Week 1 Flashcards
Three tenets of the cell theory
- All organisms are composed of one or more cells.
- The cell is the basic unit of life.
- Cells can only arise by division from preexisting cells.
What three things are all living organisms made of?
- Cells
- Stuff produced by cells.
- Stuff assimilated from the environment by cells.
How can cells be considered “containers”?
A single cell contains small molecules and macromolecules enveloped in a lipid bilayer membrane.
What are the two basic cell types?
- Prokaryotes
- Eukaryotes
Give the four essential characteristics of prokaryotes.
- Peptidoglycan cell wall.
- Genome on 1 or 2 chromosomes
- Small cell size
- Single closed compartment
Give the five essential characteristics of eukaryotes.
- Cell wall in plants and fungi, not animals
- Large genome on multiple chromosomes
- Large cell size
- Multiple membrane bound organelles
- Cytoskeleton
What three components make up the complex and dynamic cytoskeleton of eukaryotic cells?
- Actin filaments
- Microtubules
- Intermediate filaments
Number of cells in a human
10^13
Number of different cell types in a human
~200 cell types
How can there be different cell types that arise from the same genome? (eg epithelial cells vs neurons)
Cell division and differentiation and different gene expression profiles.
What are the six broad categories of cell type in humans?
- Epithelial cells
- Contractile/muscle cells
- Neurons
- Blood cells
- Sensory cells
- Connective tissue cells
Give two characteristics of enterocytes.
- The brush border increases apical membrane surface area.
- Optimized for nutrient absorption/transport.
What category of cell type are enterocytes?
Epithelial cells
What category of cell type are pancreatic acinar cells?
Epithelial cells
What is the role of pancreatic acinar cells?
These cells are optimized for large-scale regulated secretion.
Four basic types of contractile cells
- Heart muscle cell
- Smooth muscle cell
- Myoepithelial cell
- Skeletal muscle fiber
What is the role of contractile/muscle cells?
These cells are optimized for generating directed mechanical force.
What is the role of neurons?
These cells are optimized for extensive cell-cell connectivity and electrical conductivity.
What do motor neurons control?
Myocyte activity
What two types of cells compose the retina?
- Neurons
- Sensory cells
What is the role of the retina?
The retina is optimized for sensitive, high resolution photo detection.
What is the role of bundles of stereocilia?
Mechanotransduction.
What is the role of connective tissue cells?
These cells are responsible for secretion and maintenance of ECM
A fibroblast is what type of cell?
Connective tissue cell
An osteoblast is what type of cell?
Connective tissue cell optimized for bone matrix production.
How many amino acids compose nearly all of the proteins on earth?
20
What is the central dogma used to describe?
The flow of information from DNA → RNA → Protein
Transcription
Converts information from DNA to RNA.
Translation
Converts information from RNA into proteins
What determines the shape of a protein?
The shape of a protein is primarily determined by its amino acid sequence.
What determines the function of a protein?
The function of a protein is determined by its shape.
Name the three basic amino acids.
Lysine
Arginine
Histidine
Name the four polar amino acids with uncharged R groups.
Serine
Threonine
Asparagine
Glutamine
Name the two acidic amino acids
Aspartic acid
Glutamic acid
Name the three special amino acids
Cysteine
Glycine
Proline
Primary structure
The chain of amino acids covalently linked together
Tertiary structure
How a single polypeptide chain folds in 3D space.
What are the two ends of a polypeptide?
Amino end (N-terminus)
Carboxyl end (C-terminus)
What type of reaction occurs when a peptide covalent bond forms?
A condensation reaction that produces a water molecule.
What effect does hydrolysis have on a peptide bond?
Hydrolysis breaks a peptide bond by adding a water molecule.
What configuration is a peptide bond usually in?
The trans configuration in which the oxygen and hydrogen are opposite each other.
What prevents rotation around the peptide bond?
Resonance in the C=O bond that results in a partial double bond character, thus restricting rotation.
Why does a peptide bond not form under neutral conditions?
There is an energy barrier to forming a peptide bond. Amino acids must be activated to undergo the condensation reaction. Entropically, the formation of a peptide bond is not favorable.
What must occur for the condensation reaction that forms the peptide bond to happen?
Amino acids must be activated. tRNAs get charged with amino acids. Adenosine triphosphate is necessary to add tRNA to an amino acid.
Where does peptide bond formation take place?
The ribosome.
In terms of the two ends of a polypeptide, in what order is the protein synthesized?
Proteins are synthesized from the amino end (N-terminus) to the carboxyl end (C-terminus). They also exit the ribosome in this order.
What are the three main forces that drive protein folding?
Electrostatic attractions
Van der Waals attractions
Hydrogen bonds
Where do hydrogen bonds typically occur?
Between side chains and in backbones
Which amino acid can form covalent bonds?
Covalent bonds (specifically disulfide bonds) can form between cysteine residues in the presence of oxygen.
What is the role of disulfide bonds in a protein?
These bonds hold the tertiary structure of the protein together.
The hydrophobic effect
A protein will fold in a conformation with nonpolar side chains in a hydrophobic core region while polar side chains on the outside form hydrogen bonds to water. This occurs in an aqueous environment.
Where are disulfide bonds rare?
In cytosolic proteins
Where are disulfide bonds common?
Secreted proteins
What determines folding pattern?
Folding pattern is determined by the primary sequence of amino acids with help from chaperones.
What can unfold (denature) proteins?
Relatively mild perturbations can unfold proteins (heat, pH extremes, urea, guanidine, reducing agents, ionic detergents (SDS))
Native state
Active or functional conformation of protein
What effect does mercaptoethanol have on a protein?
It denatures the protein by breaking disulfide bonds.
What happens if you denature a protein and cause it to lose its enzymatic activity, but then remove the denaturing agents?
It will refold and regain its enzymatic abilities.
Give examples of chaperone proteins.
Hsp70, Hsp60 (GroEL/GroES)
How does the chaperone protein GroEL facilitate protein folding?
GroEL is an ATPase. Proteins enter GroEL and leave properly folded.
What causes chaperone proteins to recognize misfolded proteins?
Misfolded proteins have exposed hydrophobic regions. These regions tend to aggregate together to form a wad of protein.
What happens when a chaperone protein recognizes a misfolded protein?
The chaperone protein clamps down on the misfolded protein and refolds it. Then, the binding and hydrolysis of ATP allows the chaperones to release the protein.
How is ∆G different for folded and unfolded proteins?
∆G is higher for an unfolded protein than for a folded protein.
What is the secondary structure of proteins?
alpha helices and beta sheets.
What are motifs and domains?
Small regions of sequence and structural similarity between different proteins.
How are motifs and domains different?
A motif is a sequence in a protein that is conserved in many proteins and often underlies a particular structure. A domain is an independently folding portion of a polypeptide and is functionally important.
Give examples of a motif.
Helix-loop=helix motif or zinc-finger motif
Quaternary structure
The number and arrangement of different polypeptides (subunits) that make up the functional protein.
What produces reactive surfaces in proteins?
Appropriate folding of proteins produce reactive surfaces.
How is the dissociation rate defined?
dissociation rate = koff [AB]
How is the association rate defined?
association rate = kon [A][B]
What is the equilibrium constant for protein association and dissociation rate?
Assuming association rate = dissociation rate, kon / koff = K = equilibrium constant.
What are the units of the dissociation constant?
Kd has molar units (M), which correspond to the concentration of ligand [L] at which the binding site on a particular protein is half occupied (ie the concentration of ligand at which the concentration of protein with ligand bound [C] equals the concentration of protein with no ligand bound [P])
How does the dissociation constant describe how tightly bond a ligand is?
The smaller the dissociation constant, the more tightly bound the ligand is, or the higher the affinity between ligand and protein.
What is the relationship between the association constant and dissociation constant?
1 / Ka = Kd
Active site
The active site on an enzyme is the specific place where the chemical reaction takes place.
Active site residues
The specific amino acids that position the substrate in place and mediate catalysis (or sometimes coordinate metals, prosthetic groups, or other molecules needed for catalysis)
Turnover number
The number of product molecules formed per minute per enzyme.
Characteristics of human ATP8A1-CDC50A
An integral membrane protein heterodimer with two subunits.
What are the two subunits of human ATP8A1-CDC50A?
ATP8A1 and CDC50A
What is the role of human ATP8A1-CDC50A?
This protein uses the energy from ATP binding and hydrolysis to transport the lipid phosphatidylserine (POPS) across the membrane bilayer.
What is the role of the A, P, and N domains of human ATP8A1-CDC50A?
These domains are involved in binding and hydrolysis of ATP, which induces conformational changes in the membrane domain (M1-M10) where the transport substrate is bound and flipped across the bilayer.
Hydrolases
General term for enzymes that catalyze a hydrolytic cleavage reaction; nucleases and proteases are more specific names for subclasses of these enzymes.
Nucleases
Enzymes that break down nucleic acids by hydrolyzing bonds between nucleotides.
Proteases
Enzymes that break down proteins by hydrolyzing bonds between amino acids.
Synthases
Enzymes that synthesize molecules in anabolic reactions by condensing two smaller molecules together.
Isomerases
Enzymes that catalyze the rearrangement of bonds within a single molecule.
Polymerases
Enzymes that catalyze polymerization reactions such as the synthesis of DNA and RNA.
Kinases
Enzymes that catalyze the addition of phosphate groups to molecules. Protein kinases are an important group of kinases that attach phosphate groups to proteins.
Phosphatases
Enzymes that catalyze the hydrolytic removal of a phosphate group from a molecule.
Oxido-Reductases
General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced. Enzymes of this type are often more specifically named either oxidases, reductases, or dehydrogenases.
ATPases
Enzymes that hydrolyze ATP. Many proteins with a wide range of roles have an energy-harnessing ATPase activity as part of their function, for example, motor proteins such as myosin and membrane transport proteins such as the sodium-potassium pump.
What are the names of the four enzymes that don’t use the standard “ase” suffix?
Pepsin, trypsin, thrombin, and lysozyme
What does the common name of an enzyme usually indicate?
The substrate and the nature of the reaction catalyzed. For example, citrate synthase catalyzes the synthesis of citrate by a reaction between acetyl CoA and oxaloacetate.
What type of enzymes are highly involved in the regulation of protein activity?
Protein kinases and phosphatases. The activity of many proteins are regulated by phosphorylation. There are hundreds of different protein kinases in eukaryotic cells that regulate the activity of 1000s of other proteins.
What regulates GTP-binding proteins?
GTP-binding proteins are regulated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs). Active GTP-binding proteins then regulate the activity of other proteins by binding to them.
What do small GTPases in the Ras superfamily do?
They regulate nearly every aspect of cell physiology
Ras
A dominant oncogene
How is Ras related to cancer?
Activating mutations in Ras are found in ~25% of all human cancers. 90% of pancreatic cancers are caused by Ras mutations.
How is Ras activated?
Growth signals activate Ras by activating its GEF (RasGEF).
How is Ras terminated?
By RasGAP
What two processes are involved in phosphorylation?
Protein kinases add phosphate to proteins.
Protein phosphatases remove phosphate from proteins
What are the classes of protein kinases?
Ser/Thr kinases, Tyr kinases, His or Asp kinases
What amino acids does glycosylation affect?
Asn for N-linked
Ser/Thr for O-linked
What processes belong to the category of lipidation?
GPI anchors, farnesylation, myristoylation, and palmitoylation
In phosphorylation, what is the phosphate donor?
ATP
What are the two substrates of kinase?
ATP and the protein target
Src
The Src gene is an oncogene. Src (the protein) is a tyrosine kinase that regulates cell proliferation.
What are the four important parts of Src?
SH3, SH2, the kinase domain, and tyrosine
What does the SH3 domain of Src bind to?
Proline-rich domains in other proteins, or to a proline-rich region in Src.
What does the SH2 domain of Src bind to?
Phospho-tyrosine
What are the three general steps of the regulation of a Src-type protein kinase?
- Phosphate removal loosens structure.
- Activating ligand binds to SH3 domain.
- Kinase can now phosphorylate tyrosine to self-activate.
Where does N-linked glycosylation take place?
On certain asparagine residues. Only found on proteins that pass through the ER lumen (eg secreted and membrane proteins).
Myristoyl group
A 14 carbon, saturated fatty acid involved in lipidation
Palmitoyl group
A 16 carbon, saturated fatty acid involved in lipidation
Farnesyl
A prenyl group that also serves as a building block in cholesterol synthesis and is involved in lipidation
What anchors Ras to the plasma membrane?
Ras is an important oncogene that is anchored to the plasma membrane by prenyl groups.
What does Src use for membrane association?
Src uses an N-terminal myrstoyl group for membrane association.
What proteolytically processes chymotrpsinogen?
Another protease called trypsin.
What activates protease activity?
Cleavage
How are acetylation and methylation related?
They are competing reactions.
Histones
Proteins that package DNA into chromatin. Genes must be turned on or turned off in the context of this packaged chromatin form.
How do histone modifications alter gene expression?
Histone modifications can produce epigenetic marks on chromatin that alter gene expression.
Epigenetics
The study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence. It refers to functionally relevant modifications to the genome that do not involve a change in the nucleotide sequence.
Result of monoubiquitylation
Histone regulation
Result of multiubiquitylation
Endocytosis
Result of polyubiquitylation
Proteasomal degradation (Lys48) and DNA repair (Lys63)
What degrades polyubiquinated proteins (Lys48)?
The proteasome, a large cytosolic protease.
