Cell and Molecular Biology

EXAM I

Similarities between Pro and Euk

DNA codes
Protein synthesis
Photosynthesis
ATP

Differences in Euk

Bound nucles and organelles
Many linear chromosomes
Cytoskeleton
Large size

Endosymbiotic Theory

Bacteria cell ate another one and became mitochondria and chloroplast proven by double membrane, DNA, size

Function of Nucleus

assembles ribosomes
rRNA
transcription processing

2 things formed by basal body

1) primary cilium
2) flagellum

Differences in Pro

No nucleus
1 Circular Chromosome
No bound organelles
Cytoskeleton
Small size

Protein for transporting IN to nucleus

importins and RanGTP

Import of proteins and RNA through nuclear pore complex by

Nuclear Localization Signal tags proteins for importins

Progeria

disease from mutation in lamina proteins

The Internal Signaling seq. will

1) Synthesized by ER
2) Goes to Golgi for modification and sorting
3) Secreted by vesicles

Catalyzes disulfide bond formation

Protein disulfide isomerase (PDI)

pH of Lysosome

acidic, 5

Determines proteins final designation after synthesis

Own unique signal sequence

3 Pathways that deliver material to lysosome

1) endocytosis
2) autophagy
3) phagocytosis

Stored energy is converted to ATP by

1) ATP synthase
2) F0 spinds F1
3) H+ rotates F1 and cause ADP -> ATP

2 types of actin bundles

1) close spaced parallel bundles
2) loose spaced contractile bundles

4 types of Euk

Protists=algae, Fungi=mushrooms, Plant cells=chloroplast, Animal cells= mitochondria

Function of Ribosomes

Synthesize proteins by translating mRNA

Protein for transporting OUT of nucleus

exportins and RanGTP

Function of Importins

Recognize NLS seq.
Take protein to nuclear pore

Function of Nuclear Lamina

Structural support
Anchors chromatin and organizes

Function of Exportins

Recognize NES seq.
Take protein to nuclear pore

Function of RanGTP

Bind to importin/exportins and releases complex bc of hydrolysis of GTP

Function of Nuclear Pore Complex

Allows passing through Nucleus of small polar molecules, ions, proteins and RNAs

Nuclear Pore Complex Regulates Transportation on
1) small polar molecules & ions
2) proteins & RNA

1) Freely diffuse
2) energy dependent in single direction

Export of proteins and RNA through nuclear pore complex by

Nuclear Exportation Signal tags proteins for exportins

RNA is transported through the nucleus as

RNA proteins complex or ribonucleoprotein

Heterochromatin is

Condensed genes
Not actively transcribed
Interacts with nuclear lamina

Euchromatin is

Decondensed gene
Actively transcribed
Interacts with nuclear pore

Composition of Nuclear Lamina

Type V intermediate filament proteins
A-type lamins
B-type lamins

Function of Rough ER

Process proteins

Function of Smooth ER

Metabolize lipids

Specific Signal Sequence

Determines if proteins is translated by ER bound or free ribosomes

ER bound ribosome synthesized proteins go to

1) Golgi
2) PM
3) Secretory vesicles
4) endosome -> lysosome

Free ribosome synthesized proteins go to

1) cytoplasm
2) nucleus
3) mitochondria
4) chloroplasts
5) peroxisomes

Proteins targeted to ER

1) N-terminal seq. recognized and attaches to receptor binding site, and SRP is released
2) Ribosome binds to translocon, signal seq. inserted into translocon

Seq. to determine
1) ER liminal protein
2) ER membrane protein

1) stop-transfer seq.
2) internal signal seq.

The ER N-terminal sequence will

initiate protein translocation & is cleaved off

The Stop-transfer seq. will

stop transfer & become transmembrane protein

Diseases from dislocation proteins

Primary hyperoxaluria
Cystic Fibrosis

Protein modification in ER can include

1) Cleavage
2) Glycosylation
3) Lipid attachment

Catalyzes ER N-terminal signal seq. cleavage

Signal peptidase

Proteins needed for folding

chaperone proteins

Protein disulfide isomerase (PDI) only functions in the

ER bc of oxidizing environment

What is glycosylation

Adding carbohydrate to protein

Location where additional protein modification like glycosylation occur

Golgi

Pulse Chase Experiment

Radioactive amino acids used
Rough ER -> Golgi -> vesicles -> PM

Function of the Golgi

Modifies and sorts proteins

Function of Lysosomes

Degrade intracellular material

Special modification in Golgi to send proteins to lysosome

Mannose 6-phosphate (M6P)

Proteins in the lysosome

Hydrolases

3 types of transport vesicles

1) clathrin-coated
2) COPI-coated
3) COPII-coated

v-snare proteins are

vesicle SNAREs on vesicle membrane surface

t-snare proteins are

target SNAREs on target membrane surface

Transport Vesicles Formed by

1) assembly
2) disassembly
3) vesicle docking
4) disassembly

Lysosomes are formed by

1) PM engulfs material outside makes endosome
2) matures to late endoscope as early fuses together
3) acidic hydrolyses in transport vesicle from Golgi

Endocytosis is

Material engulfed outside of cell

Autophagy is

Recycled parts of cell form autophagasome and fuse with lysosome for rejuvenation

Phagocytosis is

swallow large particles; macrophages + neutrophils

Lysosomal Storage Disease is

Build up of undegraded material bc of incorrect target of proteins

Structure of mitochondria

Double membrane
Circular + small genome
Dynamic

Peroxisomes are regenerated by

1) division
2) de novo biogenesis

Mitochondrial vs Nuclear genome

1) circular vs linear genome
2) many vs one copies
3) lacks vs has histone
4) few vs many non-coding DNA
5) 1 protein vs many proteins per mRNA
6) specific vs universal codon pattern

Mitochondrial proteins are encoded by

mostly nuclear genome and some of own

Proteins in mitochondrial matrix

Presequence, Tom complex, Tim complex, Stop-transfer sequence

Name for the insertion of mitochondrial genome into nuclear genome

Polymorphic Nuclear Mitochondrial Insertion (NumtS)

3 Functions of Mitochondria

1) Energy production
2) Cell death
3) Oxidative breakdown of carbs and fatty acids

Overall reaction of glucose oxidation

glucose + 6O2 -> 6CO2 + 6H2O

3 Steps of oxidative breakdown

1) glycolysis
2) pyruvate oxidation
3) Krebs cycle

Glycolysis 1) occurs in 2) inputs 3) outputs 4) produces this in anaerobic conditions

1) cytosol
2) glucose
3) 2 pyruvate, 2 NADH, 2 ATP
4) lactic acid

Pyruvate oxidation 1) occurs in 2) inputs 3) outputs

1) mitochondrial matrix
2) 2 pyruvate
3) 2 acetyl-CoA, 2 NADH, 2 CO2, 2 H+

Pyruvate Oxidation

1) occurs in 2) inputs 3) outputs

1) mitochondrial matrix
2) 2 pyruvate
3) 2 acetyl-CoA, 2 NADH, 2 CO2, 2 H+

Krebs cycle 1) occurs in 2) inputs 3) outputs

1) mitochondrial matrix
2) 2 acetyl-CoA
3) 2 CO2, 3 NADH, FADH2, ATP, CoA-SH

Equation for oxidative breakdown of glucose

Glucose -> 6 CO2 + 10 NADH + 2 FADH2 + 4 ATP

The election transport chain (ETC) is

Energy released by electron transfer from NADH and FADH2 to O2, drives synthesis of ATP from ADP

Donates elections to ETC complex

NADH and FADH2

Receives electrons in ETC complex

O2

ETC generates energy by

1) Proton gradient on inner membrane of mitochondria
2) High [H+] in intermembrane
3) Low [H+] in matrix

Number of ATP generated by 1 NADH in ETC

3 ATP

Number of ATP generated by 1 FADH2 in ETC

2 ATP

Number of ATP generated by 1 acetyl-CoA in Krebs cycle

12 ATP

Location for oxidative breakdown of fatty acids

Mitochondria

Proteins targeted to peroxisome

1) PS1
2) PS2

Function of Peroxisome

1) Oxidative reactions
2) lipid biosynthesis; plasmalogens

Peroxisomes oxidize what

FA, AA, UA, decomposes H2O2

Defects leading to peroxisome disorder

Mistargeting
Loss of function

Examples of Peroxisomal mutations

1) X-ALD
2) kidney stones

3 types of Mitochondrial Mutations

1) Point mutations
2) Deletion
3) DNA depletions

Structural characteristics of PM

Lipids & proteins
Asymmetrical lipids
Fixed proteins
Flipping lipids

3 types of lipids in lipid bilayer

1) phospholipid
2) cholesterol
3) glycolipids

2 types of proteins in lipid bilayer

1) integral proteins
2) peripheral proteins

Function of lipid bilayer in PM

Cell signaling
Stable barrier

Function of proteins in PM

Selective transporting of molecules

Purpose of Cholesterol in PM

Regulates membrane fluidity

Purpose of Glycolipids in PM

Cell recognition
Stability

A liposome is

artificial lipid bilayer in pharmx

Location of lipid synthesis

Smooth ER or Golgi

Catalyzes translocation of lipid on leaflet of PM

phospholipid bilayer

Glycocalyx is

Sugar residue on outer surface of cell included in recognition

Membrane molecules that contribute to glycocalyx

1) glycolipid
2) glycolipid-attached protein
3) glycoproteins