Nah Flashcards
What is an independent variable?
Independent variable is the variable that is changed in an experiment to test the effects on the dependent variable.
In what way are elements in the same row of the p table the same?
They have the same number of electron shells.
A solution has a pH of 5 what is the concentration of OH- ions?
10^-9 M
A solution has a pH of 8. What is the concentration of H+ ions?
10^-8 M.
Bleach has a pH of 13, how would it be classified from acidic to basic?
Extremely basic, higher pH means more H+ ions, more H+ ions the more basic.
Why does ice float in water?
When water freezes the hydrogen bonds stabilize arranging the water molecules farther apart from each other than when in a liquid state, lower density.
How many protons, neutrons and electrons does 27/13 Al 3+ have?
Protons = Atomic # = 13 protons
Neutrons = Atomic mass - Atomic # = 27 - 13 = 14 neutrons
Electrons = Atomic # - charge = 13 - (+3) = 10 electrons
Nitrogen is much more electronegative than hydrogen. In relation to electro negativity what can you say about the atoms in ammonia (NH3) .
The hydrogen atoms would have a partial positive charge and the nitrogen would have a partial negative charge.
What is a common chemical reaction mechanism by which cells make polymers from monomers?
Dehydration reactions
Which type of interaction stabilizes the a helix and b pleated sheet structures of proteins?
Hydrogen bonds
What is an asymmetric carbon?
A carbon attached to 4 different groups.
What are buffers and how do they work?
Buffers resist changes in pH by either donating or accepting H+ or OH- ions.
What is the main bond that allows the bases from two poly nucleotides to stay together?
Hydrogen ponds.
What are the different levels of biological organization from biggest to smallest?
Biosphere, Eco-system, Community, Population, Organisms, Organs, Tissues, Cells (smallest unit capable of performing all the activities required for life), Organelles, Molecules.
What are emergent properties?
Novel properties that arise at each level that allow the systems at higher levels to function. Cells group together to form tissues which the form organs.
What are the principles of cell theory?
All living things are composed of cells
The cell is the smallest unit of life
Cells only arise from preexisting cells.
Inductive reasoning
Derives generalizations from specific observations.
Deductive reasoning
Starts with a general theory or statement and examines the possibilities to reach a specific logical conclusion.
A=B, B=C, C=A
Example: All spiders have 8 legs, Tarantulas are spiders, tarantulas have 8 legs.
Qualitative vs Quantitative data
Qualitative data is interpretation based, descriptive and normally expressed in words.
Quantitative data is expressed in numbers, answer “how much/ how many?” Questions.
What is a theory?
A theory is an explanation of a phenomenon. Usually has a broad scope and is supported by a large amount of evidence.
Ex: Theory of gravity, theory of evolution.
What is a molecule?
A molecule is two or more atoms joined chemically.
Example: O2
What is a compound?
Molecule made up of two or more elements.
What is a control group?
The control group receives no treatment or receives the usual treatment. Resembles the native/wild conditions.
What is specific heat?
Specific heat is the amount of heat that must be absorbed or lost for 1g of a substance to change temp by 1 degree Celsius.
What are some properties of water?
Cohesion: Hydrogen bonds between water molecules give water a cohesive property.
Adhesion: Water molecules stick to other substances by forming hydrogen bonds with the surface.
High surface tension due to the cohesion of water molecules.
Strong solvent due to its polarity, water can dissolve polar and ionic compounds very well.
Water becomes less dense as it freezes
High specific heat - water can absorb a lot of heat.
What is evaporative cooling?
The hottest molecules of water are turned into gas leaving the cooler molecules behind.
Solvent vs Solute?
Solvent is the dissolving agent
Solute is being dissolved
Covalent bonds
Sharing of a pair of valence electrons
Ionic Bonds
The electronegative atom strips away an electron from its partner; forms a positively charged cation and a negatively charged anion.
What happens to strong and weak acids and bases in a solution.
Strong acids and bases will completely dissociate in solution.
Weak acids and bases will not dissociate 100% but will instead reversibly accept and release back ions into the solution. (Reactions are reversible)
What makes a compound organic?
Compounds containing carbon are organic.
If glucose has a molecular mass of 180.5g/mol, how would you make a 1 molar solution of glucose.
Add 180.5g of glucose to a container then fill the container up to a litre.
What facilitates the breaking down and building up of polymers?
Enzymes
What are the differences between alpha and beta glucose?
For alpha glucose the OH on Carbon 1 is facing downwards and is on the same side as the OH on Carbon 4 and is on the opposite side of carbon 6.
Beta glucose has the OH on carbon 1 facing upward and is on the opposite side of the OH on carbon 4. The OH on carbon 4 is also on the same side as carbon 6.
What are the 4 macromolecules?
Proteins, Carbohydrates, Lipids, and Nucleic acids.
What are the monomers for each of the four macromolecules?
Carbohydrates - Monosaccharides
Proteins - Amino acids
Nucleic acids - Nucleotides
Lipids - Glycerol and fatty acids
Functions of carbohydrates?
Material to build cell membrane
Rapid energy in the breakdown of glucose.
Energy storage in the form of glycogen which is stored in the liver and muscles.
What is the function of lipids?
Long term energy storage
Cushion and insulate organs
Material used for cell membrane
Function of Nucleic acids
Stores and transfers genetic info
Directs growth and development
Functions of proteins
Controls rate of reactions
Forms cell structures
Regulates cell processes
Enzymes
Transport in and out of cells.
Immunity
Aids in muscle movement
Provides structure
What are some examples of disaccharides?
Sucrose (glucose + fructose)
Maltose (glucose + glucose)
Lactose (galactose + glucose)
Common polysaccharides and their differences
Starch - Branched polysaccharide found in plants used to store glucose. Built with alpha glucose.
Glycogen - Heavily branched PS found in animals used to store glucose.
Cellulose - Unbranched PS used in the cell wall of plants for structure. Built with beta glucose.
Glycosidic linkage
A covalent bond that joins a carbohydrate to something else.
How does starch link glucose monomers? Cellulose?
Starch links alpha glucose molecules
Cellulose links beta glucose molecules
What makes carbon special?
Can form single, double and triple covalent bonds.
Can form up to four single covalent bonds with a variety of atoms.
Can form molecules of various lengths with branches or even rings
These things result in a large molecular diversity
Van der Waals interactions
Weak attractions between molecules or parts of molecules resulting from transient local partial charges
Dehydration vs Hydrolysis
Dehydration reactions remove a water molecule forming a new bond.
Hydrolysis adds a water molecule breaking a bond.
Saturated vs unsaturated fats
Saturated fats have no double bonds which results in having the maximum amount of H. Can pack together closely and solidify at lower temps.
Unsaturated fats have double bonds and due to these double bonds do not pack as closely together (oils).
Trans fats
Unsaturated fats that have been hydrogenated to solidify.
What are fats made of?
Fats are made of a glycerol backbone attached to three fatty acids.
Known as triacylglycerols
Phospholipids
Phospholipids have two fatty acid tails, the third glycerol hydroxyl is attached to a phosphate.
Amphipathic meaning they have a hydrophilic head and a hydrophobic tail.
Very important for forming lipid bilayer.
Steroids
Lipids with four rings arranged in a specific configuration.
Examples: Cholesterol, testosterone.
What are proteins constructed from?
Proteins are all constructed from a set of 20 amino acids.
How are amino acids joined?
Amino acids are joined by covalent peptide bonds creating polypeptides.
What is the structure of an amino acid?
Each amino acid has a central alpha carbon, an amino group, carboxyl group, a hydrogen and a unique side chain (R group).
In general are non-polar amino acids hydrophobic or hydrophilic?
Hydrophobic
What are the four structures of proteins?
Primary - Amino acid sequence
Secondary - Sequence of amino acids coils and folds due to hydrogen bonds.
Tertiary - R group differences cause different folds; hydrophobic/philic, ionic bonds, van der waals.
Quaternary - Reserved for proteins consisting of multiple polypeptide chains; kept together by H bonds or disulphides bonds.
What would you predict to happen if you had two drops of oil in a cup of water that bumped into one another?
The drops of oil would come together to reduce their overall surface area due to their hydrophobic nature.
What three parts make up a nucleotide?
Phosphate group, Penrose sugar and nitrogenous base.
What are the differences between deoxyribose and ribose sugar?
Ribose sugar which is found in RNA has a hydroxyl group on the 2’ carbon.
Deoxyribose sugar which is found in DNA has a H instead oh OH on the 2’ carbon, hence deoxygenated.
Which nitrogenous bases are pyrimidines and what shape do they have?
Cytosine, Thymine in DNA, and Uracil in RNA.
6 membered ring.
Which nitrogenous bases are purines and what shape do they have?
Adenine and Guanine both have a 6 membered ring fused with a 5 membered ring.
How are nucleotides joined together?
Nucleotides are joined together through phosphodiester bonds. Covalent bonds.
They are joined together to forma sugar-phosphate backbone with a repeating pattern.
What would be found at the 5’ end vs the 3’ end of the sugar-phosphate backbone?
The 5’ end is home to the phosphate group, whereas the 3’ end has a hydroxyl group.
What is the site of protein synthesis?
Ribosomes
Proteome
Full set of proteins expressed by an organism
How many polynucleotides make up a DNA molecule and how are they positioned relative to each other.
Two sugar phosphate backbones that run anti-parallel and are connected by hydrogen bonds between paired nitrogenous bases.
What is endosymbiosis theory?
The theory that ancient prokaryotes engulfed other prokaryotes forming eukaryotic organelles.
What are the differences between scanning electron microscopy and transmission electron microscopy?
SEM uses a beam of electrons that scans the surface of a specimen that has been coated in a heavy metal.
Produces a 3D image.
TEM uses a beam of electrons that passes through the specimen which is stained by a heavy metal. The electrons are scattered by the heavy meal and it produces a 2D image.
What is magnification?
Ratio of the objects image size to real life size.
What is resolution?
The minimum distance between two points that can still be distinguished as separate points.
What is contrast?
The difference in brightness between light and dark parts.
What are some differences between prokaryotes and eukaryotes?
Prokaryotes have no nucleus.
Prokaryotes lack membrane bound organelles.
Divide by binary fission as opposed to mitosis.
Prokaryotes are generally much smaller.
What are similarities between prokaryotes and eukaryotes?
Both have a plasma membrane and a cytoplasm.
What happens to the ratio between surface area and volume as a cube gets larger.
Surface area to volume ratio decreases as cube gets larger.
1x1x1cm cube has a SA of 6cm^2 and a volume of 1cm^3 - 6:1 ratio
3x3x3cm cube has a SA of 54cm^2 and a volume of 27cm^3 - 2:1 ratio
What are gap junctions?
Protein channels that form between the plasma membranes of two cells. This protein channel is large enough for ions and small molecules to pass from one cell to the other.
What are plasmodesmata?
Channels between two plant cells that pass through the cell wall.
What is the pathway of a protein destined for secretion from an animal cell?
Rough ER —> Transport vesicle —> Golgi —> Transport vesicle —> Plasma membrane
A cell with a predominance of free ribosomes is most likely:
A cell that is producing cytoplasmic enzymes.
How does transcribed mRNA exit the nucleus?
Through nuclear pores.
At what level of DNA organization would i expect to see the most transcriptional activity?
Nucleosomes
22% of an organism’s bases are G. What is the relative proportion of bases that will be A?
28%
44% are G and C
The remaining 56% would be split evenly between A and T.
RNA is synthesized in the _____ direction as it advances along the template DNA in the _______ direction.
5’ to 3’ ; 3’ to 5’
What is the function of the poly-A tail in mRNA?
To help protect the mRNA from degradation by hydrolytic enzymes.
What is the primary role of DNA polymerase III
Synthesizes the DNA after the primer.
What is the primary role of DNA polymerase I?
REPLACES RNA PRIMERS WITH DNA NUCLEOTIDES.
Primary role of DNA ligase?
Binds two Okazaki fragments in the lagging strand together.
Main role of topoisomerase?
Relieves torsional strain on the DNA double helix as it is unwound ahead of the helicase.
Main role of helicase?
Unwinds the DNA double helix.
What makes up the plasma membrane and how could it be described?
Made up of a phospholipid bilayer with a negatively charged phosphate hydrophilic head, as well as two non-polar hydrophobic tails. Suspended in bi-layer is proteins that help regulate traffic.
Phospholipids and proteins drift around the membrane creating a “fluid mosaic”.
Nucleus
Contains majority of the genetic information of a eukaryotic cell.
Enveloped by a nuclear envelope which is made up of two membranes; an outer and inner nuclear membrane.
Nuclear lamina
Protein filaments on the inside of the nucleus that help maintain the structure of the nucleus.
Nucleolus
Region of nucleus where rRNA is synthesized. rRNA is combined with protein components to form ribosomes then transported out through the nuclear pore envelopes.
Ribosomes
Responsible for protein synthesis
Found in the cytosol, attached to outside of nucleus or the rough ER.
DNA transfers into to mRNA in nucleus —> mRNA exits nucleus and binds to ribosome —> mRNA moves through ribosome translating the genetic message into a specific protein.
What organelles are included in the endomembrane system?
Nuclear envelope
ER
Golgi apparatus
Lysosomes
Various vesicles and vacuoles
Plasma membrane.
All related to one another either through direct physical continuity or by transfer of segments via vesicles.
Smooth ER
Lipid synthesis
Metabolism of carbohydrates
Drug and poison detoxification
Calcium storage
Smooth ER is smooth duh
Endoplasmic Reticulum
Connected to the nuclear envelope.
Rough and smooth ER are connected but have different functions.
Rough ER
Studded with ribosomes.
Newly made proteins from the ribosomes enter the ER where enzymes may change the proteins before being transported elsewhere by vesicles.
Location where carbohydrates are added to proteins ( glycosylation).
Golgi apparatus
Receives, refines, stores and transports products around the cell.
Products from ER are shipped to Golgi by vesicles.
One side serves as a receiving dock (cis face)where vesicles are received and then modified as they travel through the Golgi.
The shipping side (trans face)then ships the modified proteins within vesicles to other organelles or the plasma membrane.
Vesicles bound to the plasma membrane either transfer proteins to it or secrete products out of the cell.
Lysosomes
Membrane enclosed sac of digestive enzymes.
Made in the rough ER and processed in Golgi.
Recycle damaged organelles through process called autophagy
Food engulfed in a process called phagocytosis can be digested
Can work in acidic environments (stomach acid)
Vacuoles
Large vesicles from the endomembrane system
Ex: Food vacuoles , contractile vacuoles pump out water.
Plant cells have one large central vacuole that stores inorganic ions and can absorb water allowing a plant call to grow without producing more cytoplasm.
Mitochondria
Generates ATP and contributes to cellular respiration
Interior space is called matrix
Have an inner and outer-membrane with an Inter membrane space in between.
Chloroplasts
Performs photosynthesis
Inner and outer membrane space with an inter membrane space between.
Flattened sacks called thylakoids are stacked into granum
Fluid inside membrane surrounding thylakoids is stroma where the DNA is contained.
Peroxisomes
Contain enzymes that produce hydrogen peroxide and can be used to detoxify harmful compounds.
Contain as to not damage the cell.
Microtubules
Stiff, hollow tubes composed of tubular heterodimers.
Cell shape, cell motility, chromosome movement, organelle/vesicle movement.
Can grow and shrink rapidly.
Centrosome
Region where microtubules come from.
Within centrosome is a pair of centrioles
Cilia
Small numerous hair like structures.
Ex: Cilia in respiratory tract move dust to be swallows, movement of eggs along oviduct.
May be used for signalling by detecting chemicals
Power and recovery stroke.
Flagella
Long, whiplike structure capable of allowing cell movement.
Longer than cilia
Sperm
Actin filaments
Built using a twisted double chain of actin subunits
Supports cell share
Work in conjunction with motor or proteins for muscle contraction, localized contractions.
Built and disassembled quickly.
Intermediate filaments
Intermediate in thickness.
Composed of multiple proteins coiled
Do not polymerize quickly
Only in animals
Contribute to cell structure (nuclear lamina.
Progeria caused by mutation in IF
Structure and function of Cell walls
Made primarily of cellulose.
Helps maintain cell shape, prevent excess water intake, resists gravity.
Made up of primary cell wall followed by a second cell wall and then a plasma membrane.
Middle lamedla helps cells stick together.
Extra cellular matrix
Composed of glycoproteins (collagen) and proteoglycans
Can provide mechanical support for cells, act as a barrier
May function in signalling.
Glycoprotein
Protein with one or more covalently attached carbohydrates
Proteoglycan
Large molecule consisting of a small core protein with many carbohydrate chains attached.
Collagen
Forms fibres
Integrins
Span the membrane and serve as attachment sites for cytoskeleton
Fibronectin
Bridges components of the ECM to the cell by binding to integrins.
Tight junctions
Binds the plasma membrane of two cells together using proteins with a watertight seal.
Desmosomes
Rivets anchoring one cell to another using protein
What is Chargaff’s rule?
A + G = T + C
A = T
C = G
How many hydrogen bonds are formed between A and T? G and C?
A and T form 2 hydrogen bonds
C and G form 3
In what manner is DNA replicated?
Semi-conservative
Can DNA polymerases initiate synthesis of a polynucleotide?
No, they require a primer.
How are RNA primers added?
They are added by an enzyme called primase.
What stops DNA from repairing after helicase?
Single stranded binding proteins
Which direction does DNA polymerase build?
DNA polymerase builds the NEW strand in the 5’ to 3’ direction. It moves along the old strand in the 3’ to 5’ direction.
How is proofreading carried out?
DNA polymerase 1 and 3 “proofread”. If there is an incorrect nucleotide nuclease will remove it.
Repair synthesis is then carried out by DNA polymerase and ligase.
What provides energy for polymerization?
DNTP’s
What are telomeres?
Telomeres are repetitive G and T rich, non-coding sequences.
They are at the end of chromosome to protect from degradation.
Enzyme telomerase elongates end of chromosomes.
How is DNA packaged?
DNA is packaged with histones to form chromatin.
Chromatin is packaged into chromosomes.
What are the levels of DNA structure and which are transcriptionally active?
DNA double helix —> Nucleosomes (beads on a string) —> 30nm fibre —> 300nm fibre —> Metaphase chromosome.
DNA packed in 30nm fibre and higher are generally transcriptionally inactive.
What level of DNA structure is expected during interphase? Mitotic phase?
DNA exists often as nucleosomes or 30nm fibre during interphase and then condensed into metaphase chromosomes during mitotic phase.
What are restriction sires and how do they work?
Restriction sites are symmetrical sequences that are cut using restriction enzymes.
Fragments cut with the same enzyme can be fused together by DNA ligase to produce recombinant DNA.
What are plasmids?
Small circular DNA molecule found in bacteria and other cells. Can replicate separately from the chromosome.
Minimal medium
Contains the minimum requirements for cellular growth
Complete medium
Contains everything a cell needs to grow plus things cells normally synthesize.
Where and when do transcription and translation happen in eukaryotes vs prokaryotes?
Translation and transcription happen concurrently in prokaryotes. No opportunity for mRNA to be modified.
In eukaryotes transcription occurs in the nucleus and translation begins in the cytoplasm. RNA processing allows pre-mRNA to be modified before translation.
What is the relationship between the coding/non-template strand and the mRNA produced?
The coding strand will mirror the mRNA produced other than the T’s in the coding strand will be replaced with U’s in the mRNA.
What is the relationship between the non-coding/template strand and the mRNA produced?
The non-coding strand is used as a template for the mRNA which base pairs with the template strand.
Template strand: 3’ - A G G C T - 5’
Resultant mRNA strand: 5’ - U C C G A - 3’
RNA polymerase
Synthesizes RNA using the DNA template
Does not need a primer however recognizes a promoter as where to start
Promoter
DNA sequence that makes where the RNA polymerase binds and begins transcription.
Often includes a TATA box.
Transcription factors
Help the RNA polymerase bind and function.
In what direction is RNA synthesized?
5’ to 3’ direction.
5’ is upstream
3’ downstream
What are the steps of transcription?
Initiation: RNA polymerase binds to promoter
Elongation: Polymerase moves downstream unwinding DNA and elongating the RNA in the 5’ to 3’ direction.
Termination: A polyadenylation signal (AAUAAA) is transcribed, resulting in proteins binding and termination of transcription.
What are the three steps in RNA processing.
- Addition of a 5’ cap consisting of a modified guanine nucleotide. Help ribosomes attach to 5’ end.
- A poly-A tail made up of 50-250 adenine nucleotides is added to 3’ end.
(Both help with export out of nucleus and protection from degradation. ) - RNA splicing
RNA splicing
Removal of introns (non-coding segments) by spliceosome and joining of exons (coding segments).
Alternative splicing is the different combinations of exons that result in different mRNA and proteins.
Spliceosome
Made of protein and small nuclear RNA which is responsible for splicing.
catalyses the removal of introns
Example of a ribozyme.
Codons
Group of three nucleotides.
64 possible codons that encode for all 20 standard amino acids.
Each codon only encodes for one amino acid but multiple codons can encode for the same amino acid,
Transfer RNA
Acts as a bridge between RNA and protein.
Contains a three nucleotide anticodon that recognizes codons on mRNA.
Carries a specific amino acid that corresponds to the anti-codon.
Composed of a single RNA strand that base pairs with itself forming a 3D upside down L shape.
Codons and Anticodons
MRNA is written in the 5’ to 3’ manner where’s the anticodon of the tRNA is written in the 3’ to 5’ manner to align with the mRNA codon.
How are tRNA linked to an amino acid?
They are attached by enzymes known as aminoacyl-tRNA synthetases.
Structure of Ribsomomes
Large and small subunit
Example of a ribozyme
Responsible for translation .
What are the three steps of translation?
Initiation: mRNA binds to the small subunit (5’ cap allows it to be recognized). Special initiator tRNA carrying MET binds to the start codon AUG on the mRNA (bound to the P site not A site).
(Binding of all proteins requires hydrolysis of GTP)
Elongation: tRNA binds to A-site, peptide bond formed between the polypeptide on the tRNA in the P site and the new amino acid on the tRNA in the A-site. Polypeptide is transferred to the new amino acid.
TRNA in P-site is moved to E-site where it exits and a new tRNA can enter into the A-Site.
Termination: At the stop codon a release factor (which is a protein) binds to the codon. RF promotes the polypeptide to hydrolase from the tRNA freeing it from the ribosome.
Post-Translational modifications
Addition of sugars, lipids or phosphates
Cleaving of parts of peptide
Brining multiple polypeptides together.
How do polypeptides reach certain locations?
Signal peptides will be recognized by SRP’s that escort it to the ER.
If a protein is embedded in ER membrane it stays there.
If it is soluble it will either stay in the lumen or be secreted.
Some proteins are produced in the cytosol and imported to different destinations in the cell by signal peptides.
Point mutation
Change in a single nucleotide pair.
Cause of sickle cell anemia.
Silent mutation
Have no effect on the amino acid sequence
Missense
Changes the amino acid sequence.
Nonsense
Mutated codon encodes for a stop codon resulting in premature termination.
Insertions/deletions
Addition or removal of a nucleotide pair that can have drastic results.
Frameshift mutations
Insertion/deletion resulting in all codons downstream to be shifted out of original frame.
What factors increase membrane fluidity?
More double bonds create a more fluid membrane
Shorter fatty acid tails increase membrane fluidity
At low temps cholesterol hinders ability to pack too closely together.
What factors decrease membrane fluidity?
Lower amounts of double bonds.
Longer fatty acid tails.
At high temps cholesterol restrains phospholipid movement.
Lower temps decrease fluidity.
Integral membrane proteins
Proteins embedded in the membrane.
If they span the whole membrane they are transmembrane proteins
Peripheral membrane proteins
Proteins associated with the membrane but not embedded.
Membrane Protein functions?
Transport, enzymatic activity, signal transduction, cell to cell recognition, attachment to cytoskeleton and ECM, intercellular joining.
What is cell to cell recognition and how does it occur?
Cells ability to discern one cell from another.
Cells recognize cells by binding to primarily glycolipids and glycoproteins.
Carbohydrates almost exclusively on extra cellular side.
What happens to plant and animal cells in a hypotonic solution?
Plant cells become turgid while animal cells will lyse or burst.
What happens to plant and animal cells in an isotonic solution?
Plant cells become flaccid or wilted while animal cells are normal.
What happens to plant and animal cells in a hypertonic solution?
Plant cells will plasmolyze where the cell membrane pulls away from the cell wall.
Animal cells will become shrivelled.
Order of most permeable to least permeable molecules across a cell membrane?
Small non-polar molecules —> Small uncharged polar molecules —> Large uncharged polar molecules —> Charged molecules
Ex: O2 —> H2O —> Glucose —> H+
What factors increase diffusion across a membrane?
Smaller size diffuse faster
Hydrophobic molecules diffuse faster
Osmosis
Diffusion of water across a selectively permeable membrane.
Diffusion
Process by which molecules move from a place of high concentration to low concentration.
Substances diffuse down their concentration gradient.
Passive vs Active transport
Passive does not require energy.
Active requires an input of energy usually in the phosphorylation of the pump by ATP.
Active transport moves a solute against its electrochemical gradient.
Example is a Na+/K+ pump.
What are some types of transport proteins and their functions?
Carrier proteins transport molecules or ions that fit into binding sites and then change their shape to move them in or out.
Channel proteins allow material to flow through a channel that discriminates based on size and charge.
Both are examples of facilitated diffusion.
What does it mean for a cell membrane to have a potential of -20mV?
Indicates that the inside of the cell is has a negative charge of 20mV.
What is an electrogenic pump?
A transport protein that generates a voltage across the membrane.
Example: Na+/k+ pump.
Electrochemical gradient
Diffusion gradient of a charged solute.
Depends on difference in concentration across membrane and relative membrane potential.
Cotransport
Form of indirect active transport involving the movement of one solute with another.
Endocytosis
Uptake of material forming vesicles at plasma membrane.
Phagocytosis
Cellular eating, uptake of large substances.
Pinocytosis
Cell drinking
Indiscriminate uptake of fluid and dissolved solutes
Receptor mediated endocytosis
Allows selective uptake of substances.
Specific solutes bind to receptors for uptake.
Exocytosis
Excretion of bio molecules by fusing vesicles to plasma membrane.
Thermodynamics
The study of the energy of systems
Bioenergetics
The study of how energy flows through living organisms
Metabolism
Totality of an organisms chemical reactions
Catabolic pathways
Pathways that release energy by breaking down complex molecules into simpler molecules.
Increases entropy
Exergonic
Decreases potential energy
Anabolic pathways
Pathway that consumes energy to build complex molecules from simpler ones.
Decreases entropy
Endergonic
Increase potential energy
Kinetic energy
Energy associated with the movement of objects
Thermal energy is a form of kinetic energy associated with the random movement of atoms or molecules. (Heat)
Chemical energy
Potential energy available for release in a chemical reaction
First law of thermodynamics
Energy cannot be created or destroyed only transferred or transformed.
Second law of thermodynamics and entropy
Second law of thermodynamics states that every energy transfer or transformation increases the entropy of the universe.
Entropy is a measure of disorder.
Endergonic vs Exergonic reactions
Endergonic reactions require energy and are non spontaneous change in Gibbs free energy is positive
Exergonic reactions release energy and are spontaneous, negative change in Gibbs free energy.
When is a reaction spontaneous?
IF the change in Gibbs free energy is negative it will be spontaneous.
Spontaneous reactions increase entropy.
Chemical work
Drive Endergonic reactions like building macromolecules
Transport work
Moving molecules across a membrane against the direction of spontaneous movement.
Mechanical work
Beating of cilia, motor proteins.
Why is ATP high in energy?
The three phosphates of ATP are negatively charged making it very unstable due to them repelling each other.
What is the change in Gibbs free energy of ATP —> ADP + Pi
-30.5 kj/mol
ADP + Pi —> ATP = +30.5 kj/mol
Phosphorylated intermediate
Reactant with a phosphate added to it.
More unstable thus more reactive.
Catalyst
Substance that speeds up the rate of a reaction by lower the activation energy of the reaction.
Not consumed by the reaction.
Enzymes are biological catalysts.
Change in Gibbs free energy is unaltered by catalysts.
Transition state and activation energy
The transition state is the point where the reactants are most unstable
Activation energy is the energy required for a reaction to occur
What is meant by induced fit in regard to enzymes?
The enzyme and substrate change shape to create a perfect fit.
Much like two people hugging as opposed to a lock and key.
What holds substrate and enzyme together?
Weak bonds such as Van der Waals, hydrogen bonds and sometimes covalent bonds.
What are some possible enzyme mechanisms?
Enzyme aligns the substrates in a certain orientation
Causes the substrate to change its geometry forcing certain bonds to be broken
Provides an environment favourable for a reaction
Directly participates in the reaction
Why do enzymes function optimally at certain pH and temperature levels?
Changes in pH and temperature can cause the enzyme to denature and lose its very specific shape due to weak bonds being broken.
Cofactor
Non-protein helpers of catalytic activity
Ex: Mg2+, Zn2+, Cu2+
Coenzyme
Organic cofactors.
What is the difference between competitive and non-competitive inhibitors?
Competitive inhibitors bind to the active site of the enzyme, competing with the substrate for real estate (can be overcome by adding more substrate).
Non-competitive inhibitors bind at a point distinct from the active site and change the shape of the enzyme.
Allosteric regulation
Binding of a regulatory molecule to a protein at one site that affects the function of the protein elsewhere.
Activators stabilize active form of an enzyme
Inhibitors stabilize the inactive form
Cooperativity
Some proteins exhibit cooperativity, where after interacting with a substrate all the other subunits become better at binding the substrate.
Feedback inhibition
The end product of a metabolic pathway acts as an inhibitor for the same pathway preventing the enzyme from overproducing a product.
Where does glycolysis occur? What are the inputs and outputs?
Occurs in the cytosol.
Splits glucose into two molecules of pyruvate, needs 2 ATP to activate glucose.
Generates 4 ATP and 2 NADH
What is substrate-level phosphorylation?
Method of ATP synthesis where an enzyme transfers a phosphate group from one substrate to ADP.
Does glycolysis involve any oxidation reactions?
Yes, although it does not require oxygen. G3P is oxidized and NAD+ is reduced to NADH.
What are dehydrogenases?
Enzymes that strip 2 hydrogens from glucose.
NAD+ accepts 2 electrons and 1 proton.
Where does pyruvate oxidation occur? What are the inputs and outputs?
If oxygen is present pyruvate will enter the mitochondria.
In the mitochondrial matrix 2 pyruvate molecules are oxidized into 2 acetyl CoA and 2 NADH. CO2 is released.
Then enters Citric Acid Cycle.
Where does the Citric Acid Cycle take place? What are the inputs and outputs?
Occurs in the mitochondrial matrix.
Inputs: 2 Acetyl CoA
Outputs: 2 ATP, 6 NADH and 2 FADH2
Where does the Electron Transport Chain take place in the mitochondria? Where is their a higher conectration of protons?
Inside the inner mitochondrial membrane.
In the inter membrane space
Where in the mitochondria is there a high proton concentration?
In the inter membrane space.
What path does NADH take through the ETC?
Complex 1 —> Coenzyme Q —> Complex 3 —> Cytochrome c —> Complex 4 —> O2
What path does FADH2 take through the ETC?
Complex 2 —> Q —> Complex 3 —> Cyt c —> Complex 4 —> O2
What is chemiosmosis?
The use of stored energy in the form of a proton gradient across a membrane to drive work.
What is oxidative phosphorylation?
The process by which electrons move down an ETC resulting in the formation of ATP from ADP.
Do enzymes change equilibrium points?
NO
Fermentation
Method of harvesting chemical energy without using oxygen or an ETC.
Allows the regeneration of NAD+ without oxygen.
Facultative vs Obligate anaerobes
Obligate anaerobes cannot survive in the presence of oxygen.
Facultative anaerobes can survive using either fermentation or respiration.
How can fatty acids be broken down into acetyl-CoA
Beta oxidation
What are autotrophs? Photoautotrophs?
“Self feeders”
Photoautotrophs convert light energy into chemical energy.
What are heterotrophs?
Consumers
Unable to make their own food.
What is detritus and what are detritivores?
Non-living organic material
Detritivores consume detritus
Where are chloroplasts found?
In mesophyll cells.
What are stomata?
Small pores in leaves that help exchange gasses.
What is mesophyll?
Tissue in the interior of the leaf; made up of mesophyll cells.
What is NADP+ and how does it become NADPH?
NADP+ is an electron carrier.
NADP+ accepts two electrons and a hydrogen from the stroma to form NADPH.
How are wavelength and energy related?
Shorter wavelengths have higher energy.
What are pigments?
Substances that absorb visible light.
What is the main light-capturing pigment?
Chlorophyll a
What is an absorbance spectrum?
Graph plotting a pigments light absorbance versus wavelength.
What is the action spectrum for photosynthesis measuring?
Plots the rate of photosynthesis vs wavelength.
What is the purpose of chlorophyll b and carotenoids?
Broaden the spectrum of light that can be used for photosynthesis.
Carotenoids mat absorb and dissipate excessive light energy to prevent damage to chlorophyll in plants.
What is resonance energy transfer?
Moving energy from one electron to another without transferring the electron.
What is aneuploidy and how is it caused?
Aneuploidy is having an abnormal number of chromosomes. Normally cause by non-disjunction.
What is the recombination frequency of unlinked genes?
50% due to independent assortment
Linked gene recombination frequency?
Results from crossing over. Less than 50%.
