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Biochemistry Flashcards

1
Q

What type of bond is a peptide bond?

A
  • A specialized form of an amide bond that is formed between the COO- group of one amino acid and the NH3+ group fo antoher amino acid
  • Peptide bonds are formed as a result of a condensation (or dehydration) reaction because it results in the removal of water
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2
Q

Why is rotation of the protein backbone around its C-N amide bond restricted?

A
  • Because amide groups have delocalizable pi electrons in the cabonyl and in the lone pair on the nitrogen, they can exhibit resonance; thus, the C-N bond in the amide has partial double bond character
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3
Q

What are conjugated proteins?

A
  • Derive part of their function from covalently attached molecules called prosthetic groups
  • Proteins with a lipid, carbohydrate, and nucleic acid prosthetic group are called lipoproteins, glycoproteins and nucleoproteins, respectively
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4
Q

What effect do enzymes have on a reaction?

A
  • Lower the activation energy
  • Increase the rate of the reaction
  • Do not alter the equilibrium constant
  • Are not changed or consumed in the reaction
  • Are pH and temperature sensitive, with optimal activity at specific pH ranges and temperatures
  • Do not affect the overall ΔG of the reaction
  • Are specific for a particular reaction or class of reactions
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5
Q

What do transferases do?

A
  • Catalyze the movement of a functional group of one molecule to another

Example: an aminotransferase can convert aspartate and α-ketoglutarate to glutamate and oxaloacetate by moving the amino group from aspartate to α-ketoglutarate

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6
Q

What do hydrolases do?

A
  • Catalyze the breaking of a compound into two molecules, using the additon of water
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7
Q

What do lyases do?

A
  • catalyze the cleavage of a single moleulce into two products
  • They do not require water
  • Because most enzymes can also catalyze the reverse of their specific reactions, the synthesis of two molecules into a single molecule may also be catalyzed by a lyase (these are synthases)
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8
Q

What do isomerases do?

A
  • Catalyze the rearragement of bonds within a molecule
  • Catalyze reactions between stereoisomers as well as constitutional isomers
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9
Q

What do ligases do?

A
  • Catalyze addition or synthesis reactions, generally between large similar molecules and often require ATP
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10
Q

What is a cofactor?

A
  • Generally inorganic molecules or metal ions and are often ingested as dietary minerals
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11
Q

What is a coenzyme?

A
  • Small organic groups
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12
Q

What is an apoenzyme?

A
  • Enzymes without their cofactors
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13
Q

What is a holoenzyme?

A
  • Enzymes with their cofactor
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14
Q

What is the effect of a competitive inhibitor on Vmax and Km?

A

Vmax: unchanged; if enough substrate is added, it will displace the inhibtor

Km: increased; the substrate concentration has be higher to react half of the maximum velocity in the presence of the inhibitor

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15
Q

What is the effect of a non-competitive inhibitor on Vmax and Km?

A

Vmax: decreased, becuse there is less enzyme available to react

Km: same; because any enzymes that are still active maintain the same affinity for their substrate

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16
Q

What is the effect of uncompetitive inhibition on Vmax and Km?

A

Vmax: decreased

Km: decreased

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17
Q

Draw out the 4 nucleotides

A
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18
Q

Draw out the Fischer projection for D- glucose

A
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19
Q

Draw the Fischer projection for D-galactose

A
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20
Q

Draw the Fischer projection for D-mannose

A
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21
Q

Draw the Fischer projection for D-ribose

A
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22
Q

What is the primary thing that cause secondary structures of proteins?

A

Secondary structures are primarily the result of hydrogen bonding between nearby amino acids

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23
Q

What is the role of proline in secondary structures?

A
  • Proline will introduce a kink in the peptide chain when it is found in the middle of an α helix or β pleated sheets
  • However, proline is often found in the turns between the chains of β pleated sheets and is often found as the residuce at the start of an alpha helix
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24
Q

What factors determine a proteins tertiary structure?

A
  • Mostly determined by hydrophilic and hydrophobic interactions between R groups of amino acids
  • Hydrophobic residues prefer to be on the interior or proteins, which reduces their proximity to water and hydrophilic residues prefer to be on the outside of the protein
  • Also determined by disulfide bonds, the form when two cysteine molecules become oxidized to form cystine
  • This creates loops in the protein chain
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25
Q

What is the quarternary structure of a protein?

A
  • Exist for proteins that contain more than one poly peptide chain; for these proteins, the quarternary strucutre is an aggregate of smaller globular peptides, or subunits and represents the functional form of the protein
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26
Q

What is the Michaelis-Menten equation?

A
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27
Q

What is collagen?

A
  • Has a characteristic trihelical fiber (three α-helices woven together to form a secondary helix)
  • Makes up most of the extracellular matrix of connective tissue
  • Is found throughout the body and is important in providing strength and flexibility
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28
Q

What are keratins?

A
  • Intermediate filament proteins found in epithelial cells
  • Contribute to the mechanical integrity of the cell and also function as regulatory proteins
  • Primary protein that makes up hair and nails
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29
Q

What are cadherins?

A

a group of glycoproteins that mediate calcium-dependent cell-adhesion

  • cadherins often hold similar cell types together, such as epithelial cells
  • different cells usually have type-specific cadherins; for example, epithelial cells use E-cadherin while nerve cells use N-cadherin
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30
Q

What are integrins?

A
  • A group of proteins that all have two membrane-spanning chains called α and β
  • Chains are very important in binding to and communicating with the extraceullar matrix
  • Also play a very important role in cellular signaling and can greatly impact cellular function by promoting cell division, apoptosis, or other processes
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31
Q

What are selectins?

A
  • Bind to carbohydrate molecules that project from other cell surfaces
  • Bonds are the weakest formed by the cell adhesion omlcules
  • Expressed on white blood cells and endothelial cells
  • play an important role in host defense, including inflammation and white blood cell migration
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32
Q

What is the function of these proteins:

Gs

Gi

Gq

A
  • Gs: stimulates adenylate cyclase, which increases levels of cAMP in the cell
  • Gi: inhibits adenylate cyclase, which decreases levels of cAMP in the cell
  • Gq: activates phospholipase C, which cleaves a phospholipid into PIP2, which can later be cleaved into DAG and IP3
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33
Q

How does electrophoresis work?

A
  • Subjects compounds to an electric field, which moves them accoridng to their net charge and size
  • Negatively charged compounds will migrate toward the positively charged anode
  • Positively charged compounds will migrate toward the negatively charged cathode

Velocity of the migration, v= Ez/f

E: electric field

z: net charge on the molecule
f: coefficient of friction

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34
Q

What is SDS-PAGE?

A
  • separates proteins on the basis of mass alone
  • SDS: a detergent that disrupts all noncovalent interactions; binds to proteins and creates large chains with net negative charges, thereby neutralizing the protein’s original charge and denaturing the protein
  • As the proteins move through the gel, the only variable affecting the velocity is f, the frictional coefficient, which depends on mass
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35
Q

What is native PAGE?

A

Native gels, also known as non-denaturing gels, analyze proteins that are still in their folded state. Thus, the electrophoretic mobility depends not only on the charge-to-mass ratio, but also on the physical shape and size of the protein

  • Most useful to compare the molecular size or charge of proteins known to be similar in size from other analytic methods like SDS-PAGE or size-exclusion chromatography
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36
Q

What is isoelectric focusing?

A
  • Separates proteins by isoelectric point
  • Mixture of proteins is placed in a gel with a pH gradient
  • Proteins that are positively charged will begin migrating toward the cathode and proteins that are negatively charged will begin migrating toward the anode
  • As the protein reaches the portion of gel where the pH is equal to the protein’s pI, the protein takes on a neutral charge and will stop moving
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37
Q

What is Edman degredation?

A

A method of sequencing amino acids in a peptide. In this method, the amino-terminal residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues.

  • Uses cleavage to sequence proteins of up to 50 to 70 amino acids
  • selectively and sequentially removes the N-terminal amino acid of the protein which can be analyzed via mass spectroscopy
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38
Q

What is the Bradford Protein Assay?

A
  • A spectroscopic analytical procedure used to measure the concentration of protein in a solution
  • It is subjective, i.e., dependent on the amino acid composition of the measured protein
  • In its protonated form, the dye exists as a brown-green color; the dye is deprotonated by the protein and gives up protons to the ionizable groups in the protein, turning blue in the process
  • Can compare the blueness of the sample to the blueness of the standard curve by measuring absorbance
  • Very accurate when only one type of protein is present
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39
Q

Draw out glyceraldehyde.

A
  • The simplest aldose (an aldotriose)
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40
Q

What is the relationship between D-glucose and L-glucose?

A

Enantiomers

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41
Q

What is an epimer?

A
  • A subtype of diastereomer; differ in configuation at exactly one chiral center
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42
Q

In glucose, what is an α-anomer? β-anomer?

A

α-anomer: Has the -OH group of C-1 trans to the -CH2OH substituent (axial and down)

β-anomer: has the -OH group of C-1 cis to the -CH2OH substituent (equatorial and up)

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43
Q

What is mutarotation?

A
  • When expsosing hemiacetals to water, the hemiacetal will spontaneously cycle between the open and closed form
  • Bcause the substituents on the single bond between C-1 and C-2 can freely rotate, either the α or β-anomer can be formed
  • This spontaneous configuration about C-1 is known as mutatrotation
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44
Q

What anomer of glucose is less stable? α or β?

A

-The α-anomeric configuratoin is less favored because the hydroxyl group of the anomeric carbon is axial, adding to the steric strain of the molecule

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45
Q

What is a reducing sugar? How can you detect them?

A
  • A reducing sugar is any sugar that is capable of acting as areducing agent because it has a free aldehyde group or a free ketone group.
  • All monosaccharides are reducing sugars, along with some disaccharides, oligosaccharides, and polysaccharides

Tollen’s Reagent: uses Ag(NH3)2+ an as oxidizing agent; in a positive Tollen’s test, aldehydes reduce Ag+ to metallic sivler

Benedict’s reagent: the adehyde group of an aldose is readily oxidized, indicated by a red precipitate of Cu2O

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46
Q

What is sucrose made up of?

A

Glucose-α-1,2 fructose

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47
Q

What is lactose made up of?

A

Galactose-β-1,4 glucose

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48
Q

What is maltose made up of?

A

Glucose- α-1,4-glucose

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49
Q

What types of bonds exist in cellulose?

A

β-1,4 glycosidic bonds

  • Humans lack cellulase, so we cannot digest these types of bonds
  • Cellulose: main structural component of plants
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50
Q

What type of bonds are in amylopectin?

A

Glucose units are linked in a linear way with α-1,4 glycosidic bonds. Branching takes place with α-1,6 bonds occurring every 24 to 30 glucose units, resulting in a soluble molecule that can be quickly degraded as it has many end points onto which enzymes can attach.

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51
Q

What types of bonds are in glycogen

A

Glucose units are linked together linearly by α-1-4 glycosidic bonds from one glucose to the next

Branches are linked to the chains from which they are branching off by α-1,6 glycosidic bonds between the first glucose of the new branch and a glucose on the stem chain

  • There is approximately 1 α-1,6 glycosidic bond for every 10 glucose molecules
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52
Q

What characteristic defines a lipid?

A
  • Insolubility in water and solubility in non-polar organic solvents
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53
Q

What is the structure of a phospholipid?

A
  • Head: a phosphate and alcohol
  • Tail: Hydrophobic fatty acid
  • Linked by a phosphodiester bond
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54
Q

What is an amphipathic molecule?

A
  • A molecule which has both hydrophilic and hydrophobic regions
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55
Q

What are glycerophospholipids?

A
  • Phospholipids that contain a glycerol backbone bound by ester linkages to two fatty acids and by a phosphodiester linkage to a highly polar head
  • The head group determines the membrane surface properties; head groups can be positively charged, negatively charged or neutral
  • Example: phosphotidylcholine is a glycerophospholipid with a choline head group
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56
Q

What are sphingolipids?

A
  • Have a sphingosine backbone (as opposed to glycerol, as found in glycerophospholipids)
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57
Q

What are glycosphingolipids? What are the subcategories?

A
  • A subgroup of sphingolipids with head groups composed of sugars bound by glycosidic linkages
  • Cerebrosides: have a single sugar
  • Globosides: have two or more sugars
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58
Q

What are gangliosides?

A
  • The most complex group fo sphingolipids
  • Glycolipids that have a polar head composed of logiosaccharides with one or more N-acetylneuaminic acid (NANA; also called sialic acid) molecule at the terminus, and a negative charge
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59
Q

What are spingomyelins?

A
  • The major class of sphingolipids that are also phospholipids
  • Have either phosphatidylcholine or phosphatidylethanolamine as a head group, and are thus boudn by a phosphodiester bond
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60
Q

What are terpenes?

A
  • A class of lipids built from isoprene (C5H8)
  • Steroids are metabolic derivatives of terpenes
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61
Q

What is the base structure of a steroid? How is functionality of a steroid determined?

A
  • Steroids are characterized by having four cycloalkane rings together: three cyclohexane and one cyclopenate
  • Steroid functionality is determined by the oxidation status of these rings, as well as the functional groups they carry
62
Q

What are prostaglandins?

A
  • 20 carbon unsaturated carboxylic acids derived from arachidonic acid, which contain one five-carbon ring
  • In many tissues, prostaglandins regulate the synthesis of cAMP
63
Q

What are triglycerides?

A
  • Three fatty acids bound by ester linkages to glycerol
  • Usually, these fatty acids are different
  • They are nonpolar and hydrophic; the polar hydroxyl groups of the glycerol component and the polar carboxylates of fatty acids are bound together, decreasing their polarity
64
Q

What are the fat soluble vitamins?

A

A, D, E and K

65
Q

What are nucleosides?

A
  • A five-carbon sugar (pentose) bound to a nitrogenous base
  • Are formed by covalently linking the base to C-1’ of the sugar
66
Q

What is a nucleotide?

A
  • Formed when one or more phosphate groups are attached to C’5’ of nucleoside
  • The building blocks of DNA
  • Often these molecules are named according to the number of phosphates bound
  • Example: adenosine di- and triphosphate (ADP and ATP)
67
Q

What is the difference between ribose and deoxyribose?

A

Ribose: -OH at the 2’ position

Deoxyribose: -H at the 2’ position

68
Q

Describe the structure of the DNA backbone.

A
  • Formed as nucleotides are joined by 3’- 5’ phosphodiester bonds (the phosphate group links the 3’ carbon of one sugar to the 5’ phosphate group of the next sugar)
69
Q

What are the rules that define if something is aromatic?

A
  1. Compound is cyclic
  2. Compound is planar
  3. Compound is conjugated (has alternating single and multiple bonds, or lone pairs, creating at least one unybridizied p-orbital for each atom in the ring)
  4. The compound has 4n+2 (n is any integer) π electrons; this is known as Hückel’s Rule
70
Q

What is Z-DNA?

A

DNA in which the double helix has a left-handed rather than the usual right-handed twist and the sugar phosphate backbone follows a zigzag course

  • Makes a turn every 4.6 nm and contains 12 bases each turn
  • A high GC content or high salt cconcentration may contribute to the formation of this form of DNA
71
Q

What is B-form DNA?

A
  • Right-handed DNA
  • Makes a turn every 3.4 nm
  • Contains 10 bases within that span
  • Creates both major and minor grooves in the strand
  • This is what we think of when we think of DNA
72
Q

What are the protein components of a histone?

A
  • A dimer of H2A, H2B and H3 and H4 make up the core protein of a histone; 200 base pairs of DNA wrap around this protein forming a nucleosome
  • H1 seals off the DNA as it enters and leaves the nucleosome
73
Q

What are nucleoproteins?

A

Proteins that associate with DNA

74
Q

What is heterochromatin?

A
  • The chromatin which remains compacted during interphase
  • Appears dark under light microscopy
  • Is transcriptionally silent
75
Q

What is euchromatin?

A
  • Dispersed chromatin
  • Appears light under light microscopy
  • Genetically active
76
Q

What is a centromere?

A
  • A region of DNA found in the center of chromosomes
  • Composed of heterochromatin, which is in turn composed of tandem repeat sequences that contain high GC-content
  • During cell division, the two sister chromatids can therefore remain connected at the centromere until microtubules separates the chromatids during anaphase
77
Q

What is the function of telomeres?

A
  • DNA replication cannot extend all the way to the end of a chromosome, resulting in a loss of DNA
  • Thus, telomeres comprise the end of chromosomes via a simple repeating unit (TTAGGG); thse serve no real purpose and can be cut off
  • Telmoseres also have a high GC-content which creates exceptionally strong strand attractions at the end of chromosomes to prevent unraveling
78
Q

How many origins of replication are there in eukaryotes? In prokaryotes?

A

Eukaryotes: many; in order to duplicate all of the chromosomes efficiently, each chromosome contains one linear molecule of dsDNA with multiple origins of replication

Prokaryotes: single origin of replication

79
Q

What is the function of DNA gyrase?

A
  • Also known as DNA topoisomerase II
  • Cut both strands of the DNA helix simultaneously in order to manage DNA tangles and supercoils, using hydrolysis of ATP
  • Introduces negative supercoiling
80
Q

What is the function of single stranded binding proteins?

A
  • Once helicase opens up the dsDNA, the free purines and pyrimidines seek out other molecules with which to hydrogen bond
  • single-stranded DNA-binding proteins will bind to the unraveled strand, preventing both the reassociation of DNA strands and the degredation of DNA by nucleases
81
Q

What is the function of a primase?

A

An enzyme that synthesizes short RNA sequences called primers

  • These primers serve as a starting point for DNA synthesis.
  • Since primase produces RNA molecules, the enzyme is a type of RNA polymerase
  • This is important because DNA cannot be synthesized de-novo, and needs another nucleic acid to “hook onto” in order begin synthesis of a new strand
82
Q

What is the function of DNA polymerase γ?

A
  • Repliacates mitochondrial DNA
  • Eukaryotic polymerase
83
Q

What is the function of DNA polymerases β and ε?

A
  • Participate mostly in DNA repair
  • Eukaryotic Polymerases
84
Q

Which polymerases are assisted by the PCNA protein?

A
  • Polymerases δ and ε
  • PCNA protein assembles with the polymerases to form the sliding clamp
85
Q

Which polymerase replaces the RNA laid down by the primase with DNA, in eukaryotes? In prokaryotes?

A
  • Eukaryotes: DNA polymerase δ
  • Prokaryotes: DNA Polymerase I
86
Q

Which polymerase(s) is/are responsible for the primary synthesis of DNA in eukaryotes? Prokaryotes?

A
  • Eukaryotes: DNA polymerases α and δ
  • Prokaryotes: DNA polymerase III
87
Q

What is mismatch repair?

A
  • Repair to the newly synthesized DNA strand during G2 phase of the cell cycle
  • MSH2 and MLH1 in eukaryotes and MutS and MutL in eukaryotes deteect and remove errors introduced in replication that were missed during the S phase of the cell cycle
88
Q

What is nucleotide excision repair?

A
  • NER removes thymine dimers from the DNA, which have been induced by exposure to UV light

Mechanism

  1. Specific proteins scan the DNA moelcule and recognize the lesion because of a bulge in the strand
  2. An excision endonuclease makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective nucleotide
  3. DNA polymerase can then fill the gap by synthesizing in the 5’ to 3’ direction using the undamaged strand as a template
  4. Ligase seals the strand
89
Q

What is base excision repair?

A
  • BER repairs alterations to bases; for example, thermal energy can be absorbed by DNA and may lead to cytosine deamination, making cytosine into a uracil

Mechanism

  1. The affected base is recognized and removed by a glycosylase enzyme, leaving behind a apurinin/apyramidic (AP) site
  2. AP site is recognized by AP endonuclease, which removes the damaged sequence from the DNA
  3. DNA polymerase and DNA ligase can then fill the gap and seal it
90
Q

What are restriction enzymes?

A
  • An enzyme that cleaves DNA into fragments at or near specific recognition sites within the molecule known as restriction sites
  • These enzymes cut at palindromic sequences, such as GAATTC
  • From this cut, some produce sticky ends, which are advantageous in facilitating the recombiantino fof the restriction fragment with the vector DNA
91
Q

How is a recombinant plasmid made and selected for?

92
Q

What is the difference between a genomic library and a cDNA (expression) library?

93
Q

How are transgenic mice created?

A
  • Ttansgenic mice are altered by their germ line by introducing a cloned gene into a fertilized ova or into embryonic stem cells (a transgene)
  • If the transgene is disease-producing, the transgenic mice can be used to study the disease process from early embryonic development through adulthood
94
Q

What direction is mRNA translated by a ribosome?

A
  • In the 5’ to 3’ direction, synthesizing the protein from the N-terminal to the C-terminal
95
Q

Is mRNA monocistronic or polycistronic?

A
  • In eukaryotes, mRNA is monocistronic, meaningt hat one mRNA molecule translates into only one protein product
  • In prokaryotes, mRNA is polycistronic
96
Q

What is the function of aminoacyl-tRNA synthetase?

A
  • An enzyme that attaches the appropriate amino acid onto its tRNA
  • It does so by catalyzing the esterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA
  • In humans, the 20 different types of aa-tRNA are made by the 20 different aminoacyl-tRNA synthetases, one for each amino acid of the genetic code
97
Q

What is the start codon?

What are the stop codon?

A

Start codon: AUG

Stop codons: UAA, UGA, UAG

98
Q

What does it mean when we say that the genetic code is degenerate?

A
  • There genetic code incldues 64 codons which code for 61 acids, and three are stop signals.
  • Although each codon is specific for only one amino acid (or one stop signal), the genetic code is described as degenerate, or redundant, because a single amino acid may be coded for by more than one codon.
99
Q

What is a missense mutation?

A
  • A mutation in which one amino acid substitutes for another
100
Q

What is a nonsense mutation?

A
  • A mutation where the codon now encodes for a pemature stop codon (also known as truncation mutation)
101
Q

What is the function of RNA polymerase I?

A
  • Located in the nucleolus and synthesizes rRNA
  • Eukaryotic RNA polymerase
102
Q

What is the function of RNA polymerase II?

A
  • Located in the nucleus and synthesizes hnRNA (pre-processed mRNA) and snRNA
  • Eukaryotic RNA polymerase
  • Binds to TATA box (located at -25)
103
Q

What is the function of RNA polymerase III?

A
  • Located in the nucleus and synthesizes tRNA and some rRNA
  • Eukaryotic RNA polymerase
104
Q

What is the function of the poly-A tail?

A
  • Added to the 3’ end of the mRNA transcript and protects the message against rapid degredation; as soon as the mRNA leaves the nucleus, it will start to get degreaded from the 3’ end
105
Q

What is the Shine-Dalgarno sequence?

A
  • A ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG.
  • The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the start codon.
106
Q

What are the sites in a ribosome?

A

A site:

  • Holds the incoming aminoacyl-tRNA complex
  • This is the next amino acid that is being added to the growing chain, and is determined by the mRNA codon within the A site

P site:

holds the tRNA that carries the growing polypeptide chain

  • It also is where the first amino acid (methionine) binds because it is starting the polypeptide chain
  • Peptidyl transferase, an enzyme that is part of the large subunit of the ribosome, passes the peptide bond from the tRNA in the P site to the tRNA in the A site

E site:

  • where the uncharged (lacking an AA) tRNA pauses transiently before exiting the ribosome
107
Q

How does the process of mRNA translation into protein end?

A
  • When any of the three stop codons moves into the A site, a protein called release factor binds the termination codon, causing a water molecule to be added to the polypeptide chain
  • The addition of this water moleucle allows peptidyl transferase and termination factors to hydrolyze the completed polypeptide chain from the final tRNA
  • The polypeptide chain will then be relased from the tRNA in the P site and the two ribosomal subunits will dissociate
108
Q

What is an inducible system?

A
  • A system in which the repressor is tightly bought to the operator system and thereby acts as a roadblock
  • To remove the block, and inducer must bind the repressor so that the RNA polymerase may move down the gene
  • Example: Lac Operon; used when glucose (the preferred sugar) is low and lactose (a more energentically expensive product to digest) is high
109
Q

What is the catabolite activator protein in regard to the lac operon?

A

CAP is a transcriptional activator used by E. coli when glucose levels are low to signal that alternative carbon sources should be used

  • Falling levels of glucose cause an increase in cAMP, which binds to CAP; this induced a conformational change in CAP that allows it to bind the promoter region of the operon, further increasing transcription of the lactase gene
110
Q

What is a repressible system?

A
  • Allow constant production of the protein product
  • The repressor is made by the regulator gene is inactive until its bound by a corepressor; this complex then binds the operator site and prevents further transcription
  • Serve as negative feedback loops; often, the final strucutral product can serve as a corepressor

Example: trp operon

  • When tryptophan is high in the local environment, it acts as a corepressor; the binding of two molecules of of tryptophan causes the repressor to bind the operator site; thus, the cell turns off its machinery to synthesize its own tryptophan, which is an energetically expensive process because its available in the environment
111
Q

What are transcription factors? What are their components?

A

Transcription factors: a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.

  • Two domains: A DNA-binding domain and an activation domain
  • DNA binding domain: binds to a specific nulceotide sequence in the promoter region or to a DNA response element (a sequence of DNA that binds only to specific transcription factors)
  • Activation domain: allows for the binding of several transcription factors and other important regulatory rotein, such as RNA polymerase and histone acetylases, which function in the remodeling of DNA
112
Q

What is the function of histone acetylation?

A
  • Acetylation of histone proteins decrease the positive charge on lysine residues and weakens the interaction of the histone with DNA, resulting in an open chromatin conformation that allows for easier access of the trascriptional machinery to DNA
113
Q

What are flippases?

A
  • Lipids can also move between the membrane layers, but this is energetically unfavorable because the polar head group of the phospholipid must be forced through the nonpolar tail region in the interior of the membrane
  • Thus, flipases, specialized enzymes, assist in the transition or “flip” between layers
114
Q

What is a lipid raft?

A

The plasma membranes of cells contain combinations of glycosphingolipids and protein receptors organised in glycolipoprotein microdomains

115
Q

With regard to the phospholipid bilayer, what are the three types of associated proteins?

A
  • Transmembrane proteins: pass completely through the membrane
  • Embedded proteins: associated only with the interior (cytoplasmic) or exterior (extracellular) surface of the cell
  • Membrane-associated (peripheral) proteins: may be bound through electrostatic interactions with the lipid bilayer, or to other transmembrane proteins
116
Q

What are gap junctions?

A
  • Allow for direct cell-to-cell communication
  • Are formed by the alignment and interaction of pores composed of 6 molecules of connexin
  • Permit movement of water and some solutes idrectly between cells
  • Proteins are generallyn not transferred through gap junctions
117
Q

What are tight junctions?

A
  • Multiprotein junctional complex whose general function is to prevent leakage of transported solutes and water and seals the paracellular pathway.
  • To be effective, tight junctions must form a continuous band around a cell, otherwise fluid could leak through the spakes between tight junctions
118
Q

What are desmosomes?

A
  • Bind adjacent cells by anchoring to their cytoskeletons
  • Desmosomes are formed by interactions between transmembrane proteins associating the intermediate filaments inside adjacent cells
  • Primarily found at the interface between two layers of epithelial tissue
  • Hemidesmosomes: have a similar function, but hteir main function is to attach epithelial cells to underlying (basement) membranes
119
Q

What is pinocytosis?

A
  • The endocytosis of fluids and dissolved particles
120
Q

What is the Goldman-Hodgkin-Katz voltage equation?

A

Used in cell membrane physiology to determine the reversal potential across a cell’s membrane, taking into account all of the ions that are permeant through that membrane.

P: permability for the relevant ion

Note: chloride is reversed because of the negative charge on a chloride ion

121
Q

What is a normal level of glucose in ther periphery?

A

5.6mM (Range: 4-6mM)

122
Q

What are some properties of GLUT2?

A
  • Low affinity transporter in hepatocytes and pancreatic cells
  • Captures excess glucose primarily for storage
  • When the glucose drops below the Km (Km≈15mM) for the transporter, much of the remainder leaves the liver and enters the peripheral circulation
  • GLUT2, along with glucokinase, serves at the glucose sensor for insulin release
123
Q

What are some properties of GLUT4?

A
  • Located in adipose tissue and muscle
  • The rate of glucose transport in these two tissues is increased by insulin which stimulates the movement of additional GLUT4 transporters to the membrance by a mechanism involving exocytosis
  • Km of GLUT4 (Km~5mM) is close to the normal glucose levels of blood; this means that the transporters are saturated when blood glucose levels are just slightly higher than normal
124
Q

Where are some places that anaerobic glycolysis can occur, normally, in the body?

A
  • Skeletal muscle where there is no oxygen
  • RBCS, where there are no organelles
125
Q

What is the function of hexokinase and glucokinase?

Where would you find these enzymes in the body? What are their relative differences?

A
  • The enzymes in the first step of glycolysis
  • Hexokinase and glucokinase take glucose and convert it to glucose 6-phosphate
  • *Hexokinase**
  • Present in most tissues
  • Low Km (reaches maximum velocity at low glucose concentration
  • Inhibited by glucose-6-phosphate

Glucokinase

  • Present in heaptocytes and pancreatic β islet cells (along with GLUT 2, acts as the glucose sensor)
  • High Km (acts on glucose proportionally to its concentration)
  • Induced by insuln in hepatocytes
126
Q

What is phosphofructokinase-1?

A
  • The rate limiting enzyme and main control point in glycolysis
  • Converts fructose-6-phosphate to fructose-1,6-bisphosphate
  • Inhibited by ATP and citrate
  • Activated by AMP
127
Q

How are insulin and glucagon related to Phosphofructokinase-1?

A
  • This process occurs in hepatocytes
  • Insulin stimulates PFK-1, indirectly
  • Glucagon inhibits PFK-1, indirectly
  • Insulin activates PFK-2 converts a tiny bit of Fructose 6-phosphate to fructose 2,6 bisphophate
  • F2,6BP activates PFK-1
  • Glucagon inhibits PFK-2, lowering F2,6BP and thereby inhibiting PFK-1
128
Q

What is glyceraldehyde-3-phosphate dehydrogenase?

A
  • Catalyzes an oxidation and addition of of inorganic phsophate to its substrate, glyceraldehyde-3-phosphate, resulting in the production of a high-energy intermediate: 1,3 bisphosphoglycerate
  • Also takes NAD+ and makes NADH
129
Q

What is 3-phosphoglycerate kinase?

A
  • Transfers the high-energy phosphate from 1,3 phosphoglycerate to ADP, forming ATP and 3-phosphoglycerate
  • This is a substrate-level phosphorylation and produces energy in a non-oxygen dependent way
  • This is the only means of ATP generation in an anaerobic tissue
130
Q

What is pyruvate kinase?

A
  • The last enzyme in aerobic glycosis
  • Catalyzes substrate level phosphorylation of ADP to ATP by converting phosphoenolpyruvate to pyruvate
  • Pyruvate Kinase is activated by PFK-1 (a feed-forward activation); the product of an earlier reaction of glycolysis stimulates, or prepares a later reaction in glycolysis
131
Q

What is the key enzyme in fermatation? Why does this process occur?

A
  • Lactate dehydrogenase: oxidizes NADH to NAD+, replenishing the coenzyme for glyceraldehyde-3-phosphate
  • Without mitochondria and oxygen, glycolysis would stop when all the available NAD+ had beed reduced to NADH; by reducing pyruvate to lactate and re-creating NAD+, lactate dehydrogenase prevents this potential problem
132
Q

How is the fermentation in yeast different from people?

A
  • In yeast, fermentation covnerts pyruvate (three carbons) to ethanol (two carbons and carbon dioxide (one carbon)
  • In people, fermentation converts pyruvate (three carbon) into lactate (also three carbon)
133
Q

What is dihydroxyacetone (DHAP)?

A
  • Used in hepatic and adipose tissue for triacylglycerol synthesis
  • Is formed from fructose 1,6 bisphosphate, which can be isomerized to glycaldehyde-3-phosphate, which can then be broken down into glycerol
134
Q

What enzymes catalyze irreversible reactions in glycolysis?

A
  • Glucokinase and hexokinase
  • PFK-1
  • Pyruvate kinase
135
Q

What is bisphosphoglycerate mutase?

A
  • The enzyme that converts 1,3BPG (from glycolysis) to 2,3 bisphosphoglycerate
  • 2,3 BPG binds allosterically to the β-chains of hemoglobin A and decreases its afinity for oxygen
136
Q

What is the rate-limiting enzyme in glycogen synthesis?

What is it activated and inhibited by?

A
  • Glycogen synthase; forms the α-1,4 glycosidic bond found in the lienar glcuose chains of the granule
  • Stimulated by: glucose-6-phosphate and insulin
  • Inhibited by: epinephrine and glucagon
137
Q

What is branching enzyme?

A
  • Responsible for introducing α-1,6 linked branches into the graule as it grows
  • Branching enzymes hyrolyzes one of the α-1,4 bonds to release a block of oligoglucose, when is then moved and added in a slightly different location
  • Forms an α-1,6 bond to create a branch
138
Q

What is the rate-limiting enzyme of glycogenolysis?

What is it activated and inhibited by?

A
  • Glycogen phosphorylase: breaks α 1,4 glycosidic bonds, releasing glucose-1-phosphate
  • Cannot break α-1,6 bonds and therefore stops when it nears the outermost branch point
  • Activated by glucagon in the liver and by AMP and epinephrine in the muscle
  • Inhibited by ATP
  • Note: a phosphorylase breaks a bond using inorganic phosphate
139
Q

What is de-branching enzyme?

A
  • A two-enzyme complex that deconstructs the branches in glycogen that have been exposed by phosphorylase
  • First, it takes the remainder of the straight chain which cannot be hydrolyzed by phosphorylase to the end of a straight chain; this leaves one glucose attached at a α-1,6 branch
  • Then, it hydrolyzes the single glucose from the former branch
140
Q

What are the most important substrates for gluconeogenesis?

A
  • Glycerol 3-phosphate (from stored fats or traiacylglycerols in adipose tissue)
  • Lactate (from anaerobic glycolysis)
  • Glucogenic amino acids (from muscle proteins, like alanine)
141
Q

What is phosphoenolpyruvate carboxykinase?

A
  • An enzyme in gluconeogenesis
  • Converts oxaloacetate to phosphoenolpyruvate (PEP) in a reaction requiring GTP
  • PEP cotinues in the pathway to fructose 1,6 bisphosphate; thus, phosphoenolpyruvate carboxykinase and pyruvate carboxylase reverses the irreversible actions of pyruvate kinase
142
Q

What is the rate-limiting enzyme in gluconeogenesis?

A
  • Fructose-1,6-Bisphosphatase
  • Reverses the action of phosphofructokinase-1, the rate-limiting step of glycolysis
  • Hydrolyzes a phosphate from fructose-1,6-bisphosphate to produce fructose-6-phosphate
  • Activated by ATP
  • Inhibited by Fructose 2,6 bisphosphate
143
Q

What is pyruvate carboxylase?

A
  • An enzyme in gluconeogenesis
  • First step in gluconeogenesis; takes pyruvate and makes oxaloacetate
  • This step occurs in the mitochondria
  • Note: oxaloacetate cannot leave the mitochondria so it gets turned into malate, which leaves, and once in the cytoplasm, malate gets turned back into oxaloacetate
  • Activated by acetyl-CoA, indicating that we have enough energy, do not need to go through the citric acid cycle and instead should rebuild sugars
144
Q

What is glucose-6-phosphatase?

A
  • An enzyme in gluconeogenesis
  • An enzyme in the ER of the liver
  • Takes glucose-6-phosphate and cleaves off the phosphate, creating glucose, which can leave via GLUT transporters
  • Note: muscle does not have glucose-6-phosphatase, so the glycogen in muscle cannot be a source of blood glucose; thus, muscle supplies only AAs for gluconeogenesis and not glycogen
145
Q

What is the primary function of the pentose phosphate pathway?

What is the rate-limiting enzyme in this pathway?

A
  • Functions: Production of NADPH and serves as a source of ribose-5-phosphate
  • Glucose-6-phosphate dehydrogenase, which is induced by insulin and NADP+ and inihbited by NADPH
146
Q

What is the function of NADPH?

A
  • Cells require NADPH for a variety of functions, including:
    1. Biosynthesis, mainly of fatty acids and cholesterol
    2. Assisting inc ellular bleach production in certain white blood cells, thereby contribuitng to bactericidal activity
    3. Maintenance of a supply of reduced glutathione to protect against reactive oxygen species (acting as the body’s natural antioxidant)
147
Q

What is the net ATP produced per molecule of glucose in glycolysis?

A
  • 2 ATP per molecule of glucose
148
Q

What is the role of pyruvate dehydrogenase?

A

Takes pyruvate and makes Acetyl-CoA for the citric acid cycle

  • Located in the mitochondrial matrix
150
Q

Draw out the glycolysis pathway.

151
Q

Draw out the gluconeogenesis pathway.

MCAT (8 decks)

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