Section 1: Introduction to Cell Biology Flashcards
(116 cards)
1
Q
Cell
A
Smallest unit of life
2
Q
Lipid Functions
A
Energy storage & forms membrane lipid bilayer
3
Q
Macromolecule
A
- It is a giant molecule that’s made up of covalently attached subunits of a particular type.
- They take on an overall 3D shape based on its chemical composition.
4
Q
Macromolecule function
A
- They are greatly responsible for the complex shape, function, and regulation of cells.
- Shape, size, physical and chemical properties of macromolecules allow them to have specific functions.
5
Q
What do macromolecules need to interact with other molecules?
A
The right shape
The right charge
The right chemical interactions
- Hydrogen bonds
- Electrostatic interactions
- Covalent bonds
6
Q
Monomer of Proteins
A
Twenty different amino acids
7
Q
Proteins
A
Long linear polymers that fold into a particular shape
8
Q
Proteins are involved in:
A
- Structure * Energy * Information transfer * Catalysis
9
Q
What are amino acids joined by and is it favorable or not?
A
- Dehydration reaction where water is removed.
- Not a favorable reaction as it requires energy to take place.
10
Q
Nucleic Acids
A
Tend to store information and are polymers.
11
Q
Nucleic Acids Monomer
A
nucleotide which is basic building block of DNA.
12
Q
Structure of DNA nucleotide:
A
sugar group called deoxyribose, a base that gives each subunit its specificity, and triphosphate.
13
Q
How are nucleotides stitched together?
A
Stitched together with covalent bonds between the sugar and phosphate that repeats, & order matters.
14
Q
RNA are involved in:
A
- Transcriptions and translation
- Gene regulation
- Enzyme RNAs: ribozymes
15
Q
What reaction forms a sugar saccharide?
A
Dehydration reaction & repeats to make polysaccharides
16
Q
Polysaccharides functions:
A
Energy storage Structural functions (cell walls)
Cell signaling (cell-cell binding)
What defines blood groups
17
Q
What gives macromolecules their properties?
A
- Polymer Length
- Linear sequence of monomers in the Polymer (Type of subunits used makes a difference).
- Properties of covalent bonds between monomers (important for polysaccharides)
18
Q
ALS
A
- Example of changes to linear sequence of monomers leading to change in macromolecule.
- About ~12 mutations in SOD1 are known to lead to inherited ALS
- Each of these mutations represent a change in a single amino acid in the protein.
19
Q
What tells us which carbons are joined together with a covalent bond in a polysaccharide?
A
beta/alpha and number
20
Q
What is beta 1-4 link and alpha 1-4 link?
A
beta is cellulose and alpha is glycogen.
21
Q
What stabilizes macromolecules?
A
Stabilized mostly by non-covalent interactions: hydrogen bonding, ionic interactions, hydrophobic interactions, van der Waals interactions.
22
Q
DNA replication
A
Makes faithful copies of living code.
23
Q
Process of DNA replication
A
- During replication, DNA strands can be pulled apart
- This doesn’t break phosphate-sugar backbone
- Strands serve as “templates” to make new DNA strands
- Sequence of new strand is determined by the bases that prefer to form base pairs at each position.
Semi-conservative nature of DNA replication
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Q
DNA Transcription
A
Converting DNA code (gene) into RNA.
Turning exact sequence of nucleotides in DNA and turning it to exact matching sequence of nucleotides in RNA.
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RNA
Intermediate of info transfer
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What permits a choice to express or repress a gene?
DNA Transcription (A gene thats on is one where cell is making RNA from the gene).
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mRNA
Intermediate encoding protein sequence.
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Codons
Each specific amino acid is represented by a specific set of three-nucleotide sequences called codons.
These codons are translated into protein by ribosome
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tRNA
An intermediate that matches the mRNA codon to the corresponding amino acid. They bind to amino acids and bring them into a new polymer of protein as it’s being made.
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rRNA
Structural RNA molecules that build the ribosome along with ribosomal proteins.
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RNA functions
Enzymes (ribozymes like rRNA)
Bind, transport, read genetic code (tRNA)
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what are proteins experts at?
Experts at creating structural diversity from only 20 building blocks (amino acids), by hierarchical structural order.
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Primary structure
linear sequence of amino acids in the polypeptide (one single polymer).
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Secondary structure
Local folds of polypeptide, often alpha-helices and beta-sheets (hydrogen bonds).
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Tertiary structure:
Global, 3 dimensional fold of the entire polypeptide or polymer (defined by sum of all interactions of amino acids in a single protein).
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Quaternary structure:
Separate protein polymers with right shape, charge, & hydrogen bonds to stick together non-covalently.
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What determines all other structures in a protein and its function?
Primary structure
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What are amino acids defined by?
Their R chain side group
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What are the 4 types of amino acids?
At cellular ph: Acidic (negative charge), basic (positive charge), uncharged polar, nonpolar
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Acidic amino acids
* introduce a big negative charge to the protein when they’re in the linear sequence.
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What reactions do basic amino acids do?
They do electrostatic interactions.
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What reactions do uncharged polar amino acids do?
They do hydrogen bonds.
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What reactions do nonpolar amino acids do?
* They participate in van der waals interactions.
* They are hydrophobic & it affects how they behave.
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What interactions are responsible for folding in the polypeptide chain of proteins?
Non-covalent interactions
* Hydrogen bonds (between polar amino acids)
* Electrostatic interactions (between charged amino acids)
* Van der Waals (between many different amino acids)
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What are the two categories of interactions that guide how a protein folds?
Interactions of amino acid subunits with one another.
Interactions of amino acids with water (hydrogen bonds)
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Two types of secondary protein structure?
Alpha-helix and Beta-helix
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Alpha-helix protein structure:
Helix is held in place by hydrogen bonds between nearby peptide bonds (stiff so it can grab stuff)
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Beta-helix protein structure
* Regions of polymer weaved together in parallel
* Beta-sheets held in place by hydrogen bonds between peptide bonds adjacent in space but may be distantly located in primary structure.
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What determines if a protein has a secondary alpha or beta helix shape?
primary structure
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Ligands
Interacting molecules can be small molecules or other macromolecules called ligands.
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How do logands bind to proteins?
Via noncovalent bonds.
(Ligand binding specificity and strength (affinity) depends on type and number of non-covalent bonds).
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Prion diseases
* A prion disease is one abnormal conformation of a specific protein.
* Rare conformational change leads to structure change in a chain reaction.
* Aren’t water soluble so they form insoluble material inside a neuron.
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Two types of protein switches:
Protein phosphorylation and binding to GTP or GDP
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What does turning proteins off and on control?
Controls enzymatic activity and protein-ligand interactions
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Protein phosphorylation and the two proteins involved
Protein modified by covalent attachment to a phosphate group at specific amino acid. Kinase and Phosphatase
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Kinase
* Protein whose function is to attach covalently to protein to turn on or off.
* Phosphate group gets attached to an amino acid that has a hydroxyl side chain, OH group to become ON.
* Kinases can become active after cues like growth factors.
* kinases can also be substrates for other kinases.
* This leads to a hierarchy of kinases, one which can turn on the next in the order.
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Phosphatase
Removal of the phosphate group is (de-phosphorylation) and is driven by phosphatase enzyme
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Phosphorylation
Covalent addition of a phosphate group.
causes change in protein conformation thus activity.
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GTPases
Proteins that have the ability to turn off or on by binding to GTP non-covalently.
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GEF and GAP
GEF turn GTPase on by loading GTP onto GTPase.
* GAP causes GTP hydrolysis to GDP by forcing it to cut off the last phosphate group.
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How covalent attachment of phosphate changes protein.
* Covalent attachment of a phosphate to a specific region of protein adds negative charges to that area.
* Negative charges repel each other or attract positive charges.
* This can cause changes in secondary, tertiary, & quaternary structure.
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How non-covalent attachment of phosphate changed protein
* GTPases have a special GTP binding pocket in their structure.
* Binding of GTP causes a movement of a specific part of protein called switch helix.
* This movement of switch helix allows GTPase to bind & control other proteins.
* Hydrolysis of GTP to GDP causes movement of switch helix, thus blocking interaction with other proteins.
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Switch helix
* The switch helix is a specific part of the protein which is the part closest to the third phosphate group that pushes the switch helix outwards to open it.
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Akt protein and its functions
- Turns genes on and off (regulates transcription).
- Controls cell metabolism (how much glucose gets broken down).
- Ensures cell survival (prevents apoptosis).
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What turns Akt on and off
* Covalent attachment of a phosphate on 2 specific regions causes Akt to change shape to be active.
* Akt itself is a kinase that is modified by other kinases.
* Growth factors trigger a reaction to happen in their target cell that causes a chain reaction.
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If Akt is left ON permanently
* Cells undergo weird metabolism.
* Cells divide when not supposed to.
* Cells survive when not supposed to.
* Akt disruption can lead to cancer.
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Why do cells have organelles?
* To separate non-compatible activities
* To protect certain materials (e.g. DNA in nucleus)
* To generate gradients (e.g. in the mitochondria)
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Ribosomes
Make proteins/ enzymes responsible for translation.
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Nucleolus
Subregion of nucleus responsible for RNA splicing.
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Centrioles
control where microtubules begin (their formation), and are part of the cytoskeleton.
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Cytoskeleton
protein filaments that give shape, strength & movement to cells (includes actin filaments, Intermediate filaments, and microtubules).
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Membrane-bound organelles
A cellular compartment that is enclosed within a lipid bilayer.
Can either have a single lipid bilayer or a double lipid bilayer.
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Plasma membrane
separates outside environment from inside of the cell. Responsible for forming semipermeable membrane around cell.
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Nucleus
A double lipid bilayer that protects the DNA, so important it has two layers of membranes.
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Endoplasmic reticulum
Makes things; biosynthesis of lipids and proteins.
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Golgi apparatus
Processing center as it packages macromolecules made in endoplasmic reticulum and processes them to different parts of the cell.
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Peroxisomes
Reduction/oxidation reactions; generate toxic byproducts; synthesis or breakdown of some lipids.
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Endosomes
Result from endocytosis (internalization) of material from plasma membrane. Storing stations for what the cell captures from outside.
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Lysosomes
Stomach of cell; reverse what ER does as it breaks down macromolecules, degradation of membranes & proteins.
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Mitochondria
Oxidation of energy molecules to make ATP.
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Chloroplasts
Specialized cells found in plants, algae and convert energy from light into chemical bonds.
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Three domains of Life
Bacteria, eukaryotes, and archaea.
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Prokaryotic cells
* Lack nucleus enclosing DNA but they have DNA and store genetic info and make proteins.
* Plasma membrane is the only membrane structure of these cells (are mainly bacteria and archaea).
* Lack other membrane bound organelles.
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Eukaryotic cells
* DNA enclosed by nucleus, a double membrane-bound organelle.
* Contain membrane-bound organelles with distinct functions.
* Contain a cytoskeleton, a network of filaments.
* Mitochondria & chloroplasts are organelles with their own genome.
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Last Universal Common Ancestor
* The single celled last organism that was a common ancestor to bacteria, eukaryotes, and archaea.
* Lived 3.5 billion years ago.
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How was LUCA a complex cell already?
* It had enzymes that could make lipids and membranes.
* It had complex metabolic enzymes and capacity to make fuel
* It could make proteins & ribosomes as it had translation.
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Plausible origin of eukaryotic cells
* Early eukaryotic cells with no nucleus who were eating other bacterial cells decided to protect dna by enclosing the dna in a nucleus so it doesn't break.
* Nuclear enclosure would be advantageous to protect DNA from entanglement and breakage when cells are eating.
* Requires change in cell shape driven by the cytoskeleton filaments.
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Endosymbiosis
Some bacteria taken in by phagocytosis didn’t get digested and lived in early eukaryote.
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Origin of Mitochondria
* Come from the phagocytosis of oxidizing bacteria.
* The two organisms became symbiotic: large cell provided protection and food molecules and bacteria oxidized food to release energy (ATP).
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Origin of Chloroplasts
* Predation of photosynthetic bacteria (cyanobacteria)
* Cyanobacteria converted sunlight to food while large eukaryotic cell oxidized food molecules to chemical energy.
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Order of origin of eukaryotic cells
1. Nucleus: Pre-eukaryotic cells eating other cells by phagocytosis.
Evolved nucleus to protect DNA molecules from damage.
2. Mitochondria: Predation of oxidizing bacteria leads to endosymbiosis & eventually mitochondria.
3. Chloroplasts: Mitochondria-containing eukaryotic cells may have internalized photosynthetic bacteria that became chloroplasts.
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When are reactions favorable?
1. Increase in entropy (disorder)
2. Decrease in enthalpy (heat)
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Entropy
Increased entropy (+S) means spontaneous. Increased number of molecules in a chemical reaction is more favorable because more disorder.
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Enthalpy
Energy content (H) derived from volume, pressure, and different numbers of bonds.
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Positive enthalpy (+H)
Increased heat content in bond, not spontaneous, energy transferred into system. Less bonds = more heat
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Negative enthalpy (-H)
Decreased heat in bond, spontaneous; more bonds means less energy in bond and more spontaneous.
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Gibbs Free Energy and formula
G is total energy derived from both enthalpy and entropy.
ΔG=ΔH-TΔS
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Negative G
Decreased energy, spontaneous, exergonic, product favored.
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Positive G
Increased energy, not spontaneous, endergonic, reactant favored.
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What type of system are cells?
Cells are an open system so they're able to access nutrients and energy from outside environment.
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What type of system are cells?
Cells are an open system so they're able to access nutrients and energy from outside environment.
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Total ΔG of a series of reactions:
Add every ΔG of every reaction to get the overall favorable or unfavorable ΔG.
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Coupling reactions
Catabolic reactions break down molecules and release energy that drive anabolic reactions that build molecules.
Anabolic pathways on their own can't work because they’re not spontaneous.
Instead of letting an unfavorable reaction happen on its own, it couples it with a super favorable reaction so the two work together and the overall reaction is spontaneous and favorable.
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Catabolism
Reactions that are highly exergonic (increase disorder and liberate energy) are spontaneous.
Breakdown of molecules like sugars and lipids.
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Anabolism
Reactions that are endergonic (decrease disorder and store energy in bonds) are not spontaneous.
Synthesis of complex molecules like proteins.
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What provides an unlimited source of energy?
Photosynthesis
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Photosynthesis
Involves conversion of energy:
* From electromagnetic energy to high energy electrons.
* Then from high energy electrons to chemical bonds.
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What is the common energy currency molecule
ATP
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ATP
* ATP is the critical energy carrier that cells have to make so they use it for other things.
* This is how the product of metabolism is used for anabolic reactions. The hydrolysis of a phosphate is very favorable.
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ATP structure
* Adenine base attached to ribose attached to three phosphate groups.
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How can we study gene function?
Make a gene non-functional to see if a specific function is affected.
Identifying what part of proteins inside the cells contribute to disease or the way cells work.
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Three strategies to impair gene function
1. Pharmacology (using existing drugs).
2. Gene silencing (getting rid of the mRNA of the gene)
3. Gene knockout
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How does inhibition of gene function by pharmacology work?
Involved adding molecules (ligands) that alter protein's function. Interferes with the protein directly.
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How does inhibition of gene function by gene silencing work?
Interfering RNA (added during experiment) has a complementary nucleotide sequence to target mRNA, leads to target mRNA getting destroyed or silenced. Interferes with mRNA directly.
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How does inhibition of gene function by gene knockout work?
Specific change (mutation) of DNA sequence for a specific gene.
* To make a knockout of a specific gene, mutation made in a gene makes the gene product with a loss of function.
* Can be done in a number of useful model organisms
* CRISPR has allowed this to be done in human cells.
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Why experiments testing gene function matter:
* Understand how genes work in essential cellular processes.
* Identify drug targets to treat specific diseases.
