined.
describe maltose
Maltose is glucose-\alphaα-1,4 glucose. This is also known of as"Grain sugar". Maltose does have an anomeric carbon and is therefore a reducing sugar.
what is a uniport
Movement of single molecule at a time
describe negative vs positive supercoiling
Negative supercoiling - left-handed - strands are underwound. Positive supercoiling - right-handed - strands are overwound
hypotonic
Net movement of water into cell, cell will burst.
hypertonic
Net movement of water out of cell cell shrinks
What type of linkage holds nucleotides together to make a nucleic acid?
Nucleotides are held together in nucleic acids by bonds between the phosphate and the ribose or deoxyribose sugar. These bonds are called phosphodiester bonds.
linkages between proteins can be
O or N
how are rings formed in a sugar
OH group on hexose will attack the C1. when rings forms a new asymmetric C is intoduced, the OH on new asymmetric c can be drwan to appear on same side of ring forming oxygen or on side away
Which molecule(s) would be expected to diffuse into a cell using passive transport?
Passive diffusion only occurs for small non-polar molecules where the concentration is lower inside the cell than outside. Carbon dioxide is the only small non-polar molecule listed.
what is phagocytosis
Phagocytosis: cell earing. Membrane sinks in and captures solid particles for transport into the cell ex: bacteria, cell debris
How do nonsteroidal anti-inflammatory drugs (NSAIDs) reduce inflammation and elevated temperatures?
Prostaglandins are a diverse set of molecules that can cause pain, inflammation, and fever. NSAIDs block their production, thus decreasing these effects.
how does chargaffs rule relate to DNA vs RNA structure
RNA doesnt follow the role while dna does
Which best describes the role of RNA in biological systems?
RNA is involved in the process in which the sequence information from DNA is translated into the sequence information specifying the sequence of amino acids in proteins.
What is the purpose of cholesterol in cell membranes?
Reduce the flexibility of the cell membrane
describe scramblases
Scramblases use calcium ions and our BI directional their purpose appears to be to degrade transverse asymmetry
what is an antiport
Simultaneous transport of two different molecules in opposite directions.
what is a symport
Simultaneous transport of two different molecules in same direction.
Which of the following statements is true about fats and oils?
Solid fats tend to contain saturated fatty acids, whereas liquid oils tend to contain saturated fatty acids. It is generally true that as the number of C=C double bonds increases, the melting point of a fatty acid decreases, thus oils tend to have lower melting points than fats.
sphingolipid
Sphingolipids = synthesized starting with an 18-carbon amino alcohol molecule (sphingosine
What is the structural difference between glycerophospholipids and sphingomyelins?
Sphingomyelins have a sphingosine group and glycerophospholipids do not. Solution:Sphingomyelins have a sphingosine replacing glycerol.
what is a ceramide
Spingosine plus fatty acyl group: core structure
describe sucrose, the bonds, is it reducing
Sucrose is comprised of glucose-\alphaα-1,2-fructose. Also known as "Table sugar", it has no free anomeric carbon so it is not a reducing sugar.
lipid nomenclature lipid numbers
Take the form C:D, where C is the number of carbon atoms and D is the number of double bonds ▪ When ambiguity exits, the notation is usually paired with a ∆ X notation
Which of the following is true If a sample of DNA is shown to be 30% adenine?
The DNA contains equal amounts of adenine and thymine, so it will contain 30% thymine. That leaves 40% for guanine and cytosine which are also equal and must be 20% of each.
In the nucleus of a cell, double-stranded DNA is bound to protein molecules called _____
The DNA is a cell's nucleus is bound to protein molecules called histones. The complex forms structures called nucleosomes, which are part of the material called chromatin that form chromosomes.
What is the complementary strand for the DNA strand 5´-AAGGCAGG-3´?
The complementary strands run in opposite directions. T binds to A, C binds to G and G binds to C. U is not found in DNA. The complementary strand is 3´-TTCCGTCC-5´.
what do all proteoglycans share in common
The glycosaminoglycan units being olinked to serine residues in the sequence Ser Gly
What is the major structural difference between PGE and PGF?
The major difference between PGE and PGF is that PGE has a ketone at carbon 9, while PGF has an alcohol. This makes PGF slightly more soluble in polar solvents.
What is the name of the three nucleotide sequence found in tRNA that identifies a particular amino acid for protein synthesis?
The three nucleotide sequence in messenger RNA which specifies a particular amino acid is called a codon. The three nucleotide sequence in transfer RNA which is complementary to the codon and therefore delivers the correct amino acid to the binding site is called the anticodon.
how does the linking number related to twist and writhe
The twist is the number of helical turns and the writhe is the number of supercoils. L= T+W Note that as long as the DNA is in a normal unbroken relaxed form the value of L is constant.
Which best describes the structure of the phospholipids of the lipid bilayer?
There are two layers of phospholipids. The polar heads are on the surfaces of the membrane, and the non-polar tails are on the inside of the membrane.
small nuclear ribonucleoprotein particles (snRNP's)
These RNAs are involved in the processing of eukaryotic gene transcripts into complete mRNA molecules for export from the nucleus to the cytoplasm.
define glucocorticoids (steriod)
These regulate carbohydrate, protein and lipid metabolism (Ex. cortisol.
define mineralocorticoids (steriod)
These regulate salt balance in tissues
define progestin (steriod)
These regulate the menstrual cycle (Ex. progesterone)
where do proteoglycans appear
They appear to be either extracellular matrix proteins (syndecan versican) or integral membrane proteins
what does amphipathic mean
They have a hydrophilic and hydrophobic region Why
what are the two enzymes involved in superociling
Topoisomerases: relax supecoiled DNA. They are enzymes that add or remove rotations from the DNA Helix by temporarily breaking the nucleotide strands rotating the ends around each other and then rejoining the broken ends DNA gyrase: introduces supercoiling
Which of the following abbreviations for a nucleotide is not commonly possible?
Uracil is not found in DNA so it is not commonly found in a nucleotide containing deoxyribose. Therefore dUMP is not a common abbreviation for a nucleotide.
what is bulk flow
Vesicles are used to transport large particles across the PM, requires energy. Types: endocytosis (phagocytosis, pinocytosis, receptor-mediated) and exocytosis
what is the purpose of supercoiling
Yield a more compact shape, can result in unwinding of DNA helix (aids in replicationg)
Which of the following base pairings is correct for RNA?
a and u
which of the following molecules is a typically FA
a molecule that has one cis double bond in a linear carbon chain
Glycolipids contain what additional chemical unit that other lipids are lacking?
a saccharide
the structure of a DNA in a chromosome is considered
a tertiary structure
what is a glucosyl group
a univalent free radical or substituent structure obtained by removing the hemiacetal hydroxyl group form the cyclic form of a monosaccharide and by extension, of a lower oligosaccharide.
Which of the following is not a component of a nucleic acid?
aa
O-glycosylation
addition can happen on the OH o on the side chain of hydroxy lysine, hydroxyproline, serine, or theronine
N-glycosylation
addition of sugar chains can happen at amide nitrogen on asparagine side chain
what bases are found in dna
adenine, guanine, cytosine, thymine
what bases are found in rna
adenine, guanine, cytosine, uracil
What four bases are found only in DNA? rna?
agct, agcu
What amino acid is coded by the codon GCC?
alanine
how are monosaccharides named
aldehyde group present: aldose sugar ketone group present: ketose sugar the aldo has carbonyl on C1, keto is on C2
describe the antifreeze glycoprotein
allow fish to live in freexing water [ala-ala-Thr]n-ala-ala n=4-6,12,17,28,45,50
what is the purpose of branching
allows several sites for simultaneous synthesis and degradation. Speeds up degradation. glycogen phosphorylase cleaves 1 glucose at a time from non-reduced end of glycogen makes glycogen an efficient way to sstore glucose
OH below the rings
alpha
what are N link glycoprotein
amide group on asparagine to N-acetul galactosamine, but also have mannose branched triad
what are the two forms of starch
amylose (linear) alpha 1-4 links and amylopectin (branched) alpha 1-6 links it is insoluble and the major storage of carbs in plants starch has one reducing end and many non reducing ends
define an ether glycerophospholipid
an ether linkage exists off the phosphate group o
what are the five main types of steriods
androgen, progestin, glucocorticoid, mineralocorticoid, and bile acids
A-D- glucose is the ____ of B-D- glucose
anomer
what adds to the diversity of the sugar code
anomeric status, linkage positions, addition of branches, site specific intro of substitutions
What is the best description of how the two strands are aligned with each other in the double helix of DNA?
anti parallel
. Homopolysaccharides
are made up of the same monomer sugars.
Heteropolysaccharides
are made up of two or more different monomer sugars.
what is the best term to describe the distribution of different types of phospholipid molecules in a plasma membrane
asymmetrical
each aldose with > or equal to 3c and ketose with > or equal to 4cs has
at least 1 chiral carbon
Which of the following is a commonly used mechanism for anchoring a protein to a membrane?
attaching a farnesyl group to a cysteine residue to form a thioether
what is a nucleoside
base + sugar via glycosidic bond=anomeric conformation is either syn or anti
D vs L sugars based on
based on configration about the single assymmetric C in glyceraldehyde they are greater than 1 chiral center, refers to the asymmetric C farthest from aldehyde or ketone
what are the functions of nucleotides
bases serve as recognition units cyclic ones are signal molecules and regulators of cell metab and reproduction
Oh above the rings
bea
which is a characteristic of both waxes and terpenes
both can contain oxygen
what is a characterisitc of both tg's and glycerophospholipids
both contain FAs and are saponifiable
Which carbon atom do steroids differ at?
c17
hemiacetals
carbons surrounded by O that are attached to 1 c group and 1 H allows to be reducing sugar
what are some common waxes
carnuba, beeswax, sebum waxes- sabaceous glands
what is pinocytosis
cell drinking, ccell brings in liquid.
Sphingolipids serve what function in biological systems?
cell membrane components Sphingolipids are found in membranes along with phospholipids and cholesterol.
what are the functions of O link glycoprotein
cell signals, nutrient sensors, regulate cell metab. Found to be altered in diseases of aging. found in 2 structural motifs: highly extended above membrane surface, support to push the active protion above membrane
active transport
cells also require transport proteins that can actively pump certain solutes across the membrane against their electrochemical gradients (uphill). This is known as active transport and is always mediated by carrier proteins. In active transport, the pumping activity of the carrier protein is directional because it is tightly couple to a source of metabolic energy such as ATP hydrolysis or an ion gradient. It is the movement of particles across the plasma membrane against the concentration gradient. That is from a region of low concentration to a region of high concentration. Energy is provided by atp molecules. This transport required a specific carrier protein to carry molecule in and out of the cell. Ex: ansorpotion of glucose and aa by cell in the small intestine (NA, K ATPASE
what is a glucoside (glycolipid)
ceramide plus 2 or more hexoses: lactosylceramide is present in erythocte membranes
what is a sphingomyelin
ceramide plus phosphocholine head group: component of erythrocyte and neuronal membranes
amylopectin
characterized by increase in viscocity, clarity, stability, and resistance to gellling.
when sugars become cyclic, the carbonyl carbon becomes
chiral
What is the most common steroid in animals AND is a precursor for all other steroids in animals?
cholesterol
what are clsed chain non-saponifiable lipids
cholesterol, steriod, derived.
glycopeptide
consists of carb linked to an oligopeptide. composed of L and or D aa's
glycosyl aa
consists of saccharide linked through a glycosyl linkage (o- or n- or s-) to an aa
what are glycoproteins
contain oligosaccharide chains (glycans) and are covalentaly attached to polypeptide
Which steroid hormone is produced in the adrenal glands?
cortisone, aldosterone, cortisol
All active transport reactions are
coupled reaction
glycosidic bond
covalent bond between anomeric OH of cyclic sugar and hydroxyl of 2nd sugar. the resultant molecule is glycoside. linkage of two monosaccharides to form disaccharide involves glycosidic bond.
describe oligosaccharides
created by glycosidic bonds, limited to hexoses: glu, mannose, galactose (all aldoses) and fructose pentoses: ribose, xylose
what is exocytosis
cytoplasmic vesicle merges with the PM and release their contents, ex: golgi body vesicles merge with the PM and release their contents, how nerve cells release neurotransmitters.
what are the four key lipid signalers
diacylglycerol (DAG), ceramides, platelet activating factor (PAF), arachidonic acid
what is an anomer
differ in stereochemistry around ring forming C. since alpha and beta differ in only 1 chiral center anomers=epimers
describe ribose sugars
difference shown at 2' carbon, nitrogenous base attach at 1' carbon
secondary structure of nucleotides (base pair)
double helix formed by 2 anti-parallel dna strands bind together by h bonding
what are carbs
either aldehydes or ketones with many OH groups or substances that form these when hydrolyzed. (simple sugars: glucose, complex: starch and cellulose
D vs L sugars are mirror images or
enantiomer
what process is directly linked to bulk flow
endocytosis
what are the functions of these nucleotides atp gtp ctp utp
energy metab protein synthesis lipid synthesis carb metab
exergonic
energy of products < energy reactants endergonic is opposite
what are the functions of carbs
energy production, cell structure, and recognition process
what is the activation energy
energy required for rxn to go from reactants to products through transition state
what are the functions of polysaccharides
energy storage and structural support. starch/glycogen: energy stores chitin/cellulose: structural
glycosylation vs glycation
enzymatic attachment of sugars to proteins non-enzymatic
what are the features of O-glycosylation
enzymes involved are located in various subcompartments of golgi apparatuse. Each reaction involves appropriate nucleotide sugar. occurs post-translationally at cetain ser and thr residues
what are coenzyme/cofactors
enzymes that require additional non-protein to be active some vitamins are cofactors
correct name for the relationship between D-fructose and D-picose
epimers
glucose and galactose are
epimers and diasteromers
isotonic
equal movement of water into and out of cell.
waxes
esters of fa with long chain monohydric alcohol
versican
extracellular matric proteoglycan
Water molecules travel through the cell membrane into the cell, passing through aquaporin, a channel protein. There is a higher concentration of water outside the cell.
facilitated diffusion
a plasma membrane with a high unsaturated FA content will be less fluid due to the higher amount of spacing created between the phospholipid tails in the interior of the bilayer true or false
falase
a glycosidic bond is formed via a hydrolysis reaction true or flase
false
Proteins that can flip and flop phospholipids from one side of a bilayer to the other are called
flippases, floppases, and scramblases
what are O links glycoproteins
formed through serine, threonine, hydroxlysine, hydroxyl groups to N-acetyl galactosamine
describe nucleotide
formed when phosphoric acid is esterified to a sugar hydroxyl of nucleoside -polyprotic -most are ribonucleotides -nucleoside phosphate=nucleotide phosphoric acid esters of nucleoside
What are the functions of n-linked glycoproteins
found in immunoglobuins g and m, ribonuclease B and ovalbumin. They affect chemical and physical properties and function as stabilizers/signals6
feats of mucin
found in secretions of gi, respiratory, and reproductive tracts, membranes of cells have high contents of o-glycan chains usually containing NeuAc have repeating aa sequences rich in serine, threonine, proline form protective physical barrier on epithelial surfaces, invovled in cell to cell interations and contain surface anetigens
how are carbs formed
from dehydration synthesis and hydrolysis
describe dna and rna
genetic materical in cells. main constituent of chromosomes transcribes/translate info into protein. acts a a messenger, carrying instructions from dna for controlling pro synthesis
what are the features of N-glycosylation
glc2Man9(giNAC)2 is transferred from dolichol-P-P- in rxn catalyzed by oligosaccharide: protein transferase. occurs in the er. protein bound oligosaccharide is then partially processed by glucosides and mannosides
what is the function of glycogen
glucose reserve, atp from glycolysis.
sugar esters
glucose, fructose, and others with added phosphate groups
what are the two simplest sugars
glyceraldehyde (Aldose) dihydroxyacetone (ketose)
fats and oils
glycerol + 3 FA by dehydration synthesis =tg
Which of the following chemical components is not found in sphingomyelins?
glycerol backbone
define a glycerophospholipid
glycerol-3-phosphate backbone + 2 fatty acids on C1 and C2 + a polar head linked through phosphate group
which lipids would be in the phospholipid categoru
glycerophospholipids and sphingomyelins
peptidoglycan
glycoaminoglycan formed by alternative residues of D-glucosamine and muramic acid
proteoglycan
glycoprotein whose carb moieties are glycosaminoglycans have repeating units of ser-gly aa's are either extracellular matrix proteins (serglycin/versican) or integral membranes (syndecan)
what are the major types of histones
h1, h2a, h2b, h3, h4
amino sugars
have amino groups instead of hydroxyl at c2
how do you make acetals/ketals
hemiacetals/hemiketals + OH in an acidic solution, through dehydration
what are the two lipid type
hydrolyzable (saponifiable) those that arent
defined disaccharide
hydrolyzed to form 2 monosaccharides
define oligosaccharide
hydrolyzed to form 3-12 monosaccharides
define polysaccharide
hydrolyzed to form many monosaccharides
superhelical forms occur only
if 2 poly nucleotide strands are unable to rotate freely
functions glycoproteins immunoglobin histocompatibility HCG,TSH
immunological antigens hrmone
How do intercalating agents affect structure of DNA? What are examples of intercalating agents?
intercalating agents are organic aromatic macrocyclic molecules that are flat and hydrophobic. They are capable of inserting themselves into the DNA helix causing unwinding. This can cause errors during the replication of DNA, and the molecules are therefore, carcinogenic. Ethidium bromide, Acridine Orange and actinomycin D are some example agents.
describe chitin
is in cell walls of fungi and exoskeletons of crustaceans, insects and spiders. Main difference between chitin and cellulose is the hydroxyl at the 2 position is replaced by -NHCOCH3. Chitin is composed of N-acetyl-D-glucosamine.
anomers
isomersthat vary only in orientiation of carbon stereocenters
What is the Arrhenius equation?
k = Ae^(-Ea/RT)
What amino acid is coded by the codon CUA?
leucine
selections role in inflammation
leukocytes: roles in inflammatory phenom. they are single chain ca binding transmembrane proteins that control domains. amino terminal ends have lectin domain which is involved in binding to carb ligands
lipids
long chain hydrocarbon, non-polar, polar motif FA that allow to be amphipathic, also has glycerol
FA
long hydrocarbon chain (12-24) with carboxyl head. found esterified to glycerol and can be saturated/unsaturated/polyunsat
glycogen
major storage form in animals. branched with alpha 1-6 branches. hydrlyzed by alpha and beta amylases to yield glucose and maltose. stored in muscle and liver.
functions of oligosaccharides
modulate physicochemical properties: solubilty, viscocity
what are the three groups of carbs
monosaccharides, disaccharides, polysaccharides, oligosaccharides
what are simple sugars
monosaccharides: defined by inability to be hydrolyzed. (CH2O)n N=3 or more.
describe polysaccharides
most common carb in nature aka glycans. They are synthesized from monosaccharides
cellulose
msot abundant natural polymer, polymer of b-d glucose. resistant to hydrolysis. cellulse is needed to hydrolyze glycosidic bonds . Cellulose is made of D-glucose with \betaβ-1-4 glycosidic linkages. Cellulose is resistant to hydrolysis. The enzyme (cellulase) is needed to hydrolyze the glycosidic bond. Some bacteria make cellulase and can therefore "eat" cellulose.
The porin proteins (e.g., maltoporin) utilize the ____ structural motif.
multiple β-sheet
what are the basic structural units of dna
nitrogenous bases found in nucleic acid are derivatives of pyrimidines/purines
simple diffusion
nonpolar, hydrophobic molecules diffuse directly through the lipid bilayer. Does not require the use of transport proteins. Ex: o2, co2, co, no, steroids other lipophilic substances, ethanol, h2o. Polar, hydrophilic substances cannot pass directly through the lipid bilayer. Ex: ions, carbs Down the concentration gradient
What component of a nucleotide consists of a sugar bound to a nitrogen-containing base?
nucleoside
describe the primary structure of nucleotides
nucleosides linked by phosphodiester links to form single strand. phosphate ester links 3' and 5' O's of 2 sugars 5' a-t-g-c-a 3'
What is the repeating monomer of a nucleic acid?
nucleotid. The repeating monomer of a nucleic acid is a nucleotide, which consists of a nitrogen base, a ribose or deoxyribose sugar, and a phosphate. A nucleoside consists only of a nitrogen base and a ribose or deoxyribose sugar.
which of the following is not a main component of a plasma membrane
nucleotides
what are the three major classes of glycoproteins
o link, n link, and those linked to the carboxyl terminal aa of a protein via a phosphoryl-ethanolamine moeity joined to an oligosaccharide (glycan) which in turn is linked via glucosamine to phosphatidylinositol (PI
what specific molecule is shown to represent passive diffusion
o2
acetals
oxygens are both attached to C's
what can endocytosis be broken down into
phagocytosis, pinocytosis, receptor-mediated
Flippases are enzymes that flip:
phospholipids across to the other side of a membrane.
what is the key difference between phospholipids and tgs
phospholipids have 2 fas, tgs have 3
where do carbs come from
photosynthesis
what are peptidoglycan
polysaccharides found in bacterial cell walls. gram positive bacteria have thick walls of this.. composed of N-acetyl glucosamine and N-acetylmramic acid with pentaglycine links and tetrapeptide (L-ala, D-glu, L-lys-d-ala) moieties
what are glycosaminoglycans
polysaccharides of combined amino sugars and sulfate containing groups, acts as a natural anticoagulant
describe B form dna
prevails under physiological conditions of low ionic strength and increase degree of hydration
chain of glycoproteins
protect proteolysis, affect proteolytic processing of precursor proteins to smaller productss. are involved in biological activity = ex: hcg affect insertion into membrans, intracellular migration, sorting /secretion affect embryonic development of differentiation
what are histones
proteins in chromatin
decorin
proteoglycan secreted by fibroblasts
purine bases form H bonds wiht
pyrimidines (base pairing)
what is receptor mediated endocytosis
receptor proteins on RM bind specific substances, membrane sinks in and forms a pit, called a coated pit. Pit pinches closed to form a vesicle around the bound substances. Cytoskeleton aids in pulling in the membrane and vesicle formation.
what are sugar acids
reducing sugars, as oxidized they become acids
sugar alchols
reduction of carbonyl group of sugars, -itol
describe z form dna
regions of helix rich in pC pG dinucleotide can exist in left handed helical form results from 180 degree change in orientation of base relative to that of a and b dna
whst are topoisomerases
relax supercoiled dna gyrase: introduces supercoiling
Normal dna is the ___ handed ___form
right, B
enol form of dna
ring nitrogrns serves a h bond donors, keto oxygens as h bond acceptros
what are the pentose sugars in dna and rna
rna: ribose + purine/pyr dna: deoxyribose
glycoamino acid
saccharide attached to a single aa by any covalent bond
Nearly all of the calcium ions in muscle are sequestered inside vesicles called:
sarcoplasmic reticulum.
Which of the following is true regarding membrane function?
scaffolding proteins, particularly those containing BAR domains, result in curvature of the cell membrane membrane fusion with vesicles is often accomplished with the aid of a snare protein
What term(s) best describe cell membranes?
semi-permeable, fluid mosaic model, phospholipid bilayer, liquid like
What amino acid is coded by the codon AGC?
serine
importance of lipids
serve as structural components of biological membranes provide energy reserves in form of triacylglycerol serve as vitamins/hormones lipophilic bile acids aid in lipid solubilization
facilitated diffusion
small polar molecules and ions diffuse through passive transport proteins (Carriers and channels) ex: glucose enters/leaves cells through facilitated diffusion. Down the concentration gradient
d-glucose vs d-fructose
structural isomers, they have different functional groups
functions glycoproteins collagen mucins transferrin immunoglobins
structural molecule lubricant/protective agent transport molecule
what are the three common disaccharides
sucrose (glu +fruc), lactose (galact +glu), maltose (glu x2)
the o linked glycoproteins of eukaryotes usually have their sugar chains attached to
the OH of Ser or Thr residues
what are proteoglycans
the carb units are polysaccharides that contain amino sugars, such polysaccharide are known as glycosaminoglycans
Active transport is uniquely characterized by:
the tight coupling of an input of energy to drive a thermodynamically unfavorable reaction.
Z dna occurs when
there are g-c rich regions in the dna strands in the helix
In passive diffusion, the transported species moves across the membrane in the ____ favored direction ____.
thermodynamically; without a specific transport system/molecule
in cell membranes, carbs in glycoproteins are oriented?
towards the outside the cell
In the Na+, K+-ATPase mechanism, ATP is involved in all EXCEPT:
transferring a phosphate group to make sodium phosphate.
Syndecan
transmembrane proteoglycan. Syndecan binds intracellularly to the cytoskeleton protein actin, and extracellularly through the glycosaminoglycan units to fibronectino
define trna rrna mrna
transports aa to site of pro synthesis combines with protein to form ribosome, site of pro synthesis directs aa sequence of protein
name of carbs based on number of C;s 3-6
trioses, tetroses, pentoses, hexoses,
what is the smallest type of Rna
trna
The Variable Arm in a tRNA (according to the lecture) will be classified as __ if it is composed of only a few nucleotides.
type 1
what are the two topoisomerase classes
type 1: breaks 1 of nucleotide strands and reduces supercoiling by removing rotation type 2: adds/removes rotations by breaking both nucleotide strands
which of the following has a double bond their hydrocarbon chains
unsaturated fats
amylose
unstable due to intermolecular attaction and association of neighboring amylose molecule. leads to increase in viscocity and retrodegradation
what is an epimer
used when comparing sugars with many chiral centers. only 1 center is differnt
