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Kaplan Biochem Flashcards

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1
Q

Migration velocity equation

A 
v=(Ez)/(f)
E=electric field strength
v=migration velocity
z=net charge of molecule
f=frictional coefficient
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2
Q

Positive vs negative control operon

A

Negative: binding of a protein reduces transcriptional activity
Positive: Binding of protein increases transcription of a gene

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3
Q

Self antigens definition

A

Proteins/carbohydrates on surface of every cell in body

  • Normally, signal to immune cells that cells aren’t foreign and shouldn’t be attacked
  • Can attack cells expressing self-antigens
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4
Q

Why are the number of DNA replications limited?

A

DNA replication cannot extend all the way to the end of the chromosome
-End of sequences is the telomere

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5
Q

6 types of enzymes:

A

Oxidoreductases: catalyze redox rxns -> transfer e- between species
-Dehydrogenases or reductases

Transferases: catalyze movement of functional groups between species
-Kinases transfer phosphate groups

Hydrolases: Catalyze breaking of ompound into two molecules using addition of H20
-Usually named for their substrates
—i.e. phosphatase: cleaves phosphate group

Isomerase: Catalyze rearrangement of bond within a molecule
-Between both stereoisomers and constitutional isomers

Ligase: Catalyze addition/synthesis rxns
-Often require ATP

Lysase: Catalyze cleavage of single molecule into two products
-Does not req. H20 as substrate

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6
Q

Isoelectric focusing function

A

Proteins separated on basis of isoelectric point

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7
Q

Telomerase function

A

Telomeres are slightly degraded between replication cycles (no loss of function results from this)

Telomerase synthesizes telomeres

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8
Q

How is the ETC regulated

A

ADP/AMPP activate

ATP inhibits

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9
Q

What happens if osmotic pressure > hydrostatic pressure

A

Cell will lyse

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10
Q

Transgenic mice production via embryonic stem cell lines

A
  • Altered stem cells injected into developing blastocysts and implanted into surrogate mothers
  • Offspring are chimera with patches of cells derived from the two lineages
  • Chimeras can be bred to produce mice heterozygous for transgene or homozygous

Advantage: cloned genes can be introduced into cultures

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11
Q

SDS PAGE

A

SDS disrupts all non covalent interactions

  • Creates large chains with negative charge
  • Neutralizes charge of protein and denatures
  • Only things affefcting migration -> mass
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12
Q

Isocitrate DeH regulation

A

ADP and NAD+ allosteric activators

ATP and NADH allosteric inhibitors

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13
Q

Coupled reaction of glycogenesis

A

Glucose-6P first converted to Glu1-P

  • Glu1P activated by coupling to uridine diphosphate (UDP) which allows it to intergrate into glycogen chain
  • Glu1P interacts with UTP to form UDP-gluc and pyrophosphate PPi
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14
Q

Recombinant Vector/DNA cloning

A
  • When cloning, ligated DNA of interest placed into piece of nucleic acid.
  • Usually bacterial/viral plasmids that can be transferred to host bacterium after insertion of DNA of interest
  • Bacteria then grown in colonies with a colony containing only recombinant vector
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15
Q

Macrophages are derived from one type of cell

A

Blood-borne monocytes

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16
Q

What is first line of defense of immune system

A

The skin

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17
Q

Does gluconeogenesis supply energy for the liver?

A

No, gluconeogenesis uses ATP provided by beta oxidation of fatty acids

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18
Q

MHC II molecules

A

Displayed by professional antigen-presenting cells

-Pick up antigens from environment process and present them on MHC II

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19
Q

Function of glycogenesis

A

Synthesis of glycogen granules

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20
Q

Restriction Enzymes Advantages of Sticky Ends

A

Some restriction enzymes can produce off cuts that yield sticky ends of fragments
-Helpful in facilitating recombination of a restriction fragments with vector DNA

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21
Q

Structure of glyogen granules

A

Composed entirely of linear chains

-When branched, glucose density highest at periphery of granule

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22
Q

Complex IV Cytochrome c oxidase

A

Includes subunits cytochrome a1, cytochrome a3, Cu 2+ ions

  • O -> H20
  • Cytochrome C’s are once again -> oxidized to Fe3+
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23
Q

Alternate Mechanism for ATP formation from ETC

A

Conformational Coupling: Indirect relationship between proton gradient and ATP synthesis

  • ATP released as result of conformational change caused by gradient
  • F1 portion becomes a turbine which spins to harness the gradient energy for chemical bonding
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24
Q

Osmotic pressure definition

A

Quantifies the driving force behind osmosis

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25
Q

How is pyruvate DeH complex regulated?

A

Deactivated by pyruvate deH kinase
Activated by pyruvate DeH phosphatase
-Acetyl CoA has negative feedback on own production also ATP and NADH

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26
Q

Autoimmunity

A

When self-antigens aren’t recognized by immune system and cells with these antigens are attacked

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27
Q

HbF Fetal hemoglobin characteristics

A

2,3 BPG does not bind to HbF

  • HbF has higher affinity for oxygen
  • Allows fetus to maintain sufficient O2 conc
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28
Q

Substrates of gluconeogenesis

A

G3P (glycerol 3P), Lactate, glucogenic amino acids

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29
Q

Wax function in animals

A

Secreted to prevent dehydration as water-repellent and lubricant

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30
Q

Vitamin K function

A

Posttranslational modifictaions reguired to form prothrombin -> clotting factor in blood
-Introduces Ca2+ binding sites and Ca2+ dependent proteins

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31
Q

What are the fat soluble vitamins?

A

You fat DEAK

-D, E, A, K

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32
Q

Citrate synthase regulation

A

ATP and NADH allosterically inhibit

-Citrate and succinyl-CoA also allosteric inhibitors

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33
Q

Naive B-cells definition

A

B-cells not yet exposed to an antigen

-Wait in lymph nodes for their antigen

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34
Q

Aka for oncotic pressure

A

Starling forces

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35
Q

B-cells function

A

Produce antibodies specific to antigens of invading microbe

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36
Q

Exocytosis

A

Secretory vesicles fuse with membrane

-REleases material from inside cell to extracellular environment

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37
Q

What other monosaccharides feed into glycolsis

A

Galactose and fructose feed into glycolysis and other metabolic processes

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38
Q

How does skin protect body

A
  • Physical barrier preventing most bacteria/invaders from entering body
  • Contain defensins antibacterial enzymes
  • Sweat has antimicrobial properties
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39
Q

What type of blot is used to analyze DNA?

A

Southern Blot

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40
Q

Roles of lipids besides membranes

A

Active roles in cellular signaling and as coenzymes

-Also produce hormones and can absorb light

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41
Q

Pyruvate carboxylase

A

Reduces OAA to malate so it can leave mitochondria via malate-aspartate shuttle
-Activated by acetyl CoA

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42
Q

Watson-Crick Model

A

Deduced double helical structure of DNA and proposed specific base pairing as basis for copying mechanism.

  1. Two strands of DNA that are anti parallel
  2. Sugar-phosphate backbone on outside of helix with nitrogenous bases on inside
  3. Complementary base pairing
    - Total number of purines = total number of pyrimidines
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43
Q

Functions of NADPH

A

Potent reducing agent (helps molecules become reduced)

  • Biosynthesis -> fatty acids and cholesterols
  • Cellular breach production in WBCs -> bactericidal activity contribution
  • Maintenance of reduced glutathione that protects against reactive oxidative agents
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44
Q

Active immunity definition

A

Stimulated to produce antibodies against specific pathogen

  • Either natural or artificial exposure
  • Manner in which immunity can be achieved
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45
Q

If more Na+ is pumped out than K+ how is electrochemical gradient maintained?

A

Cell membranes are more permebale to K+ ions than Na+ ions at rest because there are more K+ leak channels

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46
Q

Debranching enzyme

A

Two enzyme comlex that deconstructs branches in glycogen exposed by glycogen phosphorylase

  1. Breaks a alpha1-4 bond releasing the oligoglucose from the branch point
  2. Transfers oligoglucose to new alpha1-4 bond at end of chain
  3. Hydrolyzes the alpha1-6 bond releasing a single glucose
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47
Q

Heterochromatin vs Eurochromatin

A

Heterochromatin: Remains compact during interphase

  • Often has DNA in highly repetitive sequences (High GC conc)
  • Appears dark under microscopy
  • Transcriptionally silent
  • Small percentage of chromatin

Eurochromatin:

  • Normally dispersed chromatin
  • Light under microscopy
  • Active DNA
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48
Q

What stage of cell cycle does mismatch repair occur?

A

Occurs in G2 of cell cycle

-Two genes detect and remove errors missed during S phase

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49
Q

Saponification

A

Ester hydrolysis of TAGs with a strong base

-Results in basic cleavage of fatty acid and leaves Na+ salt of fatty acid and glycerol -> soap

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50
Q

Alpha ketoglutarate DeH complex regulation

A

Succinyl CoA and NADH allosteric inhibitors

Activated by Ca2+ ions and ADP

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51
Q

Lac Operon

A

Inducible Operon system: Usually off, can be turned on

  • Only digest lactose if glucose low
  • when gluc lvls low, cAMP binds to CAP -> induces conformational charge
  • -CAP binds to promoter region and increases transcription of lactase gene
  • -Allolactose binds to repressor and removes it from operator region
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52
Q

Nucleosides vs Nucleotides

A

Sides: Composed of 5C sugar bonded to nitrogenous base and formed by covalently linked base to C1’ of sugar

Tides: When one or more phosphate groups attached to C5’ of nucleoside

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53
Q

In what direction is leading strand read in and in what direction are complementary strands synthesized in?

A

Read in 3’-5’ direction

Synthesized in 5’-3’ direction

Results in anti parallel orientation of new double helix

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54
Q

Which enzyme adds in nucleotides where the primers previously were located?

A

Prok: DNA polymerase I
Euk: DNA polymerase delta

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55
Q

Feedback regulation

A

Feedforward: Enzymes regulated by intermediates that precede enzyme in pathway

Feedback: Enzymes regulated by products later in pathway
-Product may bind to active site of enzyme or enzymes earlier in pathway

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56
Q

Terpenes function

A

Metabolic precursors to steroids and other lipid signaling molecules

  • Class of lipids from isopropene moieties
  • Grouped according to number of isopropene units present
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57
Q

ATP yield for Reduced cofactors

A 
NADH = 2.5 ATP
FADH2 = 1.5 ATP
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58
Q

Antioncogenes

A

Function to stop tumor progression

-Tumor suppressor genes

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59
Q

Preferred gel for DNA electrophoresis

A

Agarose gel

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60
Q

Chemiosomotic coupling

A

Process that allows the chemical energy of the proton gradient to be harnessed as a means of phosphorylation ADP to ATP

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61
Q

Na+/K+ ATPase

A

Maintains low concentration Na+ and high concentration K+

  • Pumps 3 Na+ ions out and 2 K+ ions in
  • Removes one positive change from intracellular space
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62
Q

Vitamin A function

A

Carotene: vision, growth, development, immune function

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63
Q

Wobble Position

A

Third base in a codon of the same aa is what changes

  • Protects against mutations in coding region of DNA
  • Mutations in wobble position tend to be silent/degenerate
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64
Q

How many primers does each strand need during replication?

A

Leading: theroretically one
Lagging: Constnatly being added

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65
Q

GlycoSphingolipids

A

Sphingolipids with head groups composed of sugars with glycosidic linkages -> glycolipids
-Not phospholipids because no phosphodiester linkage

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66
Q

Why do proteins stop at pH equal to their pI

A

Molecule gains neutral charge and stops

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67
Q

Gene duplication

A

Can be duplicated in series on same chromosome
-Many copies in a row of multiple genes
Can also be in parallel by opening gene with helicases
- DNA replication only on that one gene

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68
Q

Eosinophils

A

Bright red granules
Allergic reactions and parasitc infections
-Release histamine for vasodilation
-Extracellular pathogens

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69
Q

Cofactor vs Coenzyme

A

Cofactor generally inorganic molecules or metal ions

Coenzymes usually vitamins or vitamin derivatives

Enzymes could have multiple cofactors/coenzymes

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70
Q

Two types of Vitamin K

A

K1 = phylloquinone

K2=menaquinone

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71
Q

Endocytosis

A

Cell membrane engulfs material to bring it into cell

-Material encased in vesicle

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72
Q

Stomach immunological role

A

Secretes acid which eliminates most pathogens

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73
Q

Effects of mutation of tumor suppressor gene

A

Loss of tumor suppression activity and therefore promote cancer
-Need both alleles inactivated for loss of function

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74
Q

Termination

A
  • When any of the stop codons moves into A site
  • -Release factor binds to termination codon and water added to polypep chain
  • –Water allows peptidyl transferase and termination factors to hydrolyze completed polypep chain from final tRNA
  • Polypep chain leaves tRNA and subunits dissociate
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75
Q

Column chromatography

A
  • Column filled with silica/alumina beads at stationary phase
  • Gravity moves solvent down column
  • Size and polarity determine how quickly compound moves through beads
  • If less polar, fast migration
  • Useful in separating and collecting macromolecules that aren’t proteins
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76
Q

Function of variable region

A

Specific polypep sequences that bind only one specific antigen sequence

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77
Q

How are nucleotides joined together?

A

3’-5’ phosphodiester bonds

-A phosphate group links the 3’ C of one sugar to the 5’ phosphate of the next sugar

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78
Q

Induced Fit Model

A

Substrate and enzyme don’t fit well together

  • Once substrate present, enzyme binds to a transition state of molecule
  • Active site then becomes complementary to substrate
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79
Q

Standard medium for electrophoresis

A

Polyacrylamide gel

  • Slightly porous
  • Solidifies at room temperature
  • Molecules move faster if small, highly charged or in large electric field
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80
Q

Glutathione function

A

Reducing agent that helps reverse radical formation done to lipid membranes by radical OH oxidizing agents

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81
Q

Big control points of TCA cycle

A

Citrate synthase, isocitrate deH, alpha ketoglutarate DeH

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82
Q

Branching enzyme

A

Introduces alpha1-6 linked branches into granule as it grows

  1. Hydrolyzes a alpha1-4 bond and releases an oligoglucose
  2. alpha1-6 bond created to form a branch with oligoglucose
  3. Glycogen synthase extends both branches
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83
Q

Origins of Replication Prokaryotes

A

Prok:Replication forks move on both sides -> one origin
-Two replication forks move away from each other around the circle and eventually meet
—Results in production of two identical circular molecules of DNA

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84
Q

What happens when soap is added to an aqueous solution

A

Forms colloid

-Micelles form -> overall solvation

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85
Q

What promotes gluconeogenesis and glycogenolysis

A

Maintenance of blood glucose levels
-Glucagon, epinephrine
Inhibited by insulin

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86
Q

Apoenzymes vs Holoenzymes

A

Apo: enzymes without cofactors

Holo: enzymes with cofactors

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87
Q

Electophoresis definition

A

Subjects compound to an electrical field and they move according to net charge and size

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88
Q

Lacteals

A

Small lymphatic vessels at center of each villus

-Transport fats packaged into chylomicrons

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89
Q

WHat enzyme synthesizes primers for replication?

A

Primase

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90
Q

Positive vs negative selection of tcells

A

Positive: Only maturation of cells that respond to presentation of antigen on MHC
Negative: Apoposis in cells that are self reactive

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91
Q

What stages of cell cycle does nucleotide excision repair and base exicision repair occur?

A

In G1 and G2 cell cycle phases

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92
Q

What other pathways are capable of forming acetyl CoA

A

Fatty acid oxidation, amino acid catabolism, alcohol

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93
Q

Nucleoside for each of the Nucleotide bases

A

Adenine: (deoxy)adennosine

Guanine: (deoxy)Guanosine

Cytosine: (deoxy)Cytidine

Uracil: Uridine

Thymine: Deoxythymidine

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94
Q

Posttranslational Processes

A 
Chaperones: protein folding
Cleavage -> peptides with signal sequences
Formation of quaternary structure -> dimerization or tetramerization
Addition of biomolecules:
- Phosphorylation
Carboxylation
Glycosylation
Prenylation
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95
Q

What does cholesterol serve as precursor for?

A

Steroid hormones, bile acids and vitamin D

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96
Q

PKas of Carbonxyl group and pKa of amino group:

A

pKacarboxyl = 2

pKa amino = 9-10

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97
Q

Waxes characteristics

A

Esters of long-chain fatty acids with long-chain alcohols

-Protection for both plant and animals

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98
Q

Cytokines function

A

Chemical substances that stimulate inflammation and recruit additional cells to area

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99
Q

GEnomic Libraries

A

-Large fragments of DNA

Contain both introns and exons of region of genome

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100
Q

Size-exclusion chromatography

A

Beads in column have tiny pores of varying sizes

  • Allow compounds to enter beads if small enough and slow them down
  • Large compounds go around the pores and migrate faster
  • Small compounds are slowed down and migrate slower
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101
Q

Operon

A

Jacob-Monod Model -> function and structure
Definition: Cluster of genes transcribed in singly mRNA
- Simple on-off switch for gene control in Prok
Structural gene: codes for protein of interest
Operator site: nontranscribable region of DNA that binds repressor protein
Promoter site: where RNA polymerase binds
Regulator gene: codes for repressor protein

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102
Q

hnRNA posttranscriptional modifications

A

Splicing
- Spliceosomes remove introns and ligate exons together
- Contains snRNA to indicate splicing sites of introns
- Introns excised in lariat form and degraded
7-methyguanylate triphosphate cap added to 5’ end
- Protects from degradation in cytoplasm
poly A tail added to 3’ end
- Protects from degradation
- Longer tail = longer survival time of mRNA in cytoplasm
- Assists with export from nucleus

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103
Q

Major differences between DNA replication in proks and euks?

A
  • Proks have one origin of replication while euks have many
  • Proks have DNA polymerase I which synthesizes the DNA, removes the RNA primers and replaces them with DNA while euks use RNase H to remove the primers and lettered DNA polymerase to perform the above functions
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104
Q

Significance of Km of GLUT 4

A

GLUT 4 is saturated when blood gluc levels are a bit higher than normal
-Permit constant gluc influx during high blood sugar bv of its saturation

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105
Q

Vmax:

A

When enzyme is working at maximum velocity/efficiency

-Can only be inc with inc enzyme conc

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106
Q

Function of glycogen

A

Storage form of glucose

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107
Q

Glycogen phosphorylase activators/inhibitors

A

Activators: glucagon in liver
-AMP and epinephrine in skeletal muscle
Inhibited by ATP

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108
Q

Cofactors

A

Non protein molecules that aid in enzyme efficiency

-Very small and bind to active site to participate in catalysis of rxn

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109
Q

Symport vs antiport

A

Symport: Both particles flow in same direction
Antiport: Moelcules flow in opposite directions

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110
Q

PEPCK

A

In cytoplasm converts OAA to PEP using up GTP

  • PEP later converted to fruc-1,6-bisP
  • PEPCK and pyruvate carboxylase revert Pyruvate Kinase step
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111
Q

What type of fermentation is used in RBCs/erythrocytes?

A

Only ATP producing pathway is glycolysis

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112
Q

How to denature DNA

A

Can be denatured if H-bonds and base pairs are disrupted

  • Heat, alkaline pH, chemicals like urea
  • When denaturing condition removed-> reannealment
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113
Q

What charge do anode and cathode have?

A

Anode: positive
Cathode: negative

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114
Q

Malate-Aspartate shuttle

A
  1. Coupled rxn of cytosolic OAA reduced to malate and cytosolic NADH oxidized to NAD+ by cytosolic malate DeH
  2. Malate crosses into matrix and reverse rxn occurs
    - NAD+ -> NADH & Malate -> OAA
    - NADH passes e- to ETC via complex I and yields 2.5 ATP
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115
Q

Thymine Dimer/Nucleotide excision repair Steps

A
  1. Proteins scan DNA molecule and recognize lesion bc bulge in strand.
  2. Excision endonuclease makes nicks in backbone of damaged stand on both side of thymine dimer and removes defective nucleotides
  3. DNA polymerase fills in gaps in 5’-3’ direction
  4. Nick in strand sealed by ligase
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116
Q

Which types of t-cells responsd to endogenous antigens

A

Cytotoxic T-cells

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117
Q

Waxes function in plants

A

Secreted as surface coating to prevent excessive evaporation

-Protects against parasites

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118
Q

Start and end terminus of protein/aa synthesis

A

Amino terminus to Carboxy Terminus

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119
Q

Linewaver Burks Plot

A

Double reciprocal plot of M-M plot
-Linear plot
X-int: -1/Km
Y-int: 1/Vmax

X-axis: 1/[S]
Y-axis: 1/v

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120
Q

Change in Gibbs free energy for different types of transport

A

Spont. processes, deltaG<0, passive transport

Nonspont. processes, deltaG>0, active transport

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121
Q

What happens when an antigen binds to surface of an antibody

A

Causes degranulation: exocytosis of granules

-HIstamines released and inflammatory allergic reaction

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122
Q

How does proofreading DNA polymerase tell between the two strands?

A

Looks at methylation to tell two strands apart

-Template strand is older and more methylated

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123
Q

What is an electrochemical gradient and why is it helpful in the ETC?

A

Both a chemical and electrostatic gradient

-Sotres energy to form ATP later

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124
Q

What types of cells produce MHC class 1 molecules

A

All nucleated cells

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125
Q

What enzyme uses the proton gradient to form ATP from ADP and inorganic phosphate?

A

ATP synthase

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126
Q

Osmosis characteristics

A

Special kind of diffusion with water

  • Water moves from region of low solute concentration. to higher solute concentration.
  • From dilute solution to more concentration solution
  • Useful when solute is impermeable to membrane
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127
Q

Three possibilities of antibody binding to antigen

A
  1. Attracts other leukocytes to phagocytize antigens
    - Opsonization
  2. Agglutination: Causes pathogens to clump together in insoluble complexes to be phagocytized
  3. Block pathogens from invading tissues to neutralize them
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128
Q

Secondary active transport

A

Harnesses energy released by one particle going down its gradient to drive a different particle up its gradient

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129
Q

Complex II Succinate-CoQ oxidoreducatase

A
  1. Succinate oxidized to FAD reduced FADH2

2. FADH2 reoxidized to FAD and CoQ reduced to CoQH2

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130
Q

Two types of sphingolipids

A

Cerbrosides: single sugar
Globosides: Two or more sugars
-Mainly found on outer surace of plasma membrane

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131
Q

Glycogen synthase activators and inhibitors

A

Activated by:
-Glu6P and insulin
Inhibited by:
-epinephrine and glucagon

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132
Q

Facilitated diffusion:

A

Molecules impermeable to membrane that req intergral membrane proteins to serve as transporters/channels

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133
Q

What type of reactions dominate the ETC?

A

Series of redox reactions

  • NADH is good e- donor
  • Oxygen is a great oxidizing agent
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134
Q

MHC class.1 molecules

A

Any protein within cell can be loaded onto MHC 1 and presented on surface of cell
-Allows immune system to monitor health of cells and detect if they’ve been infected

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135
Q

Hydrostatic pressure definition

A

Exerted by water level in high solute side that will eventually oppose influx of water
-Water rises to point at which it exerts sufficient pressure to counterbalance tendency of water to flow across membrane

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136
Q

Glycogen synthase functino

A

Forms alpha1-4 glycosidic bond in linear glucose chains

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137
Q

Two steps of the ETC

A
  1. Electron transport along IMM
  2. Generation of ATP via ADP phosphorylation
    - Coupled process
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138
Q

N-terminus vs C-terminus

A

N: amino terminus -> free amino end

C: free carboxyl terminus

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139
Q

Bradford protein assay

A

Mixes protein in solution with Coomassie blue dye
-Dye is green-brown before mixed with proteins
-Dye gives up protons when binding to aa groups and turns blue
-Ionic attractions between dye and protein and stabilize blue form of dye
Increased protein concentration = more intensely blue dye

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140
Q

Kinetics: K1, K-1 and Kcat

A

K1: forward rxn: E+S -> ES

K-1: reverse rxn: ES -> E+S

Kcat: ES -> E+P
-Rate limiting step

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141
Q

Point Mutation

A

One nucleotide substituted

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142
Q

Colligative property definition

A

Physical property of solution dependent on concentration of dissolved particles but not their chemical identities

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143
Q

Contant region function

A

Houses natural killers, macrophages, monocytes, eosinophils and can initiate complement cascade
-Each B-cell only has one type and produces one isotype

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144
Q

What types of WBCs are agranulocytes

A

lymphocytes and monocytes

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145
Q

Nonsense Mutation

A

Codon now encodes Stop codon -> Truncation mutation

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146
Q

How many chromosomes of DNA

A

46

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147
Q

Occluded state definition

A

When carrier is neither open to either side of membrane

-Can also be channels which can be in either open or closed conformation

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148
Q

Centromeres

A
  • Regions of DNA found in center of chromosomes
  • Sites of constriction -> form noticeable indentations
  • Composed of heterochromatin and have highly repeating sequences -> high GC content
  • During cell division, two sister chromatids remain at centromere until microtubules separate chromatids during anaphase
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149
Q

Van’t hoff factor definition

A

Number of particles obtained from molecule when insoluble
Ex: NaCl in solution, i = 2
Ex: Gluc in solution, i = 1

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150
Q

What is supercoiling?

A

Wrapping of DNA on itself as helical structures pushes toward telomeres during replication

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151
Q

What hormone facilitates selection of T cells and secretion

A

Thymosin -> peptide hormone

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152
Q

Edman Degradation

A

Uses cleavage to sequence proteins of up to 50-70 aa’s

  • Sequentially removes N-terminal aa of protein
  • Analyzed with mass spectroscopy
  • Creates smaller fragments that can be analyzed by electrophoresis
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153
Q

Fructose-1,6-bisPase

A

In cytoplasm and removes phosphate from fruc-1,6-bisP to produce fruc-6-P.

  • Activated by ATP
  • Inhibited by AMP and fructose 2,6-bisP
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154
Q

STOP codons

A

U Are Annoying -> UAA
U Go Away -> UGA
U Are Gone -> UAG

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155
Q

Cytotoxic T cells aka

A

CD8+ T-cells

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156
Q

Active transport

A

Net movement of solute against its concentration gradient

-Requires energy

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157
Q

What four enzymes circumvent the irreversible steps of glycolysis

A

pyruvate carboxylase, phosphoenolpyruvate carboxykinase (PEPCK), fructose1-6bisphosphatase, glucose-6-phosphatase

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158
Q

What happens to plasma cells after pathogen has been eliminated

A

They die

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159
Q

Resident population immune definition

A

WHen a type of cell becomes a permanent resident in a tissue

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160
Q

Restriction Enzymes

A

Recognize specific DNA sequences

  • Isolated from bacteria
  • Able to cut through. backbones of double helix
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161
Q

T vs R Conformation + Application to PFK-1 conformational equilibrium

A

T: low affinity to S
R: high affinity to S

Binding of S induces equil. shift to R form

For PFK1:

R state has Arg that increases S affinity
-Conformational change to T inhibited by AMP/ADP allosteric binding

T state has Glu that decreases S affinity
-Conformational change to T induced by ATP/Citrate binding

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162
Q

What is the key enzyme of fermentation?

A

Lactate DeH -> oxidizes NADH to NAD+

  • Reduces pyruvate to lactate
  • Regenerates cells NAD+ supply
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163
Q

Two functions of pentose phosphate pathway

A

production of NADPH and source of ribose5phosphate for nucleotide synthesis

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164
Q

Effects of glucagon and insulin on gluconeogenesis

A

Glucagon lowers F2,6BisP stimulating gluconeogenesis

Insulin increases F2,6BisP inhibiting gluconeogenesis

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165
Q

Humoral vs cell-mediated immunity which WBCs are in each

A

Humoral: driven by b-cells and antibodies

Cell-mediated: T-cells

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166
Q

What are terpenes metabolic derivatives of

A

Steroids

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167
Q

Passive immunity

A

Transfer of antibodies to an individual

-Transient immunity because antibodies not plasma cells that produce antibodies are transferred

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168
Q

Hypotonic soln

A

Concentration of solute inside cell higher than concentration in surrounding solution
-Water rushes into cell -> lysing/bursting

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169
Q

When is chromatography preferred over electrophoresis

A

When large amounts of protein are being separated

170
Q

Where is glycogen stored

A

Stored in the cytoplasm as granules
Also stored in liver
Also muscle glycogen stored as energy reserve

171
Q

Helicase

A

Enzyme response for unwinding DNA and generating two single stranded template strand of polymerase
-Unzips

172
Q

How does pH change as a result of H+ concentration increasing in intermembrane space?

A

pH drops in intermembrane space

pH of matrix increases

173
Q

Facilitaed diffusion steps

A
  1. substrate binds to transporter
  2. substrate remains in transporter during conformational change -> occluded state
  3. Dissociates from substrate-binding site of transporter
174
Q

Basophils

A

Large purple granules

-Release large amounts of histamines in response to allergens

175
Q

Eukaryotic Origins of Replication

A

Must copy much more bases than prokaryotes
-To do this efficiently, each chromosome has multiple origins of replication
-As replication forks move toward each other -> sister chromatids created
—Chromatids remain connected to the centromere and are separated during mitosis

176
Q

Hypermutation

A
  • B-cells undergo alteration in which only those with high affinity to antigen survive -> clonal selection
  • Reason why specific immunity takes long
177
Q

Transgenic mice production via surrogate mother

A
  1. Cloned gene micro injected into nucleus of fertilized ovum
    -Surrogate mother has offspring with the transgene
    -Transgene can be passed onto more offspring
    Difference: Transgene coexists in animals with copies of their own gene
    -useful only for looking at dominant genes
178
Q

What is the rate limiting enzyme of gluconeogenesis

A

Fructose-1,6-bisPase

-Reverses the action of PFK-1

179
Q

Native PAGE

A

Does not denature protein

-Gel not stained

180
Q

Pinocytosis

A

Endocytosis of fluids and dissolved particles

181
Q

Interferons function

A

Produced by cells infected with viruses

  • Prevent viral replication and dispersion
  • Cause nearby cells to dec production of viral and cellular proteins
  • Decrease permeability of nearby cells so harder to viruses to infect them
  • Upregulate MHC class I and II molecules for inc antigen presentation of infected cells
182
Q

How much carbon is lost when pyruvate is converted to lactate by Lactate DeH?

A

No net loss of carbon

-Pyruvate and lactate both are 3C molecules

183
Q

Natural killer cells function

A

Nonspecific lymphocyte able to detect downregulation of MHC

-Induces apoptosis in virally infected cells

184
Q

Proline

A

Introduces kinks in peptide chains when found in middle of alpha-helices

  • Rarely found in alpha-helices except when they cross the cell membrane
  • Rarely found in middle of sheets
  • Often found in turns between sheets or at start of alpha-helix
185
Q

What are prostaglandins

A

20 Carbon molecules derived from arachidonic acid and have one 5C ring

186
Q

How is the overall process of PCR performed?

A

DNA of interest is denatured, replicated and then cooled/reannealed several times until enough copies of DNA sequence are available.

187
Q

What types of cells do natural killer cells kill?

A

Virally infected cells and cancer cells

-Both downregulate MHC production

188
Q

Cholesterol function

A

Major component of phospholipid bilayer and responsible for mediating membrane fluidity

189
Q

Three types of RNA polymerase in eukaryotes

A

RNA polymerase I: in nucleolus and makes rRNA
RNA polymerase II: in nucleus and makes hnRNA and some snRNA
RNA polymerase III: In nucleus and makes tRNA and some rRNA

190
Q

What is a vitamin

A

Essential nutrient that cannot be adequately synthesized by body

191
Q

Self-reactive definition immune

A

Cells that are acivtaed by proteins produced by the organism itself

192
Q

Pentose Phosphate irreversible step

A
  1. Gluc6P converted to ribulose 5 phosphate

- converts two NADP+ to two NADPH

193
Q

Denaturation

A

When a protein loses its tertiary structure and function

-High temp -> hphobic interactions can be overcome and protein unfolds
-Solutes can be introduced to denature as well
—Urea breaks disulfide bridges

194
Q

Where does gluconeogenesis occur

A

Mostly in the liver but in kidneys also to smaller extent

195
Q

Germinal centers

A

Places where B-cells proliferate and mature

-Located in lymph nodes

196
Q

Enhancer

A

Outside of normal promoter regions

  • Several response elements grouped together
  • DNA has to bend in hairpin loop to bring promoter and enhancer regions closer
  • -Can be 1000 bp away or even in an intron
  • Increased likelihood of gene amplification bc variety of signals
197
Q

Glycogen phosphorylase

A

Breaks alpha1-4 glycosidic bonds releasing 1-phosphate from periphery of granule
-Cannot break alpha1-6 bonds so stops near branch points

198
Q

Gut bacteria function

A

Large bacterial gut population competes with invading bacteria to keep them at bay

199
Q

Southern blot function

A

Detects presence and quantity of various DNA strands in a sample

  • DNA cut by restriction enzymes and separated by gel electrophoresis
  • DNA fragments carefully transferred to a membrane
  • This membrane is probed which bind to complementary sequences and form DNA
  • Probes are labeled radioactively so can be tracked
200
Q

Why does the range of total ATP from respiration range from 30 to 32?

A

Variability of cytosolic NADH shuttle mechanisms into the mitochondrial matrix

201
Q

Trp Operon

A

Repressible System: usually on but can be turned off
- Repressor made by regulator gene inactive until bound to corepressor
When trp is high, acts as corepressor
- Two trp molecules bind to form repressor-corpressor complex and bind to operator site
- Transcription or trp is hindered

202
Q

Macrophage is a granulocyte or agranulocyte?

A

agranulocyte

203
Q

How are steroids different from steroid hormones?

A

Secreted by endocrine glands into bloodstream and travel on protein to be carried to distant sites

204
Q

Memory T-cells

A

Similar to memory B-cells

-Carry out more robust and rapid response to next exposure of same antigen

205
Q

What type of reactions are autoimmunity and allergic reactions classified as?

A

Hyper sensitivity reactions

206
Q

Complex III

A
  1. CoQH2 passes two e- to cytochrome C

- Cytochrome C reduced from Fe 3+ to Fe @+

207
Q

Where does remaining fluid in tissues in blodo vessels go

A

Drained into lymphatic vessels

-Then return to bloodstream

208
Q

Why does ligase have a higher likelihood of mutations in lagging strand

A

Ligase lacks proofreading ability

209
Q

Sphingomyelin function

A

Major component in plasma membranes

-Produces myelin to insulate sheath of axons

210
Q

What types of WBCs are granulocytes

A

neutrophils eosinophils and basophils

211
Q

Why is replication semi conservative?

A

One parental strand is retained in each of the two resulting initial double stranded molecules

212
Q

When does GLUT 4 transport increase?

A

When insulin is released

-Stimulates movement of more GLUT 4 transporters to membrane via exocytosis

213
Q

GLUT 4 Transporter Location and Km

A

In adipose tissue and muscle and responds to gluc concentration in peripheral blood
-Km is similar to normal blood gluc levels

214
Q

How does a tRNA become activated?

A

when aa’s are bound to a tRNA they become activated/charged.

  • Each tRNA/aa complex is activated by a different aminoacyl-tRNA synthetase
  • High energy amino acyl-tRNA bond supplies energy needed to create peptide bond in translation
215
Q

X-ray crystallography

A

Proteins isolated and crystallized

  • Measures e- density on extremely high-resolution
  • Small dots in diffraction pattern interpreted to determine protein structure
216
Q

Primary Structure

A

Linear arrangement of aa’s in an organism’s DNA

  • Listed from N-terminus to C-terminus
  • Encodes all info needed for folding at other structural levels
217
Q

What enzyme adds Okazaki fragments to lagging strand?

A

Prok: DNA polymerase III

Euk: DNA polymerase alpha, delta and epsilon

218
Q

Granulocytes vs agranulocytes

A

granulocytes contain granules in their cytoplasm

219
Q

Variables of catalytic efficiency

A

Kcat/Km

Kcat represents turnover rate of enzyme (# of [s] converted to [P] per second

Km represents specificity

High Kcat + low km -> efficient

220
Q

Why can’t PCR use normal DNA polymerase

A

Performed at high temperatures so must use Taq polymerase

221
Q

Helper T-cells function

A

Coordinate immune response by secreting chemicals

  • REcruit other immune cells
  • Respond to antigens on MHC II molecules
222
Q

What types of cells activated in humoral immunity

A

T-cells

223
Q

Terpenoids

A

Modified terpenes that share similar characteristics of terpenes

224
Q

Phagocytosis

A

Ingestion of large solids like bacteria

225
Q

Lymph nodes fucntion

A

Space for cells of immune system to be exposed to possible pathogens
-Also filters blood

226
Q

Function of glycogenolysis

A

Breaking down glycogen

227
Q

Topoisomerase

A

Introduce negative supercoils

  • Relaxes torsional pressure and then reseals cut strands
  • Prevents supercoiling of DNA
228
Q

Hypertonic soln

A

Solution surrounding cell has higher concentration than concentration in cell
-Water will move out of cell

229
Q

Soap functino

A

Soap can act as surfactant -> lowers surface tension

-Can be detergent and emulsifier

230
Q

What amino acids are not glucogenic

A

Leucine and Alanine

231
Q

Why does GLUT 2 have a high Km for glucose?

A

Liver picks up glucose in propotion to its concentration in blood

  • This means that GLUT 2 collects glucose when its in excess only
  • Remainder bypasses liver and goes to peripheral circulation
232
Q

Examples of passive immunity

A

When mother transfers antibodies across placenta to protect fetus
-Also when mother transfers antibodies to infant rhough breast milk

233
Q

Vitamin D function

A

Cholecalciferol -> converted to calcitrol in liver/kidneys

  • Inc. Ca2+ intake and phosphate uptake in intestines
  • Leads to bone production
234
Q

Reversible steps of pentose phosphate pathway

A
  • Ribulose5P can be converted to ribose5P for nucleotide synthesis
  • Fructose6P and G3P can also be converted to Ribose5P without GDPD
  • -Done by transketolase and transaldolase
  • Ribose5P can also be converted into glycolysis intermediates (G3P and Fructose6P)
235
Q

What is the overall net charge of DNA/RNA?

A

Phosphates have a negative charge -> net negative charge for these nucleic acids

236
Q

Promoter Regions

A

Regions in DNA in targeted by RNA polymerase

  • RNA polymerase II binds to TATA box (high A and T conc)
  • Transcription factors help RNA polymerase locate/bind to this region
237
Q

How many bonds between the base pairs:

A

A to T: 2 H-bonds
G to C: 3 H-bonds

-H-bonding and H-phobic interactions between bases provide stability

238
Q

How is an Electrochemical gradient created?

A

Impermebaility of cell membrane and selectivity of ion channels lead create an electrochemical gradient

239
Q

What is the main glucogenic amino acid?

A

alanine

240
Q

Function of prostaglandins

A

Act as paracrine and autocrine signaling molecules

  • Regulate synthesis of cAMP
  • Downstream effects
241
Q

Sugar Pentose backbones of RNA/DNA

A

RNA: Pentose=ribose

DNA: Pentose=deoxyribose

242
Q

Would a longer DNA strand migrate faster or slower via gel electrophoresis

A

Slower

243
Q

What is the rate limiting enzyme of pentose phosphate pathway

A

glucose6phosphate deH (G6PD)

244
Q

Secondary Structure

A

Local structure of neighboring aa’s
-Result of h-bonding between nearby aa’s

alpha-helix: peptide chain coils clockwise around central axis
—Stabilized by intramolecular H-bonds between carboxyl-C and amine-H four residues down the chain
—side chains point away from the core

beta-pleated sheets: peptide chains lie alongside one another
—Form rows held together by intramolecular H-bonds between carbonyl-O and amide H of different chains
—Parallel more common than anti-parallel
—R groups point above and below plain of sheet
—In rippled shape to fit more aa’s

245
Q

Oncogenes

A

Mutated genes that cause cancer
-Primarily encode cell cycle-related proteins
Proto-oncogenes: Before these genes are mutated

246
Q

How is the malate aspartate shuttle regenerated after OAA is reformed in the mitochondria?

A

OAA can be converted to aspartate via aspartate transaminase and then trasnported back into cytosol
-Conversely, in cytosol, aspartate transaminase can convert this aspartate into OAA to participate in this shuttle as needed

247
Q

GLUT 2 Transporter location and Km

A

Low affinity transporter in hepatocytes and pancreatic cells

-High Km

248
Q

How are functions of steroids determined?

A

Functionality determined by oxidations states of rings and ring functional groups

249
Q

Role of gangliosides

A

Interaction, recognition and signal transduction

250
Q

What does lipid soluble mean?

A

Stored in fat

251
Q

Initiation

A

Prok: small subunit binds to Shine-Dalgarno sequence in 5’ end of mRNA
Euk: small subunit binds to 5’ cap
-Charged initiator tRNA binds at P site
-Large subunit binds to small
-Initiation factors help and transiently associate with ribosome

252
Q

What do oncotic pressures do?

A

Draws water back into vessel at venule end

-Pressure pushing fluid out of arterial end is higher

253
Q

Missense Mutation

A

One aa substitutes for different aa

254
Q

B-cells origination and activation locations

A

Originate and mature in bone marrow

-Activated in spleen and lymph nodes

255
Q

Pattern recognition receptors function

A

Able to recognize category (virus/bacteria/fungi) of invader

-Allos for production of appropriate cytokines to recruit right types of immune cells

256
Q

Innate vs Adaptive immunity

A

Innate: Defenses always active against infection
-Lack ability to target specific invaders -> nonspecific
Adaptive: Defenses that target a specific pathogen
-SLower to act but maintains immunological memory and mounts faster attack in subsequent infections -> specific

257
Q

What happens if body encounters same antigen

A

Memory cells produce secondary response

-More rapid and robust response to Infection

258
Q

Equation of hydrostatic pressure

A 
pi = iMRT
pi = hydrostatic pressure
i=van't hoff factor
R=ideal gas constant
T = absolute temp in K
259
Q

What do his tone proteins do?

A

They form chromatin by winding DNA

  • 5 his one proteins form this complex and form a nucleosome which adds stability
  • Histones: nucleoproteins that associate with DNA
260
Q

Frameshift Mutation

A

Nucleotides are added to or deleted from mRNA sequence

  • Reading Frame = three nucleotides
  • Typically more serious than point mutations
261
Q

What type of pathway is MHC 1 pathway

A

Endogenous: Binds antigens that come from inside of cell

262
Q

Two domains of transcription factors

A

DNA-binding domain: binds to specific nucleotide sequence in promoter region or DNA response element
- aids in transcription
Activation domain: allws for binding of several transcription factors and other regulatory proteins

263
Q

Elongation

A
  • Next aminoacyl-tRNA complex at A site
  • P site has tRNA with growing polypep chain
  • -Peptide bond between polypeptide between tRNA in P site and in A site
  • –Needs peptidyl transferase and GTP as energy
  • Uncharged tRNA in P site moves to E site and leaves
  • -tRNA in A site moves to P site and is still charged

Elongation factors help in bringing in GTP and amino-acyl-tRNA

264
Q

Gangliosides function

A

Glycolipids with polar head groups composed of oligosaccharides with one or more N-acetylneuraminic acid at terminus and a negative charge

265
Q

Primary active transport

A

Uses ATP or other energy molecule to directly power transport of molecules across a membrane
-Transmembrane ATPase

266
Q

What is function of Recombinant DNA technology

A

Allows a DNA fragment to be multiplied by either gene cloning or PCR

  • Can analyze or alter genes/proteins
  • Can also provide source of specific protein
267
Q

How are autoimmune reactions prevented

A

Via maturation of T-cells and B-cells

  • T-cells that respond to self-antigens are eliminated via negative selection
  • Immature B-cells that react to self-antigens eliminated before leaving bone marrow
268
Q

How does RNA polymerase proofread its work during transcription?

A

Trick question

269
Q

What must be done to flanks of desired regions of DNA to allow for amplification via PCR?

A

PCR requires primers complementary to DNA at flanks of region of interest
-Primers have high GC content to provide more stability

270
Q

Hill’s Coefficient

A

Measure of cooperativity

If>1, positively cooperate binding occurring
If<1, negatively cooperative binding
-Binding of one ligand inhibits binding affinity of another
If =1, no cooperative binding present

271
Q

Bone marrow function

A

Produces all leukocytes/WBCs in immune system

272
Q

Fermentation in yeast cells

A

Converts pyruvate into ethanol and CO2

-Still replenishes NAD+

273
Q

Isoelectric steps

A

Mix of proteins placed in gel with pH gradient

  • Acidic gel at positive anode and basic gel at negative cathode
  • Electric field generated and proteins migrate to one of the ends and stop at pH equal to pI
274
Q

What type of pathway is MHC II

A

Exogenous: Presents antigens originated from outside the cell

275
Q

Glucose 6 Phosphatase

A

Found only in lumen of ER in liver cells

  • Converts Glu6P to glucose
  • Glu6P transported to ER and free glucose transported back to cytoplasm
  • Circumvents glucokinase and hexokinase
276
Q

F0 function

A

Portion of ATP synthase that functions as an ion channel for protons to travel along their gradient back into the matrix

277
Q

Suppressor T cells

A

Can be differentiated from helper-T-cells

  • Help tone down immune responce once infection is contained
  • Turn off self-reactive lymphocytes
278
Q

ETC Complex I NADH-CoQ oxidoreducatse

A
  1. NADH transfers e- to CoQH2

- Pumps four protons into intermembrane space

279
Q

Lymph nodes function

A

Place for immune cells to communicate and mount an attack

-B cells can be activated here

280
Q

Isoelectric focusing mnemonic

A

A+: anode has acidic (H+ gel) and positive charge

281
Q

Thymus function

A

Small gland in front of pericardium

-T-cells mature here

282
Q

GALT examples

A

Gut-associated lymphoid tissue

-Tonsils, adenoids, Peyer’s patches in small intestine and appendix

283
Q

G3P shuttle

A
  1. On outer face of IMM, FAD-dependent G3P DeH oxidizes cytosolic NADH to NAD+ via G3P deH isoform
  2. This FADH2 transfers its e- via complex II of ETC and yields 1.5 ATP
284
Q

Km

A

Michaelis constant: binding affinity between E&S

  • Lower km = higher affinity
  • Cannot be altered by changing [E] or [S]
285
Q

Classical vs alternative pathway of complement system

A

Classical req binding of antibody to pathogen

Alternative does not req antibodies

286
Q

How can GLUT 4 intake of gluc be increased?

A

Only way is to produce more GLUT 4

287
Q

Base excision repair

A
  1. Affected base recognized and removed by glucose lapse enzyme
    - apurinic/apyrimidinic AP site left aka abasic site
  2. AP site recognized by AP endonuclease that removes damaged sequence from DNA
  3. DNA polymerase fills it in and DNA ligase seals strand
288
Q

Tertiary Structure

A

3-dimensional shape

-Determined by hphilic/hphobic interactions between R-groups
—If hphobic: interior
—If hphilic: exterior

-Can also be determined by H-bonding/acid-base interactions
—Charged R-groups can create salt bridges

-Protein folding is extremely rapid

289
Q

Where does Pentose Phosphate pathway occur?

A

In the cytoplasm

290
Q

Isotonic soln

A

Concentration of solution in and out of cell are equimolar

  • Prevents net movement of particles
  • H20 still moves in and out of cell but cell doesn’t have any net change of H20
291
Q

Gene therapy Steps

A
  1. Transfer normal copy of gene into affected tissues
    - Pathology should be fixed and individual should be cured
    - Requires efficient gene delivery vectors to transfer cloned gene into target cell DNA
292
Q

How does cholesterol impact fluidity

A

Interacts with both h-phobic tails and h-phobic heads to maintain relatively constant fluidity in cell membranes

  • Low temps: keeps membrane from solidifying
  • High temps: holds membrane intact and keeps it from becoming too permeable
293
Q

How do prok and euk accomplish gene diversity

A

Prok: polycistronic
Euk: alternative splicing
- some hnRNA transcripts can be spliced in different ways
– Produces multiple variants of proteins encoded by the same gene

294
Q

Lysozyme function

A

Nonspecific bacterial enzyme secreted in tears and saliva

295
Q

Components of antibody

A

Y-shaped molecules with two identical heavy and two identical light chains

  • Antigen-binding region at end (variable region)
  • Constant region (domain)
296
Q

Quaternary Structure

A

Proteins with more than one polypeptide chain
-Aggregate of subunits -> each with a. functional form

Roles:

  1. Can provide stability
  2. Can reduce amount of DNA needed to encode protein complex
  3. Can bring catalytic sites closer together
  4. Can induce cooperativity or allosteric effects
297
Q

STrand copied in transcription

A

Template/antisense strand

  • Coding/sense strand not used as template
    • This strand is also complementary/antiparallel to template strand and is identical to mRNA transcript
  • –Only difference is Uracil instead of Thymine
298
Q

What does a lack of vitamin D entail

A

Rickets

-Underdeveloped, curved long bones

299
Q

BPG in RBCs

A

RBCs have BPG mutase -> produces 2-3 BPG from 1-3 BPG

  • 2,3 BPG binds allosterically to HbA and dec. affinity for O2
  • Causes rightward shift in curve to allow unloading of O2
300
Q

What three things does an activated macrophage do

A
  1. Phagocytizes invader via endocytosis
  2. Digests invader using enzymes
  3. Presents pieces of invader to other cells with MHCs
    - Also release cytokines
301
Q

What are ketogenic amino acids?

A

Can be converted into ketone bodies like acetyl-CoA for alternative fuel

302
Q

Which genomic library can be used reliably to sequence specific genes and produce recombinant proteins

A

cNA libraries

-Genomic libraries can’t because they could split genes by chance

303
Q

Difference between knockout mice and transgenic mice

A

Knockout mice have a gene intentionally knocked out

Transgenic mice have a gene added

304
Q

How is acetyl CoA converted back to glucose

A

Cannot be converted to glucose

-Can be converted to ketone bodies for alternative fuel

305
Q

Artificial vs natural exposure of active immunity

A

Natural: B-cells activated when individual is infected
Artificial: Individual never experiences true infection
-Receives injection of weakened/killed form of microbe so B-cells can produce antibodies

306
Q

Structure of steroids

A

Four cycloalkane rings fused together

-Three cyclohexane, one cyclopentane

307
Q

Storage form of vitamin A

A

Retinol

-Can be oxidized to retinoic acid -> regulates gene expression during epithelial development

308
Q

How are rates of passive transport by temperature?

A

Diffusion and osmosis generally inc. in rate with inc. temperature

309
Q

Where do most lymphatic vessels meat to deliver fluid back to circulatory syste,

A

Large thoracic duct

-Delivers fluid into left subclavian vein near heart

310
Q

Which types of t-cells respond to exogenous antigens

A

Helper T-cells

311
Q

Sphingomyelin structure

A

Has either phosphocholine or phosphoethanolamine head group with a phosphodiester bond

312
Q

Why are Okazaki Fragments needed?

A

DNA polymerase can’t read the lagging strand bc its oriented in 5’-3’ polarity.

Must read it in 3’-5’ direction while synthesizing in 5’-3’

  • Reads short segments of strand and adds in Okazaki Fragments
  • Once an Okazaki fragment is completed, DNA polymerase turns around to find another gap to fill in
313
Q

How is endocytosis actiavted?

A

Both activated by stubstrate binding to specific receptors embedded within a plasma membrane
-Leads to invagination by vesicle-coating proteins

314
Q

Affects of pH, Temp, Salt on Enzyme activity

A

Enzyme catalyze rxns double for every 10 degC increase until optimum temp reached
-AFter about 37 degC, activity falls dramatically

pH affects ionization of active site and can lead to denaturation of enzyme
-Optimal pH: 7.4
-Only exception: digestive tract
—Stomach pH: 2, small intestine pH: 8.5

Increasing salt levels can disrupt H-bonds and ionic bonds
-Would cause partial change in conformation of enzyme and denaturation

315
Q

Fructose metabolism

A

Abosrbed into hepatic portal vein and phosphorylated by fructokinase to trap in cell
-Cleaved into G3_ and DHAP by aldolase B

316
Q

Examples of macrophages forming resident population in nervouos, skin, and bone tissues

A

Bone: osteoclasts
skin: Langerhans cells
CNS: microglia

317
Q

Lock and Key Theory

A

Enzyme active site already in appropriate conformation with substrate

  • Can easily fit in active site
  • No conformational change req. in structure when binding
318
Q

Three enzymes of the pyruvate deH complex?

A
  1. pyruvate dehydrogenase: pyruvate oxidized to yield CO2
    - acetyl group binded covalently to TPP
  2. Dihydrolipoyl Transacetylase: acetyl group transferred to lipoc acid -> forms thioester linkage
    - Acetyl group transferred to CoA coenzyme
  3. Dihydrolipoyl deH: FAD reoxidizes lipoic acid
    - Resulting FADH2 reoxidized to FAD by NAD+
319
Q

Why do we need branched glycogen

A

Allows for more rapid release of glucose

320
Q

Where is the Pyruvate DeH complex located?

A

In mitochondrial matrix

321
Q

Affinity chromatography

A

Column with high affinity for a specific protein

  • Beads coupled with receptor that binds protein or specific antibody -> protein retained in column
  • After being retained in column, eluted by washign column with free receptor and outcompete bead-bound receptor to free protein from column
322
Q

How does the body produce vitamins?

A

Cannot be adequately produced

-Must be consumed in diet

323
Q

How are the compounds stuck in Ion Exchange chromatography eluted?

A

After all compounds have eluted, salt gradient used to elute charge molecules from stuck column

324
Q

Which portion of ATP synthase utilizes chemiosomotic coupling?

A

F1 portion

325
Q

Main difference between Euk. and Prok. mRNA?

A

Euk: monocistronic -> each mRNA molecule translates into only one protein product
Prok: polycistronic -> starting translation at different locations in mRNA could result in different proteins

326
Q

End of Transcription

A

When reaches termination sequence or receives stop signal

  • DNA reforms and primary mRNA transcript is known as hnRNA (pre-processed mRNA)
  • hnRNA now needs posttranscriptional modifications
327
Q

Two enzymes of glycogenesis

A

glycogen synthase (rate-limiting enzyme) and branching enzyme

328
Q

Single Stranded DNA-Binding proteins

A
  • Free Purines and Pyrimidines want to H-bond with other molecules
  • Bind to unraveled strands
  • Prevents reassociation of DNA strands and degradation of DNA by nucleases
329
Q

Hybridization Biotech

A

Joining of complementary base pair sequences

  • Can be DNA-DNA or DNA-RNA recognition
  • Uses two single-stranded sequences
  • Vital for PCR and Southern blotting
330
Q

Chromatin Structure regulation

A

Heterochromatin: tightly coiled -> inaccessible to transcription -> genes are inactive
Euchromatin: Looser and can be accessed
-Histone Acetylation: decreases positive charge on Lys and weakens interaction between histone & DNA
–Open conformation change -> easier access
–Histone acetylases add acetyl groups to histones
-Can be reversed by histone deacetylases that remove these acetyl groups -> closed conformation
-DNA methylation: DNA methylases add methyl groups to C and A nucleotides
–Linked w silencing of gene expression
–Heterochromatin is highly methylated -> gene experssionless

331
Q

What type of cells use MHC II and are considered professional antigen-presenting cells

A

Macrophages, dendritic cells, certain activated epithelial cells

332
Q

Start Codon

A

AUG -> Methionine

Prok: AUG -> N-formylmethionine

333
Q

What is the function/composition of telomere’s?

A

Located at the end of DNA and has repeating units

  • Telomeres are progressively shortened
  • High GC content prevents unraveling
334
Q

What is the main secondary structure of DNA?

A

beta-DNA: right handed helix

335
Q

Function of granules

A

Contain toxic enzymes and chemicals released via exocytosis

-Effective against bacterial, fungal, parasitic pathogens

336
Q

Ribosomal Subunits

A

Euk: 60s and 40s = 80S
Prok: 50S and 30S = 70 S
- S is how fast subunits sediment experimentally

337
Q

Helicase/Topoisomerase Transcription

A

Unwind DNA and prevent supercoil formation

338
Q

Structure of DNA/RNA + stability

A

Both are aromatic heterocyclic
-Unusually stable
-Stability due to delocalized pi e- that can travel throughout the entire compound
—Forms two pi e- clouds
—All 6 C atoms in the benzene are sp2 hybridized

339
Q

gluc-6PdeH activators and inhibtors

A

Inhibited by insulin and NADPH

Activated by NADP+

340
Q

RNA synthesis direction, ribsome translation direction

A

5’ to 3’ Direction

341
Q

Spleen function

A

Blood storage and B-cell activation

-B cells turn into Plasma cells produce antibodies

342
Q

Catalyst Characteristics

A
  • Lower activation energy
  • Do not alter equilibrium constant
  • pH/temperature sensitive
  • Do not affect deltaG of a rxn
  • Not consumed in rxn
  • Increase rxn rate greatly

Enzymes: biological catalysts

343
Q

cDNA libraries

A

0Constructed by reverse-transcribing processed mRNA

  • Lacks non coding regions like introns
  • Only includes genes expressed in tissue from mRNA
  • Known as expression libraries
344
Q

Endergonic vs Exergonic

A

Endergonic: nonspont. deltaG > 0, requires energy input, reversible

Exergonic: energy given off, irreversible, deltaG<0, spont.

345
Q

Galactose metabolism

A

Reaches liver via hepatic portal and phosphorylated by galactokinase
-converted to Gluc 1P by galactose-1-phosphate uridyl transferase

346
Q

Membrane Potential

A

Vm: difference in potential across cell membranes

-Resting potential for most cells between -40mV to -80 mV

347
Q

Which part of the ETC coupled processes are ender/exergonic?

A

Formation of ATP -> endergonic
e- transport -> exergonic
-Coupling them means energy yielded by one fuels the other

348
Q

Helper t-cells aka

A

CD4T+ cells

349
Q

Neutrophils

A
  • Most populous leukocytes in blood
  • Short lived
  • MOve up concentration grandient to source of chemical stimuli from bacteria via chemotaxis
  • Acute bacterial
350
Q

What type of respiration occurs in absence of oxygen?

A

Fermentation

351
Q

Purines vs Pyrimidines

A

Pure As Gold Rings: Purines: Two rings -> Adenine and Guanine

Pyrimidine: Have only one ring

  • Cytosine in DNA and RNA
  • Thymine only in DNA
  • Uracil only in RNA`
352
Q

What types of lymphocytes included in adaptive immune system

A

B-cells and T-cells

353
Q

Dideoxyribonucleotide Function

A

Modified base added that have C-3’ hydrogen instead of hydroxyl

  • Once incorporated polymerase cannot add to the chain
  • Sample eventually contains fragments each terminate with one of these modified bases
  • Separeate fragment by size with gel electrophoresis and read them in order
354
Q

When does an allergic reaction occur

A

When cell idenfities a foreign antigen as dangerous when it isn’t
-Immune system becomes overactivated

355
Q

Activation of B-cells steps

A
  1. Exposed to correct antigen -> proliferation
  2. Plasma cells produce large amounts of antibodies
  3. Memory B-cells stay in lymph node for reexposure to same antigen
356
Q

Metastasis

A

Migration of cancer cells to distant tissues by the bloodstream or lymphatic system

357
Q

What inhibits pyruvate deH complex?

A

Accumulation of acetyl CoA and NADH

358
Q

Cytotoxic cells

A
  • Direct killing of virally infected cells by injecting toxic chemicals that promote apoptosis in infected cells
  • Respond to antigens presented on MHC I molecules
359
Q

How can colony with recombinant vector be multiplied?

A

Can ensure recombinant vector also has a gene for antibiotic resistance

  • Abx can be used to kill off all other colonies that don’t have recombinant vector
  • Resulting colony can then be grown in larger quantities
360
Q

What enzyme removes the primers?

A

Prok: DNA polymerase I
Euk: RNase H

361
Q

DNA ligase

A

Seals the ends of the DNA molecules together

-Creates one continuous strand of DNA

362
Q

Respiratory system mechanisms to prevent pathogens in the body

A
  • Respiratory passages lined with cilia to trap matter and push it up to oropharynx to be swalowed and expelled
  • Mucus prevents bacteria and viruses from accessing tissues below
363
Q

Complement system immune definition

A

Proteins in blood that act as nonspecific defense against bacteria
-Punches holes in bacterial cell walls -> makes them osmotically instable

364
Q

Trans gene

A

The altered gene introduced into the germ line of the mice

365
Q

Mast cells

A

Closely related to basophils but smaller granules

-Release large amounts of histamine in response to allergens

366
Q

Vitamin E function

A

H-phobic and antioxidants

-Destroys free radicals -> prevents oxidative damage

367
Q

How is glycogen synthase inactivated?

A

Protein kinase phosphorylates it

368
Q

Steps of TCA cycle in order

A
  1. Citrate Synthase: OAA + acetyl CoA -> citrate
  2. Aconitase: citrate -> isocitrate
    - Dehydration and rehydration
  3. Isocitrate DeH: Isocitrate -> alpha-ketoglutarate
    - Produces NADH & CO2
    - Rate-Limiting Enzyme
  4. Alpha ketoglutarate DeH: alpha-keto -> succinyl-CoA
    - Produces 2nd NADH & CO2
    - Similar to Pyruvate DeH complex
  5. Succinyl CoA Synthetase: Succinyl CoA -> succinate
    - Substrate Level phosphorylation: Produces GTP
    - Nucleosidediphosphate kinase GTP -> ATP
  6. Succinate DeH: Succinate -> Fumarate
    - Produces FADH2, located in IMM
  7. Fumarase: Fumarate -> L-Malate
    - Addition of H20 across double bond
  8. Malate DeH: L-Malate -> OAA
    - FInal NADH producing step
    - OAA ready for next turn of cycle
369
Q

Ion exchange chromatography

A

Beads in column attract/hold negatively charged protein as it passes through

370
Q

Micelles composition

A

Clusters of amphipathic lipids that are soluble in aqueous environment of intestinal lumen

  • Water solube sphere exterior
  • Lipid soluble exterior
371
Q

Function of micelles

A

Digestion, transport, absorption of lipid soluble substances in small intestine
-Diffuse to brush border of intestinal mucosal cells where they are absorbed

372
Q

Where do lipids go after being absorbed by intestinal mucosal cells

A

They are re-esterified to form TAGS and cholesteryl esters

-Packaged into chylomicrons and leave intestine via lacteals

373
Q

Lipase function

A

Hydrolyzes TAGS into fatty acids and glycerols

374
Q

Lipase hormone control

A

Activated by dec insulin, inc epi or inc cortisol

375
Q

What do digested TAGS get converted into

A

They are released as fatty acids

376
Q

How are free fatty acids transported through blood

A

When associated with albumin

-Transported as lipoproteins

377
Q

Components of lipoproteins

A

Apolipoproteins + Lipids

378
Q

Ratios of lipoproteins from least to most dense

A 
Chylomicrons are least dense
-VLDL
-IDL
LDL
HDL
379
Q

What does density of lipoproteins mean

A

Density of proteins

Low density = high fat to protein ratio

380
Q

What lipoproteins carry TAGS

A

VLDLs and chylomicrons

381
Q

What liporoteins carry cholesterol

A

LDLs and HDLs

382
Q

Function of chylomicrons

A

TAGs, and cholesterol from intestine to tissues

383
Q

Function of VLDLs

A

Transport TAGS and fatty acids from liver to tissues

384
Q

Function of ILDLs

A

Pickup cholesteryl esters from HDL to become LDL

385
Q

Function of LDLs

A

Delivers cholesterol to the cells

386
Q

Function of HDLs

A

Pick up cholesterol from tissues and return it to liver and steroidogenic tissues
-Transports apolipoproteins to other lipoproteins

387
Q

How do apolipoproteins become lipoproteins

A

Combine to make lipoproteins

388
Q

Cholesterol formed by what type of synthesis

A

De Novo Synthesis in liver

-Formed from acetyl-CoA and ATP

389
Q

Function of citrate shuttle

A

Carries mitochondrial acetyl-CoA to cytoplasm

390
Q

What is the rate limiting step in cholesterol biosynthesis

A

Synthesis of mevalonic acid by HMG-CoA reducatse

391
Q

Lecithin-Cholesterol Acyltransferase (LCAt)

A

Adds a fatty acid to cholesterol and produces soluble cholesteryl esters

392
Q

Fatty acid function

A

Used for uel and can be converted to TAGS to be stored as enegy

393
Q

Steps of Fatty acid synthesis

A
  1. Attachment to an acyl carrier protein
  2. Bond formation between malonyl-CoA and growing chain
  3. Reduction of Carbonyl group
  4. Dehydration
  5. Reduction of double bond
394
Q

What enzyme comlex is used to create fatty acids

A

Fatty acid synthase

-Multienzyme complex in the cytosol

395
Q

What cofactors are used in fatty acid synthesis

A

NADPH reduces the acetyl groups added to the fatty acid

-Needs B5 for the acyl carrier protein

396
Q

Structure of TAGs

A

Three fatty acids attached to glycerol

-Packaged into VLDLs and LDLs to transport to tissues

397
Q

Where does beta oxidation occur

A

In mitochondria and peroxisomes

398
Q

Beta oxidation function

A

Converts fatty acids into acetyl CoA and reduced carrier proteins (NADH, FADH2)

399
Q

Function of acetly CoA in liver

A

Stimulates gluconeogenesis by activating pyruvate carboxylase

400
Q

Steps of beta oxidation

A
  1. Oxidation of fatty acid to form a double bond
  2. Hydration of double bond to form hydroxyl group
  3. Oxidation of hydroxyl group to form a carbonyl
  4. Splitting of beta ketoacid into shorter acyl-CoA and one Acetyl CoA
401
Q

What happens after the 4 steps of beta oxidation

A

The chain conitnues to be shortened by those 4 steps repeating by two Cs each time

402
Q

What type of fatty acids undergo beta oxidation

A

Even numbered fatty acids usually

403
Q

Products of beta oxidation for even numbered fatty acids

A

Two acetyl CoA

404
Q

Products of beta oxidation for odd numbered fatty acids

A

One acetyl-CoA and one propionyl coA for each cycle

405
Q

How is propionyl-CoA used

A

Converted to metyl-malonyl-CoA by propionyl-CoA carboxylase

-Methyl malonyl-CoA converted to succinyl-CoA which enters TCA cycle

406
Q

How are unsaturated fatty acids converted to Acetyl-CoA during beta oxidation

A

Must first be converted to saturated fatty acids

407
Q

What does body do while fasting

A

It converts excess acetyl-CoA from beta oxidation into ketone bodies

408
Q

What does the body do in excessive fasting

A

Brain runs out of glucose energy and starts to metabolize ketone bodies

409
Q

Ketogenesis def

A

In mitochondria

-During excess acetyl-CoA in liver

410
Q

Ketolysis def

A

Acetoacetate oxidized to Acetoacetyl-CoA

411
Q

Under even more deprivation than excessive fasting what does body use for energy

A

Proteins are broken down via proteolysis in the stomach by pepsin

412
Q

How does proteolysis continue in the pancreas

A

Trypsin, chymotrypsin, carboxypeptidases A and B break it down

413
Q

How does proteolysis continue in the small intestine

A

Brush border enzymes like dipeptidase and aminopeptidase break it down

414
Q

End product of proteolysis

A

Energy and amino acids and di/tripeptides

415
Q

Where do the amino acids go after proteolysis

A

Absorbed through luminal membrane via secondary transport

416
Q

How are amino acids used for energy after proteolysis

A

Lose their amino group via transamination or deamination

-Remaining Carbon skeleton for energy

417
Q

Which aa’s are glucogenic

A

All aa’s except for Lys and Leu

418
Q

Which aa’s are ketogenic

A

Ile, Phe, Thr, Tyr, Trp, Lys, Leu

419
Q

Which aa’s are both gluco and ketogenic

A

Trp, Ile, Phe, Tyr, Thr

420
Q

Function of glucogenic aa’s

A

Can be converted into glucose in gluconeogensis

421
Q

Function of ketogenic aa’s

A

Can be converted into Acetyl-CoA andd ketone bodies

422
Q

How are amino groups removed from the body following transamination and deamination

A

Via the urea cycle in the liver

MCAT (12 decks)

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