Cell Biology Flashcards
1
Q
Acidic Amino Acids
A
Asp and Glu
2
Q
Basic Amino Acids
A
Lys, Arg, and His
3
Q
Amino Acids
A
Only L-aa in natural proteins
aa are modified to change effects
4
Q
Isoelectric Point
A
pI = [pKa1 + pKa2]/2
Used for electrophoresis
5
Q
Proteins
A
aa’s linked by peptide bonds
Synthesis requires a lot of energy
Cysteine residues form disulfide bonds (cystine)
Have primary, secondary, tertiary, and quaternary structure
Primary structure is sole determinant of folding
6
Q
Beta Sheets
A
H bonding btw CO and NH groups on different chains
Either parallel or anti-parallel (anti make a Beta turn)
7
Q
Carbohydrates
A
Aldehyde or ketone group Named off glyceraldehyde 2^n stereoisomers (n= chiral centers) D-isomer - OH group to the right L-isomer - OH group to the left Non-reducing carbs have an hemiacetal bonded forming an acetal
8
Q
Anomers
A
Differ only at C1
Alpha - OH group is opposite CH2OH group
Beta - OH group is cis w/ CH2OH group
9
Q
Fatty Acids
A
Saturated - all carbons full complement of H’s
-Low melting temperature
Unsaturated - contains double bonds btw carbons
-Higher melting temperature
Usually found in triglycerides (glycerol and three fatty acids)
10
Q
Glycerophospholipids
A
Lipid component of membranes
Nonpolar tails/polar heads
Composed of glycerol, two fatty acids, and a phosphate
11
Q
Sphingolipids
A
Composed of sphingosine backbone
One fatty acid and one sugar
12
Q
Cholesterol
A
Synthesized in cytosol
Membrane constituent
Used to make steroids in mitochondria
13
Q
DNA
A
Composed of deoxyribose, nitrogenous base, and phosphoric acid
A/G - purines
T/C - pyrimidines
Phosphoric acid gives (-) charge making backbone polar
Runs anti-parallel 5’ –> 3’
14
Q
RNA
A
Composed of ribose, nitrogenous base, and phosphoric acid
A/U/G/C
Phosphoric acid gives (-) charge making backbone polar
Either mRNA, tRNA, rRNA
Can have enzymatic activity
15
Q
Phosphoric Acid
A
Used to help buffer pH
H3PO4 H2PO4- + H+ HPO4 2- + H+ PO4 3- + H+
16
Q
Eukaryotic Cells
A
Nucleus holds genetic info
Chromatin - Found in interphase, linear dsDNA and histone
Chromosomes - condensed chromatin in prep for cell division
17
Q
Human cells
A
23 chromosomes
Diploid cells have 46 (23 pairs)
Metaphase is best time to view chromosomes
18
Q
Histones
A
Basic proteins ( (+) charged) that bind to DNA backbone ( (-) charge)
H1, H2a, H2b, H3 and H4 subunits
-These associate to form a nucleosome
Nucleosome repeats every ~200 bp
Linker histone binds btw nucleosomes
Core histone (H2a, H2b, H3, H4) bind 1.75 turns of DNA
19
Q
Cell Cycle
A
The major stages:
1) Interphase (G1, S, G2)
2) Mitosis: Prophase, metaphase, anaphase, telophase
3) Cytokinesis (partitioning of cell contents)
20
Q
Interphase
A
G1: RNA and proteins synthesized
-centriole pair separates in prep for synthesis
-Cells that don’t divide stay here
S: chromatin is replicated
G2: chromatin begins to condense, cell prepares for mitosis
21
Q
Prophase
A
Centrioles begin to move apart
Microtubules radiate from each pair forming aster
Chromatin is completely condensed
Microtubules attach at kinetochore
Nucleolus disappears and nuclear membrane breaks down
22
Q
Metaphase
A
Chromosomes align on equator of cell (metaphase plate)
Nuclear membrane has completely disappeared
23
Q
Anaphase
A
Centromeres divide and sister chromatids are now daughter chromosomes (now 92 chromosomes, 46 to one side, 46 to the other)
Movement by microtubule depolymerization at kinetochore
24
Q
Telophase
A
Daughter chromosomes reach poles -Begin to uncoil Microtubules disappear Nuclear membrane reforms, nucleolus reappears Cleave furrow forms
25
Cytokinesis
Cytoplasmic division of cell into two daughter cells
| Begins during anaphase
26
Meiosis
Formation of gametes by two nuclear divisions
Meiosis I (prophase I, metaphase I, anaphase I, telophase I)
-Results in two haploid cells
-Crossing over occurs in prophase I
Meiosis II (prophase II, metaphase II, anaphase II, telophase II)
-Results in 4 haploid cells (23 chromosomes)
27
Lipid Structure
Form either bilayers, liposomes, or micelles
Micelles - spherical structures formed when phopholipids congregate so polar heads interact w/ water and hydrophobic tails exclude water
Bilayers - Stabilized by H bonding and van der waals
-form liposome when it folds in on itself to form aqueous hollow center
28
Membrane Proteins
Integral - embedded in bilayer
- Transmembrane - span the bilayer
- Peripheral - attached to just one side
29
Glycolipids
Membrane proteins attached to a carbohydrate
| -Carb is found on exterior surface
30
Glycoproteins
Membrane protein attach to carbohydrate
31
Simple diffusion
Spontaneous movement of solute through lipid bilayer from high to low concentration
-Hydrophobic and small molecules diffuse quickly
32
Facilitated Diffusion
Solute travels down a concentration gradient
Diffusion depends on interaction w/ transmembrane protein
Uniport - one solute passes down gradient
Symport - two solute pass in same direction
Antiport - two solutes pass in opposite directions
33
Primary Active Transport
Uses ATP
ex: Na+-K+ ATPase
- maintains [Na+] and [K+]
- Pumps 2 K+ in and 3 Na+ out against concentration gradient
ex: Ca 2+ ATPase
- Ensures low [Ca 2+] in cell
- pumps two Ca 2+ out of cell for every ATP
34
Secondary Active Transport
Uses ionic gradients to provide driving force of cotransport of another molecule against its concentration gradient
ex: cotransport of Na+ w/ glucose in kidney cells
- protein binds Na+ and glucose, uses Na+'s travel down a concentration gradient
35
Bulk Transport
Endocytosis - form vesicles that contain part of ECM
-Pinocytosis - contains liquid of env.
-Phagocytosis - contains particulate matter
Exocytosis - Release of material
36
Nucleus
Double membrane bound
Holds genetic info
Perinuclear space - btw inner and outer membrane
Replication and transcription occurs in nucleus
Pores allow flow of material from cytoplasm
37
Nucleolus
Within the nucleus
Centered around parts of chromosomes that synthesize rRNA
Larger if cells is actively synthesizing proteins
38
Ribosomes
Sites of protein synthesis
Composed of 40S and 60S subunits (euk)
Found in ER
39
Endoplasmic Reticulum
Network of membranes in cytoplasm
Smooth ER - Involved in lipid synthesis
-Does hydroxylation rxns that detoxify drugs
-Helps catabolize glycogen
Rough ER - Ribosomes are bound here
-Synthesize membrane and secretory proteins
-Modification happens in lumen
40
Golgi Apparatus
Protein from Rough ER are transported by vesicles to golgi
Cis face - faces nucleus and ER
Trans face - faces plasma membrane
Proteins travel cis --> trans
41
Lysosomes
Has low pH (due to ATPase pump)
Has phosphatases
Include many hydrolytic enzymes
42
Peroxisomes
Hold catalse
| Degrade H2O2
43
Mitochondria
Not found in red blood cells
Double membrane
-Outer is permeable; inner is impermeable
Matrix hosts biochemical rxns
44
Microtubules
Made of tubulin
| Grow from organizing centers (centrosome, kenetochores, centrioles)
45
Microfilaments
Made of actin
46
Prokaryotic Cells
```
Lack membrane bound organelles
Ribosomes found in cytoplasm (30S and 50S)
No nucleus
Circular dsDNA, can have plasmids
Cell wall is G+ or G-
Flagella move by propeller motion
```
47
Conjugation
Exchange of DNA by cell to cell contact
Donore - F+, recipient F-
Pass on copy of plasmid to recipient
48
Transformation
Uptake of genetic info from surrounding env.
49
Transduction
Transfer of genes by viruses
50
Viruses
Obligate intracellular parasites
Capsomers are proteins that form capsid
Enveloped viruses - surrounded by lipid membrane
51
Virus Genome
Can be DNA or RNA
-must convert to mRNA to make proteins
(+) strand - mRNA that can synthesize proteins
(-) strand - complimentary to mRNA
52
Catalysts
Changes transition state to lower energy
Does NOT alter equilibrium
Changes rate of reaction
53
Transition State Analogs
Synthetic structures that look like transition state and therefore impede rxn
54
Michaelis Menten
Enzymes have active sites where a substrate binds
E + S ES --> E + P
-If [S] is small, then v is directly proportional to [S]
-If [S] is large, then v is independent of [S]
v = v_max*[S]/([S] + Km)
High Km - weak binding of ES
Low Km - strong binding of ES
55
Lineweaver Burk
Plot of 1/v and 1/[S]
1/v = (Km/v_max)(1/[S]) + 1/v_max
y-int = 1/v_max
56
Competitive Inhibition
Molecule resembles normal substrate and binds at active site (forms EI, not ES)
Decreases catalysis rate
Can be overcome by increasing [S]
Increases Km, but maintains v_max
57
Noncompetitive Inhibition
Bind at a site other than the active site
Allows conformation to inhibit catalysis
Cannot be overcome by increasing [S]
Lower v_max, same Km
58
Chymotrypsin Mechanics
Catalyzes hydrolysis of either ester of peptice bond
Uses catalytic triad: His, Ser, Asp
His take proton from Ser, making Ser very reactive
Ser is a nucleophile and passes e-'s to carbonyl
Forms unstable tetrahedral TS
-Causes cleaved amine LG
Water enters to deacylate intermediate
His donates H+ to Ser (resets enzyme) and carbonyl end of peptide is released
59
Enzyme Precursors
Enzymes initially synthesized as proenzymes or zymogens
Zymogens - inactive precursor of active enzyme
-undergo proteolytic activation (irreversible)
60
Cofactors
Substances other than aa that are needed for an enzyme to function
ex: NAD
61
Glycolysis
Occurs in cell cytoplasm
Produces 2 net ATP, 2 pyruvate, 2 NADH
Starts w/ phosphorylation by Hexokinase to keep glucose in cell
Regulation occurs at irreversible reactions: hexokinase, phosphofructokinase, pyruvate kinase
High ATP and high [H+} (low pH) allosterically inhibits phosphofructokinase
High citrate levels inhibit phosphofructokinase
High AMP levels stimulate phosphofructokinase
62
Fructose Metabolism
Fructose is phosphorylated by fructokinase and then enter glycolysis
63
Galactose Metabolism
Galactose is converted to glucose-6-P and enter glycolysis
64
Pyruvate Decarboxylation
Pyruvate is converted to Acetyl-CoA by pyruvate dehydrogenase complex
- TPP adss carbonyl function to pyruvate causing decarboxylation
- Transferred to lipoamide to form acetyl-lipoamide
- Transferred to CoA to form Acetyl CoA
- Resetting the complex creates an NADH
65
Citric Acid Cycle
Acetyl-CoA is oxidized to create reduced e- carriers and CO2
Acetyl CoA is added to oxaloacetate (6C) which is then decarboxylated to reform oxaloacetate (4C)
Per pyruvate: 3 NADH, 1 FADH2, 1 GTP, 2 CO2
66
Electron Transport
NADH and FADH2 are oxidized causing e-'s to pass btw membrane carriers ad forming a proton gradient across inner mit. membrane
Intermembrane space has high [H+] (low pH), and matrix has low [H+] (high pH)
67
Oxidative Phosphorylation
Proton gradient provide energy for ATP synthase to phosphorylate ADP to ATP
NADH: 3 ATP
FADH2: 2 ATP
Can only function w/ O2 present
68
Glycerol Phosphate Shuttle
Shuttle cytoplasmic NADH into mitochondrial matrix
| Lose one ATP in process, therefore one cytoplasmic NADH only produces 2 ATP
69
Malate-Aspartate Shuttle
Shuttle cytoplasmic NADH into mitochondrial matrix
| No loss of ATP, therefore one cytoplasmic NADH produces 3 ATP
70
Pentose Phosphate Pathway
Creates ribose-5-P (5C sugar used for nucleotide synthesis) and NADPH (reducing power)
Starts w/ glucose-6-P
Phase 1 produces NADPH and ribulose-5-P
Phase 2 generates 6C and 3C sugars to be put back into glycolysis
71
Toxic Oxygen
Superoxide Dismutase catalyzes conversion of superoxide into H2O2 and O2
Catalase catalyzes H2O2 into O2 and H2O
72
Gluconeogenesis
Occurs in liver to convert non-carbohydrate precursors into glucose (lactate, alanine, glycerol)
Animals cannot make glucose out of 2C segments
If NADH/NAD+ is low, favor lactate --> pyruvate
Pyruvate is converted to oxaloacetate and then PEP to go around irreversible step of glycolysis (costs 2 ATP)
73
Fatty Acid Oxidation
Fats can only be broken down by ox-phos
Triglycerides are hydrolyzed by lipases to glycerol and 3 fatty acids
Fatty acids are converted to acetyl CoA, degraded 2C at a time by Beta-Oxidation.
-2C fragments are activated releasing one FADH2 and one NADH to make acetyl CoA which then enters Krebs cycle
Glycerol is also converted to acetyl CoA
74
Urea Cycle
Proteins can be broken back down into aa's
Phase 1: aa degradation to alpha-keto acid
-Amino transfer to alpha-ketoglutarate (makes glutamate and alpha-keto acid)
-Glutamate is oxidatively deaminated (makes NADH and releases NH4+)
Phase 2: some aa's provide carbon skeleton for gluconeogenesis, some are degraded to acetyl CoA (gives ketone bodies)
75
Law of Segregation
Proposed by Gregor Mendel
| States: alternative alleles segregate from each other in heterozygous individuals and retain their identity
76
Law of Independent Assortment
Segregation of one gene pair is independent of other gene pairs
77
Auxotroph
Mutant that only grows in a supplemented medium
78
Pedigree
An individual w/ dominant genetic trait will have one parent who is affected
An autosomal disease affects both genders
Recessive disease often skips generation
79
Central Dogma
DNA RNA --> Protein
| DNA and RNA can reproduce themselves
80
DNA Melting Temperature
A=T bonds denature first due to less H-bonding
| The more GC bonds the higher the melting temperature
81
DNA Synthesis
Replicated semi-conservatively
Goes 5' --> 3'
DNA pol I
-Has exonuclease to remove RNA primer and close gap
Primer added by primase (RNA) is needed to start replication
DNA replication begins at origin site, unwound by enzymes, kept open by single stranded binding protein
Both strands serve as templates
Leading and lagging strands develop (lagging has Okazaki fragments)
DNA pol III is more processive and does most synthesis
Ligase joins gaps caused by primer
82
RNA Synthesis
RNA polymerase TRANSCRIBES DNA into RNA
Synthesizes 5' --> 3'
Does not need a primer
83
Prokaryotic RNA Synthesis
One bacteria RNA pol
Specific starting spots (TATAAT (pribnow box) at -10; and -35 region)
Termination at terminator sequences (GC rich regions followed by AT rich regions)
Rho-Independent: hairpin after a sequence of U's pulls RNA off DNA
Rho-dependent: uses rho protein
84
Eukaryotic RNA Synthesis
1) Initiation; 2) Elongation; 3) Termination
Synthesizes 5' --> 3' (pol moves 3' --> 5')
Have promoters and enhancer sequences
-enhancers help stimulate transcription
-can be upstream, in the gene, or downstream
85
Eukaryotic RNA Polymerases
rRNA - RNA pol I
mRNA - RNA pol II
tRNA - RNA pol III
Polymerase lacks editing function and no repair system, therefore more erros
86
Transcription Modifications
```
5' Capping
-5' end can easily be degraded in cell, therefore its modified w/ GTP and methyl group
3' Poly A Tail
-About 200 A's are added to 3' end
-Protests 3' end from degradation
Splicing
-euks splice out introns
-snRNP's involved in bp rxns
-Some RNA is self splicing
```
87
Protein Synthesis
1) Initiation; 2) Elongation; 3) Termination
RNA is TRANSLATED to a peptide chain
aa's are brought to ribosome by tRNA
Synthesized from amino end to carboxyl end
Translation is from 5' --> 3'
Need aminoacyl-tRNA, mRNA, ribosomes, initiation factors, and GTP
88
Prokaryotic Protein Synthesis
Initiation: 16S (part of 30S) binds at Shine-Delgarno sequence
-GTP binds w/ 50S; forms 70S for translation
Elongation: next aminoacyl-tRNA attaches to A-site
-Peptidyl transferase form a peptide bond btw aa's
-old tRNA leaves P site, mRNO moves and new aa enters P site (translocation); A site is now empty
Termination: stop codon enters A site
-Protein release factor recognizes and peptide chain is released
89
Protein Synthesis Energetics
Each aa activation costs 2 ATP
Binding of aminoacyl-tRNA costs 1 ATP
After first aa, each one costs 1 ATP per translocation
90
Lac Operon
Allows switch btw sugars used for glycolysis
W/o lactose, operon should be off
-Repressor protein is made and freely binds to operator to stop transcription
W/ lactose operon should be on
-Lactose binds repressor and prevents repressor from binding to operator
-Allows RNA pol to transcribe lac operon
91
Catabolite Represson
Bacteria prefer glucose for energy
CAP protein binds to DNA and mediates catabolite repression
-Can only bind if cAMP presen; cAMP is high when glucose is low
CAP-cAMP complex is an activator that activates lac operon
92
Constitutive Mutant
Genes of lac operon always synthesize
| Repressor gene has been mutated, so repressor doesn't work
93
Operator Constitutive Mutants
Mutation in operation gene, allows for continual transcription
94
Trp Operon
Trp acts as corepressor
-If high [trp], then repressor binds trp and binds operator; operon OFF
-if low [trp], then repressor cannot bind to operator; operon ON
Four GC rich regions in operon and can hairpin together
-if high [trp] then 1=2 and pol pauses and 3=4, which causes early termination. No trp made
-if low [trp] then ribosome pauses on 1 and 2=3 and transcription is not terminated. trp made
95
Wobble Rules
1) U can pair w/ A or G
2) G can pair w/ C or U
3) I can pair w/ A,U, or C
96
Point Mutation
One nucleotide is substituted for another
| Silent mutation if aa sequence doesn't change
97
Frameshift Mutation
Insertions or deleation shift reading frame
98
Deamination Mutation
Cytosine can lose an amine to become a U
- Cell can recognize U and remove it (gives apurinic site)
- Fixed by DNA pol I
99
Mismatch Repair
Tautomerism and slippage during replication
- Causes a bulge in DNA
- Mismatch repair enzyme finds bulge and fixes new base
- Detects new base by methylation on old strand at GATC (new DNA hasn't been methylated yet)
100
Mutagens
External agents that cause or increase mutations
Base analog - subbed for a natureal base
Chemical - causes deamination to be more likely
UV radiation - cause Thymine dimers
Intercalators - slip btw adjacent bases in DNA molecules
101
Ames Test
Uses his- organisms (can't make histadine)
The transition point mutation can be reverted back to his+
Ames tests adds mutagens to determine rate of back mutation
-Need to use only a little mutagen to cause only a small # of mutations
102
Restriction Enzymes
Recognize specific DNA sequences and cleaves
| -Doesn't cut own DNA b/c of methylations
103
Sanger DNA sequencing
Uses ddNTP which inhibit DNA pol I
1) Select DNA strand
- add dNTP's, polymerase, and ddNTP, and primer
2) DNA pol will add dNTP's
- Stops when ddNTP is added
3) Spearate by size on a polyacrilic gel
