Section 1 - Cells and Genomes Flashcards
How much diversity is there with species on Earth?
Lots. Between 10-100 million species have been identified
How are the characteristics of offspring determined?
Parent organism provides genetic material to (partially) determine characteristics
What hereditary information does the cell contain?
Generate machinery to gather raw materials for life, and form new cells (to survive!)
True or false: single cells are very similar
True: cells have many similarities
True or false: matured organisms are very similar
False: matured organisms are very different
True or false: different matured organisms come from different single cells
False: even though the matured organisms are different, the single cells are fairly similar
How do living cells store hereditary information?
DNA
What is DNA comprised of?
A, T, C, and G
What makes DNA different than engineered data storage methods?
DNA can be read and used by any cell type
How is DNA replicated?
From a template strand (semi-conservative)
What is the central dogma?
DNA -> RNA -> Protein
What is the most fundamental information in BME 501?
The central dogma
What does the central dogma describe?
How information flows in molecular biology
What is the process to turn DNA -> DNA?
DNA synthesis / replication
What does DNA synthesis do?
DNA -> DNA
What is the process to turn DNA -> RNA?
Transcription
What does transcription do?
DNA -> RNA
What is the process to turn RNA -> protein?
Translation
What does translation do?
RNA -> protein
Is DNA disposable or reusable?
Reusable (stable molecule)
Is RNA disposable or reusable?
Disposable (rapidly created and degraded)
Are proteins disposable or resuable?
Somewhat disposable (depends on the protein)
What is the intermediate of the central dogma?
RNA
What is a codon?
A group of 3 nucleotides
How controlled is gene expression?
Tightly controlled (feedback, protection, etc.)
Why is gene expression so tightly controlled?
Don’t want to waste energy making proteins randomly
How much free energy is needed for DNA replication?
A large amount
Why is a lot of energy needed for DNA replication?
DNA is a very stable molecule (high energy)
What are on/off processes?
Protein machinery binding / dissociating for useful work
Do on/off processes require energy?
Yes, binding and work of proteins requires energy
True or false: All cells use the same basic building blocks
True: all cells use nucleotides, amino acids, simple sugars, and ATP
True or false: Since all cells use the same basic building blocks, they all have the same function
False: just because all cells have the same tools does not mean that they have the same function
What structure are all cells enclosed in?
Plasma membrane
What are the two basic functions of the cell membrane?
- Differentiate between inside and outside
2. Be selective with materials that enter or exit the cell
Chemically, what are the vast majority of cellular molecules based on?
Carbon compounds
What environment do cellular reactions take place in?
Aqueous environments
What are some advantages of doing reactions in aqueous environments?
Use water binding in some cell processes
What are some disadvantages of doing reactions in aqueous environments?
Water can bind to polar molecules, expend energy to move water out of the way
What are atoms composed of?
Neutrons, protons, and electrons
What is the atomic weight?
Sum of the protons and neutrons (weight of the atom)
What electrons determine binding?
Valence (outermost electrons)
What is the size of an atom dependent on ?
Orbital paths of the electrons
What are the 4 most common elements in living organisms?
Carbon, nitrogen, hydrogen, and oxygen (HONC)
True or false: The most common elements in living organisms is the same as the most common elements in Earth’s crust
False: the two have largely different makeups
True or false: The environment organisms live in is different than their biological environment
True: the compositions are different
True or false: The only elements living organisms need is hydrogen, oxygen, nitrogen, and carbon
False: trace elements (such as Zinc) are also needed
If an element is reactive, what can you say about its electron shell?
It is unfilled
If an element is nonreactive, what can you say about its electron shell?
It is filled
What is an ionic bond?
Exchange of electrons to create of bond
What is a covalent bond?
Sharing of electrons to create a bond
When is a covalent bond in equilibrium?
When the repulsive and attractive forces are equal
What happens to the bond when it is in equilibrium?
There is a particular bond strength, length, and angle
What is the importance of bond strength?
Tells you how much energy is needed to break it
True or false: you can tell the bond strength by the elements in a covalent bond
True: covalent bonds have a particular bond strength in equilibrium
True or false: you can tell the bond strength by the elements in an ionic bond
False: ionic bonds do not follow a particular bond strength
What is a polar covalent bond?
Unequal sharing of electrons, leading to dipoles
Which side of water is electronegative?
Oxygen
Which side of water is electropostivie?
Hydrogen
What are single bonds?
Sharing of two electrons
How much movement is possible with single bonds?
Complete rotation around the bond
What are double bonds?
Sharing of four electrons
How much movement is possible with double bonds?
No rotation around the bond
What is a hydrogen bond?
An attraction between hydrogens on polar atoms / molecules
What can be said about the direction and strength of hydrogen bonds?
The bond is fairly weak (weaker than covalent bonds) and directional
What are Van der Waals forces?
Transient forces between changes in electron density
What are hydrophobic forces?
Interactions between nonpolar molecules to move away from environments with lots of hydrogen bonding
How do energetics dictate binding?
Specific binding has specific energies that are optimized for specific substrates
What is the primary function of sugars?
Energy source for cells
What form (chemically) do monosaccharides follow?
(CH2O)n
True or false: Since the formula for monosaccharides is simple, there are relatively few sugars
False: different arrangements and handiness increase the amount of sugars
How are polysaccharides formed?
Through condensation reactions
In cell biology, what are the primary form of sugars?
Monosaccharides (with some disaccharides)
What are the functions of fatty acids?
Secondary energy storage, and the cell membrane
What is the structure of a fatty acid?
Long hydrocarbon tail, and carboxyl group
What are the properties of a long hydrocarbon tail?
Hydrophobic and not very reactive
What are the properties of a carboxyl group?
Hydrophilic and reactive
What are some properties and characteristics of saturated fatty acids?
Only single bonds, increases packing density and strength, straight chained, usually solid
What are some properties and characteristics of unsaturated fatty acids?
Double or triple bonds, decreased packing density and strength, kinked chained, usually liquid
What is a chemical model of a molecule?
Writing out the chemical formula
What is the advantage of a chemical model?
Can clearly see what atoms make up the molecule
What is a wire model of a molecule?
Showing the bonds between atoms
What is the advantage of a wire model?
Can clearly see how the bonding occurs between the elements
What is a space filling model of a molecule?
Showing the space that an atom takes up in a molecule
What is the advantage of a space filling molecule?
Can see where the molecule can get attacked (based on structure) (reactivity)
How are fatty acids normally stored in cells?
In triacylglycerols
What is a triacylglycerol?
3 fatty acids chains connected to a glycerol molecule
What is the structure of a phospholipid?
Two fatty acid tails and one polar head group, connected by glycerol
What is the primary function of phospholipids?
Cell membrane
What does it mean to be amphipathic?
A molecule that has both hydrophilic and hydrophobic parts
What is an example of an amphipathic molecule?
A phospholipid (hydrophilic head, hydrophobic tails)
How many amino acids are in living cells?
20
What is the function of amino acids?
Building blocks of proteins
What is the same among all amino acids?
An amino group and a carboxylic acid group connected by a central carbon
What is different among all amino acids?
The R group (side chain)
What type (handiness) of amino acids are used in proteins?
L amino acids
What is a peptide bond?
Bond between amino acids in a protein
What bond binds amino acids in a protein?
Peptide bond
When are D amino acids seen in the body?
To monitor the age of a protein (older proteins degrade, and have more D amino acids)
What is the structure of a nucleotide?
Nitrogen containing ring linked to a 5 carbon sugar, and one or more phosphate groups
How do nitrogen bases interact with protons?
Nitrogen bases act as proton absorbers
What is the structure of a pyrimidine?
One 6-membered ring
Which of the bases are pyrimidines?
C, T, U
What is the structure of a purine?
One 6-membered ring fused to one 5-membered ring
Which of the bases are purines?
A, G
What is a mneumonic to memorize pyrimidines?
Pyramids CUT the sky (C, T, U)
What is a mnemonic to memorize purines?
Pure As Gold (A, G)
What are the functions of nucleotides?
Energy (ATP) and information storage (DNA)
What is metabolism controlled by?
Enzymes
How come reactions cannot occur in the body without enzymes (think temperature)?
Most reactions can only occur at temperatures higher than 37 C
Where does the extra external energy come from to power reactions?
Enzymes
What do enzymes control?
Function and energetics of cells (rate of reactions)
What are catabolic pathways?
Pathways that break down molecules, and produce energy
What are anabolic pathways?
Pathways that build up molecules, and use energy
What is meant by “engineering control theory” for cell biology?
Important to consider the level of control that these reactions in the cell have
What three things do catabolic pathways create?
Useful forms of energy (to use in anabolic reactions), building blocks for biosynthesis, and lost heat
What is the second law of thermodynamics?
The entropy (disorder) of a system must increase with time
How does the disorder of a cell change over time?
Decreases disorder
How does the disorder of the extracellular environment change over time?
Increases disorder
Why does the extracellular environment change over time?
Heat released by the cell increases the disorder
How does the 2nd law of thermodynamics relate to the cell system?
The sum of the cell losing entropy, and the extracellular environment gaining entropy, tends towards increasing disorder (and thus doesn’t break the 2LoT).
How is energy extracted from food molecules
Gradual oxidation (controlled burning)
What is the most chemically stable form of carbon in the cell?
CO2
What is the most chemically stable form of hydrogen in the cell?
H2O
True or false: All processes have an innate barrier based on the energy needed to break or form bonds
True: this activation energy is present for all reactions
What element is useful for controlled burning?
Oxygen
How do enzymes catalyze reactions?
By lowering the activation energy needed
True or false: enzymes change the activation energy of a reaction
True: this is how enzymes catalyze reactions
True or false: enzymes change the energy of products / reactants in a reaction
False: this is not changed. Only the activation energy is changed
How do enzymes determine the end product of a reaction?
Through quantity and type of enzyme
How does the quantity of enzyme determine the end product?
Dictates speed
How does the type of enzyme determine the end product?
Dictates branching pathway to follow
How does the type of enzyme relate to control?
Enzyme can control which reaction is happening to get a certain output
How can reactions can a typical enzyme catalyze in one second?
A thousand
What must the enzyme do to repeatedly catalyze reactions?
Bind and release substrates, and find new ones quickly
What process dictates the probability of molecules interaction with each other?
Diffusion
What parameters does diffusion depend on?
Temperature, media, etc.
What is the requirement to spontaneously undergo a chemical reaction?
The free energy change (delta G) must be negative
True or false: An enzyme changes the equilibrium point of the reaction
False: it only affects the speed of the reaction
What is meant by coupling reactions?
An favorable reaction can be coupled to a unfavorable one to help complete it
What are activated carriers?
Molecules that store energy in an easily exchangeable form
What are some examples of activated carriers?
ATP, NAD+, NADP+
What is the purpose of activated carriers?
Store energy to be used for other reactions
How is energy from food derived?
Breakdown of chemical bonds in food molecules
How are sugars broken down?
Sugars are oxidized into CO2 and H2O
What happens if the oxidation of glucose is done in one step?
Huge energy loss than cannot be harvested
What is the disadvantage of oxidizing glucose in one step?
There is a lot of energy lost as heat
What happens if the oxidation of glucose is done in a series of steps?
Each step can be coupled to create activated carriers
What is the advantage of oxidizing glucose in a series of steps?
Can harness more energy as activated carriers
What is the process of breaking down glucose in a series of steps called?
Controlled oxidation
What is the first stage of food breakdown?
Digestion
What is digestion?
Enzymatic breakdown of large food molecules into monomers
In digestion, what are proteins broken down into?
Amino acids
In digestion, what are lipids broken down into?
Fatty acids and/or glycerol
In digestion, what are polysaccharides broken down into?
Simple sugars
What is the second stage of food breakdown?
Glycolysis
What occurs during glycolysis?
Glucose is broken down into pyruvate
How is pyruvate used by the mitochondria?
Converted into CO2 by the Citric Acid Cycle for more activated carriers
What type of molecule is acetyl CoA?
Activated carrier
Where does digestion occur?
Stomach and intestines
Where does glycolysis occur?
Cytosol of the cells
How is acetyl CoA formed?
Attaching coenzyme A to an acetyl group
What is the purpose of phosphates in glycolysis?
Charge the molecules, and then use them to create activated carriers
In the absence of oxygen, what occurs after glycolysis?
Fermentation
What are some possible products of fermentation?
Lactate and ethanol / CO2
What is the third stage of food breakdown?
Oxidative phosphorylation
Where does oxidative phosphorylation occur?
Mitochondria
What happens during oxidative phosphorylation?
NADH is used to power the electron transport chain (ETC) to generate ATP and consume O2
What are the waste products of oxidative phosphorylation?
H2O, CO2, and NH3
True or false: oxidative phosphorylation requires excess oxygen
True: oxygen is needed as the final electron donor
What is pyruvate dehydrogenase, and what is its function?
Enzyme complex to convert pyruvate into CO2, NADH, and acetyl CoA
In stage 3 of food breakdown, what are fatty acids converted into?
acetyl CoA, NADH, and FADH2
Why is it advantageous to have pyruvate dehydrogenase as an enzyme complex (as opposed to separated)?
Can efficiently couple reactions in series, since the product of one reaction can be used as a reactant of the next. Thus, substrates don’t have to diffuse to find the second enzyme
What is the general trend of the citric acid cycle (think carbons)?
Add 2 carbon molecule to a 4 carbon molecule to make a 6 carbon molecule, which is oxidized (by losing carbons) to produce energy
What are the functions of the byproducts of glycolysis and the citric acid cycle?
Biological building blocks for other biomolecules
How do other foods feed into glycolysis / citrus acid cycle?
They all converge at different points in the food breakdown cycle
How many ATP molecules are found in a given cell?
10^9 (1 billion) molecules
How frequently is ATP consumed and replenished in a given cell?
Every few minutes
What is the rate of ATP consumption?
10^9 ATP / every few minutes
How is GTP similar to ATP?
Similar amount of energy released
How is GTP different from ATP?
Different structure (may not be used in reactions), ATP is more common in the body
