CMB Week 1 Flashcards
what is the function of the plasma membrane of cells?
- compartment separation - receptor sites and signal transduction -movement in and out of the cell through channels and carriers on the plasma membrane -cell to cell adhesion
The nucleus is composed of …
nuclear membrane, chromatin, nucleolus
what is the nuclear envelope?
double membrane of nucleus
What is the nucleolus?
site of rRNA transcription and ribosome subunit assembly
What is the purpose of the ribosome?
site of protein synthesis
what is glycosylation?
addition of glycans to proteins, lipids and other organic molecules
what is the function of the smooth ER?
lipid synthesis, glycogenolysis, detoxification, Calcium metabolism
What is the function of the rough endoplasmic reticulum?
contains enzymes for protein folding and glycosylation; membrane specialized for ribosome binding
What is glycogenolysis?
breakdown of glycogen to glucose-6-phosphate and smaller glycogen (n-1)
what is the function of the golgi apparatus?
- Glycosylation and deglycosylation of proteins and lipids - Assembly of proteoglycans - Phosphorylation and sulfation of proteoglycans and proteins - Transport of proteins and lipids from RER to lysosomes, secretory granules or plasma membrane
what is an endosome?
membrane bound compartment in eukaryotic cells, provides an environment for materials to be sorted before it reaches the degradative lysosome
what is the function of lysosomes?
cellular organelles that contain acid hydrolase enzymes that break down waste materials and cellular debris
What is the function of peroxisomes?
contains the enzyme catalase, which metabolizes hydrogen peroxide. Also contains enzymes for beta oxidation of long chain fatty acids
what is the primary function of the mitochondria?
production of ATP and cellular metabolism
What is the function of microtubules?
part of the cytoskeleton, functions - mechanical support, organization of the cytoplasm, transport, motility and chromosome segregation
What are microfilaments (actin filaments)?
thinnest filaments of the cytoskeleton, involved in cytokinesis, movement and changes in cell shape
What is the cytoskeleton?
a meshwork of protein filaments within the cytoplasm that is responsible for cell morphology and movement
What is the composition of microtubules?
Alpha and beta tubulins form a protofilament. 13 protofilaments align side by side in a circle to form a microtubule
what are intermediate filaments?
part of the cytoskeleton, involved in regulating cell shape
what is desmin?
intermediate filament found in muscle cells
What is vimentin?
intermediate filament found in mesenchymal cells
what is neurofilament protein?
intermediate filament found in neuronal cells
What is keratins?
intermediate filament found in epithelial cells
What is epithelium tissue?
lines or covers organ surfaces, regulates the transport of materials, forms glands
What are the four main types of tissue?
epithelium, connective, muscle and nerve
How are subtypes of epithelium tissue classified?
by the number of cell layers and the shape of the cells forming the epithelium
What are the functions of connective tissue?
forms skeletal structures (bone, cartilage, tendon and ligament) provides conduit for blood vessels and nerves provides attachment and support
What is the function of muscle tissue?
specializes in contraction
What are the three types of muscle tissue?
skeletal, cardiac, and smooth
What is the function of skeletal tissue?
attached to the skeleton for voluntary body movement
What is the function of smooth tissue?
responsible for autonomic visceral movement
What is the function of cardiac tissue?
muscle forming the walls of the heart chambers
What is the function of nerve tissue?
specialized for transmission of electrical signals which regulate brain function, muscle and gland activity
What are the two major cell types in nerve tissue?
neurons and glia
What is the function of neurons?
cells that generate and receive electrical signals
What is the function of glia cells?
provides metabolic and structural support to neurons
What is a globin fold motif?
protein motif with 8 alpha helices (A-H) in a specific 3D orientation
What is hemoglobin (Hb)?
a globular, tetrameric protein found primarily in red blood cells and functions to deliver O2 from lungs to peripheral tissues and eliminate CO2 and protons.
What is myoglobin?
globular protein found primarily in muscles that binds oxygen molecules delivered by Hb
What is heme?
an iron-chelated porphyrin prosthetic group found in hemoproteins
What is the principle type of heme found in oxygen binding proteins?
Heme B
What is the composition of heme B?
protoporphyrin IX (4-linked pyrrole groups) and a ferrous ion Fe2+
Which histidine molecule is replaced when O2 binds to the ferrous ion?
the distal Histidine
What is the composition of Hb?
two alpha type subunits and two beta type subunits
What are the alpha type subunits that can be found in Hb?
5’ - zeta - alpha2 - alpha1 - 3’
What are the beta type subunits that can be found in Hb?
5’ - epsilon - gamma G - gamma A - delta - beta - 3’
Which chromosome are the genes for alpha subunits of Hb localized on?
chromosome 16
Which chromosome are the genes for beta subunits of Hb localized on?
chromosome 11
What are the two types of Hb found in embryos?
Hb Gower-1 and Hb Portland
What is the chain composition of Hb Gower-1?
ζ2ε2
What is the chain composition of Hb Portland?
ζ2γ2
What is the chain composition of fetal Hb (HbF)?
α2γ2
What % of adult Hb is composed of HbF?
less than 1%
What is the composition of HbA1 (adult Hb)?
α2β2
What % of adult Hb is composed of HbA1?
98%
What is the composition of HbA2 (adult Hb)?
α2δ2
What % of adult Hb is composed of HbA2?
2%
Approximately how long after birth is HbF replaced with HbA?
12-18 weeks
What is the deoxygenated form of Hb and myoglobin called?
Tense state (T-state)
What is the oxygenated form of Hb and myoglobin called?
Relaxed (R-state)
What is the effect of 2,3-biphosphoglycerate (BPG) on Hb?
Increase quantities of BPG —> Increased affinity of Hb to BPG —> decreased affinity of Hb to O2 —>Hb releases O2 (right shift in curve)
What is the oxygen-binding curve for myoglobin?
Hyperbolic (simple dissociation)
What is the oxygen-binding curve for hemoglobin?
sigmoidal
What is the Bohr effect?
Decrease in pH (periphery -tissues) –> decreases Hb affinity for O2 —> Hb releases O2. Shifts the equilibrium to T-state (right shift in curve)
What is the mutation for sickle cell anemia?
HbS B6 (beta -6): glutamine to valine
what is the mutation for anemia (HbC)?
HbC (beta -6): glutamine to lysine
What is the mutation for mild anemia (HbE)?
HbE (beta 26): glutamine to lysine
What is the mutation for Hb M-Boston (methemoglobin)?
beta58 (histidine to tyrosine)
What is the mutation for Hb M-Saskatoon (methemoglobin)?
beta63 (histidine to tyrosine)
What is carbon monoxide poisoning?
Hb has very high affinity for CO —> CO binds Hb 200x stronger than O2, displacing the oxygen. Carboxyhemoglobin circulates in blood for an extended time without releasing the CO
What is the treatment for CO poisoning?
Using 100% oxygen to compete with the CO, reducing carboxyhemoglobin levels rapidly
What is collagen?
most abundant (fibrillar) protein in the human body, with 20 different types
Abnormal collagen synthesis or structure causes dysfunction of…
- cardiovascular organs - bone (fragile) - skin - joints (hyper mobility and arthritis) - eyes (dislocation go lens)
What is the amino acid composition of collagen type I?
33% glycine, 10-13% proline, 10% hydroxyproline (OH-Pro), and 1% hydroxylysine (OH-Lys)
What are the three enzymes that are required for post translational modification (hydroxylation) of Pro and Lys?
Lysyl hydroxylase Prolyl-4-hydroxylase Prolyl-3-hydroxylase
What is Prolyl-4-hydroxylase?
hydroxylates the proline in X-Pro-Gly to 4-OH-Pro
What is Prolyl-3-hydroxylase?
hydroxylates the proline in Hyp-Pro-Gly to 3-OH-Pro
What is a polyproline type II helix?
Secondary structure of collagen - each strand is a loose, left-handed helix, with three residues per turn
What is required in post translational modification of collagen?
Fe2+, oxygen, alpha-ketoglutarate, and ascorbic acid (Vit C)
pinocytosis
the non-specific ingestion of fluid and small molecules via small vesicles
phagocytosis
ingestions of large particles, cell debris, bacteria via pseudopodia
receptor mediated endocytosis
allows entry to specific molecules via receptors in the plasma membrane and clathrin coated pit/vesicles
methemoglobinemia
Mutations cannot bind O2, since the Fe2+ ion is oxidized to Fe3+
thallasemia
general term for an autosomal recessive disorder where one of the globin genes is not expressed properly, leading to anemia
What is the advantage of having glycine in collagen?
-small structure allows the formation of triplex - the 3 collagen chains are able to be packed tightly together
What helps stabilize the triplex of collagen (besides Gly)?
- Hydrogen bonds between the neighboring chains - Disulfide chain interactions
telopeptides
- N and C terminus segments in collagen triple helical region -site of cross linking
What are the steps in the biosynthesis of collagen inside the cell?
- Translation of alpha chains (two alpha-1 and one alpha-2 chains) on the ribosomes of the RER 2. Peptide chains sent to lumen of RER 3. Signal peptidase cleaves the signal peptides from end of preprocollagen –> procollagen 4. Hydroxylation of Pro and Lys 5. Glycosylation on specific hydroxylysines (helps stabilize the triple helix) 6. Intra and inter chain disulfide bond formation 7. Triple helical structure formed inside RER 8. Procollagen goes to the Golgi Apparatus, glycosylation is completed, and procollagen is secreted via exocytosis
preprocollagen
precursor peptide chains of collagen, with signal peptide that directs the chains to the ER
What are the steps in the biosynthesis of collagen outside of the cell?
- Registration peptides are cleaved from both end of the molecule by procollagen peptidase forming tropocollagen 2. multiple tropocollagen molecules self assemble into collagen fibrils, which form into collagen fibers 3. Maturation - intra and inter molecular cross-links of the tropocollagen
catalyzes the hydrolysis of collagen
collagenases - a matrix metalloproteinase (MMPs)
after hydrolysis of the collagen by collagenases, this enzyme finishes the degradation
gelatinases
What are the two major categories of collagen?
fibrillar and network-forming
Name the fibrillar type collagens
types I, II, III, V and XI
Name the network-forming collagen
type IV
Name the fibril-associated collagens
types IX and XII
What is scurvy?
nutritional condition cause by deficiency in vitamin C. very diverse symptoms
What is Ehler-Danlos Syndrome?
group of connective tissue disorders (10 types)
Describe type IV Ehler-Danlos Syndrome
- autosomal dominant mutation resulting in deficiency in type III collagen formation - symptoms: thin skin, easily ruptured arteries and internal viscera
Describe type VI Ehler-Danlos Syndrome
- autosomal recessive deficiency in lysyl hydroxylase - Symptoms: scoliosis, velvety skin, hypermobile joints, tendency towards ocular injuries
Describe type VII Ehler-Danlos Syndrome
- autosomal dominate mutation leads to an inability to remove the N terminal propeptide - Symptoms: hypermobile joint, prone to joint dislocations, soft skin
Describe type IX Ehler-Danlos Syndrome
- X-linked recessive deficiency in lysyl oxidase that results in decreased cross linking - could also be due to copper deficiency - Symptoms: hyper extensible skin, bladder diverticula, skeletal deformities
What is elastin?
- fibrillar protein that provides elasticity to tissue - fibrous and insoluble in H2O
Explain secondary structure in elastin
- lacks a secondary structure, has a coiled structure in which the amino acid residues are highly mobile
What is allysines?
modified lysine residues
enzyme that catalyze lysine to allysine
lysyle amino oxidase also lysyl oxidase
structure of elastin
3 allysines and an unmodified lysine from different regions of the polypeptide chain react to form the heterocyclic structure of desmosine and isodesmosine desmosines covalently cross-link the chains in elastin
what is needed for protein glycosylation?
-an activated sugar (UDP-glucose) - glycosyl transferase enzyme - acceptor protein
In protein glycosylation, how are sugars linked?
covalently through O-links: glycans attach to the hydroxyl oxygen (OH) on serine or threonine N-links: glycans are attached to the nitrogen on asparagine
In N-linked glycosylation, what is the composition of the sugar precursor being added?
14 sugar precursor contains 3 glucose, 9 mannose, and 2 N-acetylglucosamine molecules
dolichol
carrier molecule that is attached to the 14-sugar precursor in N-linked glycosylation, transfers the glycans to the asparagine
What are the two major saccharides from N-linked glycosylation
- high mannose oligos (two N-acetylglucosamines with many mannose residues) - complex oligos: contains any number of of types of saccharides
Inclusion (I)-cell disease
a lysosomal storage disease: defective phosphotransferase - enzyme that transfers phosphates to mannose residues on specific proteins, which serves as a marker for these proteins to be moved to the lysosome. Without the marker, the proteins are not transferred to the lysosome, without these proteins, the lysosome cannot degrade substances, leading to a buildup
gamma carboxyglutamic acid (Gla)
- glutamate side chain modified with addition of a second carboxyl group - found in clotting factors and other protein of the coagulation cascade - requires vitamin K
kinases
enzymes that phosphorylate proteins
phosphatases
enzymes that remove phosphates from proteins
in animal cells, which three amino acids are subject to phosphorylation
serine, threonine, and tyrosine
which amino acid has sulfate modification
tyrosine
proteasome
major mechanism for destruction of cellular proteins
Where is the proteasome located?
cytosol and nucleus
ubiquitin
before being recognized by the proteasome, proteins are tagged by ubiquitin, a small 76 amino acid protein
steps of ubiquitin process
1) ubiquitin-activating enzyme binds ubiquitin to the enzyme via a high energy (ATP) bond 2) this ubiquitin intermediate is transferred to the substrate protein by ubiquitin-conjugating enzymes 3) the ubiquitin is covalently attached to the amino group of an internal lysine of the protein, carried out by ubiquitin-protein ligases 4) ubiquinated proteins are recognized by the proteasome for degradation
disease states associated with the ubiquitin modification system
- defective ubiquitination in cancer result from defective growth promoting proteins - defection ubiquitination is associated with neurodegenerative diseases such as Alzheimer’s, Parkinson’s.
What is SUMO-ylation?
post-translational modification involved in - transcriptional modification - apoptosis - response to stress - progression through cell cycle
free energy of activation
available energy used to form the reaction intermediate
name the 6 functional classes of enzymes
- oxidoreductases 2. transferases 3. hydrolases 4. lyases 5. isomerases 6. ligases
oxidoreductases
act on many chemical groupings to add or remove hydrogen atoms
transferases
transfer functional groups between donor and acceptor molecules
lyases
Add water, ammonia or carbon dioxide across double bonds, or remove these elements to produce double bonds.
hydrolases
Add water across a bond, hydrolyzing it
isomerases
Carry out many kinds of isomerization (optical or geometric isomers): e.g. L to D isomerizations
ligases
Catalyze reactions in which two chemical groups are joined (or ligated) with the use of energy from ATP.
Klenow fragment
5’—>3’ exonuclease activity is located on a portion of the enzyme (30kDa) that can be separated from the larger portion of the enzyme (70kDa). The 70kDa fragment contains the 5’—>3’ polymerization and the 3’–>5’ exonuclease activity - this is the Klenow fragment
(Prokaryotes) Single-stranded DNA-binding proteins (SSB)
during replication, binds to the DNA to keep the two strands from annealing (keeps it open)
(Eukaryotes) Replication protein A (RPA)
during replication, binds to the DNA to keep the two strands from annealing (keeps it open)
Primosome
complex consisting of primases, ligases, helicases, and other proteins that bind to the Ori and are necessary to synthesize the primer
Replisome complex (OriC)
contains the primosome and other molecules like SSB, pol III and I that are necessary for DNA replication
replicons
In eukaryotic DNA replication, these are the segments between Oris
Modification of the primary transcript (precursor to mature RNA) includes:
- removal of both external and internal nucleotides by ribonucleases 2. base modification 3. addition of nucleotides
tRNA post-transcriptional modification
- 5’ end of tRNA is removed by ribonuclease P (a ribozyme) - 3’ end is removed, the terminal CCA (cytosine-cytosine-adenine) is synthesized - nucleotide bases are modified
mRNA post-transcriptional modification
- addition of a 3’ terminal poly A tail - addition of methylated internal nucleotides and the methylated inverted cap at the 5’ terminus -splicing
initial velocity (Vo)
measured at the very beginning of an enzyme reaction when very little product has been made
steady state
point at which the enzyme-substrate (ES) intermediate remains constant
Assumptions for the Michaelis-Menten rate equations
- [S] >> [E] so only small amount of S bound to E. 2. [ES] does not change, stays at steady state. 3. Initial velocities (Vo) are used so no P is converted to S.
Michaelis-Menten equation
v = Vmax * [S]/K m + [S]
What is Km?
- measure of [S] required for effective catalysis to occur - [S] at 1/2 Vmax - estimate of the equilibrium constant for a given enzyme - small Km: tight binding of S to E - large Km: weak binding
What is Vmax?
- theoretical maximal rate of a reaction - at Vmax, all active sites of the enzyme are saturated with substrate
What is kcat?
- turnover number: max number of substrate molecules converted to product per enzyme per unit of time - kcat = Vmax/E * t
Competitive enzyme inhibition
- inhibitor binds specifically at the catalytic site, competes with substrate for binding - reversible by substrate - Km increased in presence of competitive inhibitor - more substrate is needed for effective catalysis - Vmax - unchanged
Noncompetitive inhibitor
- Binds E or ES complex other than at the catalytic site - substrate can still bind, but with the inhibitor altering the enzyme configuration, the ESI (enzyme-substrate inhibitor) complex becomes inactive - Km - no change, no competition for the substrate binding site - Vmax decreased proportionately to inhibitor concentration (more inhibitors = slower rate)
ACE inhibitors (angiotensin-converting enzyme)
- group of drugs used for treatment of hypertension and congestive heart failure - inhibits ACE to lower blood pressure
Methotrexate
- competitively inhibits dihydrofolate reductase (DHFR) - DHFR synthesizes tetrahydrofolate (folic acid), needed for synthesis of DNA, RNA, thymidylates, and proteins
Aspirin (as an inhibitor)
causes irreversible inactivation of cyclooxygenase (enzyme required for prostaglandin and thromboxane synthesis)
Allosteric inhibition
allosteric inhibitor binds to the allosteric site —> causes the active site to become distorted —> substrate cannot bind
Allosteric activation
there’s a distorted active site on enzyme (S cannot bind) allosteric activator binds to the allosteric site —> active site changes shape to fit substrate
heterotropic effectors
Activating and inhibiting effectors that bind at the allosteric sites
homotropic effectors
Substrate induces distant allosteric effect when it binds to the catalytic site
Feedback inhibition
Product of a metabolic pathway inhibits the activity of an enzyme involved in its synthesis
The vast majority of the cells in the body at any given time are in the …
Go phase (resting phase)
Cell cycle
G1 –> S —> G2 —> Mitosis –> cytokinesis —> Go
G1 phase
cellular contents (excluding chromosomes) are duplicated
S phase
Chromosomes duplicated
G2
Cell ‘double checks’ duplicated chromosomes for error, making any needed repairs
Retinoblastoma protein (pRb)
- tumor suppressor that when hypophosphorylated is ACTIVE: inhibits cell cycle progression - when phosphorylated, pRb is INACTIVE: allowing cell cycle progression
When it is time for a cell to enter S phase, pRb is..
phosphorylated by CDKs (cyclin dependent kinases) and cyclins, which inactivates pRb, allowing cell cycle progression
pRb becomes more and more…
phosphorylated as it goes further in the cell cycle and then becomes hypophosphorylated after mitosis (to inhibit a new cycle)
pRb encoded by…
Rb1 gene
If both alleles of the Rb1 gene are mutated early in life…
the pRb becomes inactivated (allowing cell progression) and results in retinoblastoma - cancer of the eye
cyclins
regulatory molecules controls a cell’s progress through the cell cycle
CDKs are activated when …
bound to a cyclin
The cyclin-CDK pair …
allows phosphorylation to either activate or inactive target proteins for coordinated entry into the next phase of the cell cycle
Cyclins are synthesized…
at specific stages of the cell cycle in response to various molecular signals
neoplasms
abnormal growth of tissue, disturbances in cell cycle control mechanisms are often seen in human neoplasms
Overexpression of cyclin C is associated with what?
Overexpression of cyclin C has been found in both neurons and astrocytes in Alzheimer’s
….. often expressed abnormally in lung premalignancy and malignancy, negative marker for prognosis
Cyclin E
Overexpression of cyclin A
accelerates pRb phosphorylation, promoting cell cycle progression
p53
- tumor suppressor protein that has a role at G1/S checkpoint. - p53 can activate DNA repair, can induce growth arrest in the presence of damaged DNA, initiates apoptosis if damaged DNA cannot be repaired
Morphological changes during apoptosis:
- DNA and organelles fragmented and disintegrated - apoptotic body formation that is quickly engulfed by nearby macrophages - no spilling out of content of cell - no inflammation of surrounding area
cell necrosis
traumatic cell death from acute injury with spillage of cell contents into the surrounding area
What are the intracellular signals for apoptosis?
Intracellular signals - can be induced to undergo cell death b/c of lack of nutrients, low oxygen, heat, hypercalcemia
The apoptotic pathway can be controlled by:
direct transduction from pro-apoptotic cytokines: - Tumor necrosis factor (TNF) - primarily produced by macrophages - Fas Ligand- transmembrane protein that binds to its receptor to induce apoptosis
Stem cells have the ability of:
- self-renewal through mitosis (indefinitely) - Differentiating into specialized cell types