Bio: Molecular Biology Flashcards
why are cells small
due to reliance on the diffusion of substances in and out ofthe cell
waht is tyhe rate of diffusion reliant upon
surface area avaliable
termpature
concentration gradient (ficks first law)
distance - larger cells means greater distance
what does greater surface area mean
means greater interaction with the environment because all substances enter and exit via the surface (membrane)
basic structural similarities between eukaryotic and prokaryotic cells
- nucleoid or nucleus where DNA is located
- cytoplasm - semifluid matrix of organelles and cytosol
- ribosomes
- synthesis proteins - translation - plasma membrane
- phospholipid bilayer, transporter proteins
bacterial walls
- Most bacterial cells are encased by a strong cell wall.
- Composed of peptidoglycan (carbohydrate matrix cross-linked by short peptides).
- Cell walls of plants and fungi are different.
- Protect the cell, maintain its shape, and prevent excessive uptake or loss of water.
- The susceptibility of bacteria to antibiotics often depends on the structure of their cell walls.
- Archaea lack peptidoglycan (only protein).
eukaryotic cells
- Possess a membrane-bound nucleus.
- More complex than prokaryotic cells.
- Hallmark is compartmentalization (achieved through membrane-bound organelles or endomembrane system).
- Possess a cytoskeleton for support and to maintain cellular structure.
stuff 2 know about the nucleus
- Store genetic information.
- Most eukaryotic cells possess a single nucleus.
- Nuclear envelope (membrane)
* two phospholipid bilayers.
* nuclear pores - control movement in and out (proteins). - In eukaryotes, the genes (made of DNA) are present in chromosomes.
- Chromatin - DNA and protein in chromosomes.
stuff to know about ribosomes
- Cell’s protein synthesis machinery.
- Found in all cell types (prokaryotes and eukaryotes).
- Ribosomal RNA (rRNA) - proper alignment of mRNA and ribosomes and catalyze the peptide bonds).
- Protein synthesis also requires messenger RNA (mRNA) and transfer RNA (tRNA - provide anticodon).
- Ribosomes may be free in the cytoplasm or associated with internal membranes (ER and nuclear membranes).
animal vs plant cells
Animal and plant cells have largely the same structure
* Both have plasma membranes.
* Contain most of the same organelles.
Plant cells have extra components usually not present in animal cells
* A cell wall outside of the plasma membrane.
* Chloroplasts and specialized vacuoles internally.
stuff to know about the endoplasmic reticulum
Rough endoplasmic reticulum (RER)
* Attachment of ribosomes to the membrane gives a rough appearance.
* Slasthan empateins to be secreted, sent to lysosomes or Smooth endoplasmic reticulum (SER)
* Relatively few bound ribosomes.
* Variety of functions - synthesis (carbohydrates, lipids steroids, hormones etc.), store Ca*, detoxification (especially in liver cells).
Ratio of RER to SER depends on cell’s function.
things to know about vescicles
- Membrane-bound (tonoplast) structures typically found in plants.
- Contractile vacuoles (very small) in some fungi and animal cells.
- Various functions depending on the cell type Storage vacuoles in plants (waste, toxins, heavy metals, NaCl or any kind of unwanted material).
things to know about the golgi apparatus
- Flattened stacks of interconnected membranes
(Golgi bodies). - Functions in packaging and distribution of molecules synthesized at one location and used at another within the cell or even outside of it.
- Has cis (near ER) and trans faces.
- Vesicles transport molecules to the destination.
things to know about lysosomes
- Membrane-bounded digestive vesicles.
- Arise from the Golgi apparatus.
- Contain enzymes that catalyze the breakdown of macromolecules.
- Fuse with a target to initiate the breakdown
- Recycle old organelles, or digest cells and foreign matter that the cell has engulfed by phagocytosis
things to know about microbodies
Variety of enzyme-bearing, membrane-enclosed vesicles.
Peroxisomes
1. Contain enzymes involved in the oxidation of fatty acids.
2. Hydrogen peroxide produced as a by-product - rendered harmless by catalase enzyme.
things to know about eukaryotic cell walls
Present in plants, fungi, and some protists
Eukaryotic cell walls are distinct from prokaryotic cell walls chemically and structurally
* Plant and protist cell walls made of cellulose and hemicellulose.
* Fungi cell walls are made of chitin.
* Plant cells have primary and possibly secondary cell walls (mostly lignin and suberin).
things to know about chloroplasts
- Organelles present in cells of plants and some other eukaryotes.
- Surrounded by two membranes.
- Contain chlorophyll for photosynthesis.
- Thylakoids are membranous sacs within the inner membrane.
Grana are stacks of thylakoids. - Have their own DNA
membrane structure
- Phospholipids arranged in a bilayer
- Globular proteins inserted in the lipid bilayer
- Fluid mosaic model - a mosaic of proteins floats in or on the fluid lipid bilayer like boats on a pond
plasmodesmata
Plant cells have plasmodesmata
*
*
Specialized openings in their cell walls.
Cytoplasm of adjoining cells are connected.
Function - communication between cells, transport of molecules between cells.
Main components of plasma membrane
- Phospholipid bilayer
* Flexible matrix, barrier to permeability. - Transmembrane proteins
* Integral membrane proteins.
membrane proteins Various functions:
- Transporters
- Enzymes
- Cell-surface receptors
- Cell-surface identity markers
- Cell-to-cell adhesion proteins
- Attachments to the cytoskeleton
enerrgy definition
capacity to do work
redox reactions
During chemical reactions, electrons pass from one atom or molecule to another
* Atom or molecule loses an electron - Oxidation
* Atom or molecule gains an electron - Reduction
* Reduced form has a higher level of energy than the oxidized form
* Reduction — Oxidation reactions (redox)
* Reactions are always paired.
first law of thermodynamics
- Energy cannot be created or destroyed
- Energy can only be changed from one form to another
- Total amount of energy in the universe remains constant
- During each conversion, some energy is lost as heat
eenrgy flow
- Sun provides energy for most living systems.
- Energy flows into the biological world from the sun.
- Photosynthetic organisms capture this energy, e.g. plants, algae and some bacteria.
- In photosynthesis, absorb energy from sunlight is used to convert small molecules (water and CO,) into complex molecules (sugars).
- Stored as potential energy in chemical bonds.
- Energy stored in chemical bonds may be used for some cellular processes, e.g. respiration.
second law of thermodynamics
Energy cannot be transformed from one form to another with 100% efficiency
* Some energy is always unavailable - Entropy
* Energy transformations proceed spontaneously to convert matter from a less stable form to a more stable form
gibbs free energy
G = Free energy available to perform work
G = H-TS
* H = enthalpy, energy in a molecule’s chemical bonds.
T = absolute temperature or Kelvin temperature
(K = 273 +°C).
* S = entropy, unavailable energy.
ΔG = ΔH - TS
ΔG = change in free energy
Positive ΔG
* Products have more free energy than reactants.
* H is higher or S is lower.
* Not spontaneous, requires the input of energy (uphill reaction).
* Endergonic.
Negative ΔG
* Products have less free energy than reactants.
H is lower or S is higher or both.
* Spontaneous.
Exergonic.
endergonic
ΔG > 0 , energy must be supplied
entropy
Entropy increases as the ice melts
Water molecules in ice form are less stable (less entropy), while in liquid form they are mostly more stable (high entropy).
Less entropy - high available energy
High entropy - low available energy
exergonic
ΔG < 0 , energy is released
ATP cycle
ATP drives endergonic reactions (uphill reactions)
* If ATP hydrolysis releases more energy than the other reaction needs - coupled reaction results in net -G or G < 0 (exergonic and spontaneous).
ATP is not suitable for long-term energy storage
* Phosphate bonds are too unstable
* Fats and carbohydrates are better
* Cells store only a few seconds worth of ATP.
ATP
Adenosine triphosphate
* Primary energy “currency” used by cells
* Cells store and release energy in the bonds of ATP
* Breakdown (hydrolysis) of ATP is an exergonic reaction (ATP has more energy than ADP or AMP)
ATP —> ADP + Pi + energy.
release energy or use for other reactions
aerobic respiration
C6H1206 + 602 → 6C02 + 6H20 + Energy
Free energy = - 686 kcal/mol of glucose (exergonic)
G OR ΔG<0)
Free energy can be even higher than this in a cell.
* This large amount of energy must be released in small steps rather than all at once.
electron acceptors
Aerobic respiration
* The final electron receptor is oxygen (O,).
Anaerobic respiration
* The final electron acceptor is an inorganic molecule (not 02), such as sulfur, nitrate, carbon dioxide, etc.
Fermentation
* The final electron acceptor is an organic molecule, such as an organic acid.
electron carriers
Many types of carriers used
* Soluble, membrane-bound, moves within the membrane.
* All carriers can be reversibly oxidized and reduced.
* Some carry just electrons, and some electrons and protons.
* NAD+ acquires two electrons (e) and a proton (H+)
to become NADH.
aerobic respiration
starts in cytoplasm (glycolysis), glucose makes two pyruvate molecules. pyruvate is the molecule that enters into the mitochondria
second step is the oxidation process, pryuvate is converted into acetyl coA, the last step happens in the inner membrane.
aerobic respiration steps
The complete oxidation of glucose proceeds in stages:
1. Glycolysis
2. Pyruvate oxidation
3. Citric acid cycle
4. Electron transport chain & chemiosmosis
step 1. glyoclysis
- Converts 1 glucose (6 carbons) to 2 pyruvate (3 carbons)
- 10-step biochemical pathway
- Occurs in the cytoplasm
- Net production of 2 ATP molecules by substrate-level
phosphorylation - 2 NADH produced by the reduction of NAD+
Net Energy production: 2ATP + 2NADH
the fate of pyruvate
Depends on oxygen availability
* When oxygen is present, pyruvate is oxidized to acetyl coenzyme A (acetyl-CoA) which enters the citric acid cycle.
* Aerobic respiration.
* Without oxygen, pyruvate is reduced in order to oxidize NADH back to NAD+
* Fermentation / anaerobic respiration.
crtic acid cycle net energy production
6 NADH
2 FADH2
2 ATP
total atp = 20
pyruvate oxidation (with O2) net energy production
2 NADH
the energy level of NADH and FADH
1 NADH = 2.5 ATP
1 FADH2 = 1.5 ATP
3rd step citric acid cycle
happens in the matrix of the mitochondria
Oxidizes the acetyl group (2C) from pyruvate (3C)
* Occurs in the matrix of the mitochondria
* Biochemical pathway of nine steps in three segments
1. Acetyl-CoA (2C) + oxaloacetate (4C) → citrate (C6)
2. Citrate rearrangement and decarboxylation
3. Regeneration of oxaloacetate
step 4. electron transport chain (again for first year you dont have to remebver intermediate stages)
location = inner mitochondrial membraine
Electron transport chain (ETC) is a series of membrane-bound electron carriers
* Embedded in the inner mitochondrial membrane
* Electrons from NADH and FADH are transferred to complexes of the ETC
ATP synthase structure
Accumulation of protons in the intermembrane space drives protons into the matrix via diffusion, but this occurs slowly since the membrane is relatively impermeable to ions
Most protons can only re-enter the matrix through ATP synthase
Uses energy of electrochemical gradient to make ATP from ADP +
* Process called chemiosmosis.
theoretical yield of respiration
ATP yield:
glycolysis = 5 ATP
pyruvate oxidation = 5 ATP
citric acid cycle = 20 ATP
theoretical energy yield of bacterias and eukaryotes
32 ATP per glucose for bacterias
30 ATP per glucose for eukaryotes
parts of the chloroplast you should be able to identify
inner membrane
outer membrane
lumen
disk-like thylakoid
stroma lamellae
intermembrane space
stroma (semi-liquid)
granum (or grana)
photosynthesis overview
Energy for all life on Earth ultimately comes from photosynthesis:
6C02 + 12H20 + Light → C6H1206 + 6H20 + 602
Oxygenic photosynthesis is carried out by:
* Cyanobacteria.
* Seven groups of algae.
* All land plants - inside chloroplasts.
Anoxygenic photosynthesis is carried out by:
* Some bacteria (purple, green sulfur, green non-sulfur)
stuff to know about light as a source of energy
- Light is a form of energy.
- Photon - a particle of light.
* Acts as a discrete bundle of energy.
* The energy content of a photon is inversely proportional to the wavelength of the light. - Photoelectric effect - removal of an electron from a molecule by light
chloroplasts
- Thylakoids (disc-like structures).
- Contains chlorophyll and other photosynthetic pigments.
- Pigments clustered into photosystems (proteins).
- Grana - stacks of flattened disks of thylakoids.
- Stroma lamella - connect grana.
- Stroma - semi-liquid surrounding thylakoids
absorption spectrum
When a photon strikes a molecule, its energy is either:
* Lost as heat.
* Absorbed by the electrons of the molecule.
(Boosts electrons into higher energy level).
Absorption spectrum - range and efficiency of photons a molecule can absorb.
structure of chlorophyll
1 Porphyrin ring.
* Complex ring structure with alternating double and single bonds.
Magnesium ion at the centre of the ring.
2 Photons excite electrons in the ring.
3 Electrons are shuttled away from the ring.
chlorophylls
Chlorophyll a
- Main pigment in plants and cyanobacteria.
- Only pigment that can act directly to convert light energy to chemical energy.
- Absorbs violet-blue and red light.
Chlorophyll b
- Accessory pigment or secondary pigment absorbing light wavelengths that chlorophyll a does not absorb.
photosystem organisation
Light is captured by photosystems, each of which consists of two components:
1. Antenna complex
* Hundreds of accessory pigment molecules.
* Gather photons and feed the captured light energy to the reaction centre.
2. Reaction centre
* 1 or more chlorophyll molecules.
* Passes excited electrons out of the photosystem.
reaction centre
Transmembrane protein-pigment complex
* When a chlorophyll in the reaction centre absorbs a photon of light, an electron is excited to a higher energy level
* Light-energized electrons can be transferred to the primary electron acceptor, reducing it
antenna complex
Also called light-harvesting complex
- Captures photons from sunlight and channels them to the reaction center chlorophylls
- In chloroplasts, light-harvesting complexes consist of a web of chlorophyll molecules linked together and held tightly in the thylakoid membrane by a matrix of proteins
noncyclic photophosphorylation
Plants use photosystems Il and I in series to produce both ATP and NADPH
* Path of electrons not a cirçle
* Photosystems replenished with electrons obtained by splitting water
* Z diagram
photosystem I
Occurs at P700
Photosystem I accepts an electron from plastocyanin
Passes electrons to NADP+ to form NADPH
photosystem II
- Occurs at P680
- Essential for the oxidation of water.
- b6-f complex/cytochrome connects 2 Photosystems
- Proton pump embedded in thylakoid membrane.
- Passes electrons to plastocyanin, then passes to Photosystem I.
carbon fixation - calvin cycle
To build carbohydrates cells use:
* Energy = ATP from light-dependent reactions.
* Reduction potential = NADPH from
Photosystem I.
calvin cycle
- Also called C3 photosynthesis
- First intermediate molecule has three carbons.
- Key step is attachment of CO, to the 5-carbon sugar, ribulose 1,5-bisphosphate (RuBP) to form
3-phosphoglycerate (PGA) - Uses enzyme ribulose bisphosphate carboxylase/oxygenase or Rubisco
output of the calvin cycle
- Glucose is not a direct product of the Calvin cycle
- G3P is a 3 carbon sugar
- Used to form sucrose.
- Major transport sugar in plants.
- Disaccharide made of fructose and glucose.
- Used to make starch.
- Insoluble glucose polymer.
- Stored for later use.
photorespiration
Rubisco has two enzymatic activities:
1. Carboxylation
* Addition of CO, to RuBP.
* Favored under normal conditions. (Photosynthesis)
2. Photorespiration
* Oxidation of RuBP by the addition of 02.
* Favored when stomata are closed in hot conditions.
* Creates low-COz and high-02*
CO, and O, compete for the active site on RuBP
types of photosynthesis
C3
* Plants that fix carbon using only C photosynthesis (the
Calvin cycle). - e.g. Dicot plants
C4 and CAM
* Add CO, to phosphoenolpyruvate (PEP) to form 4 carbon molecule.
* Use PEP carboxylase.
* Greater affinity for CO,, no oxidase activity.
* CAM - temporal solution to photorespiration.
C4 pathway
- C4 pathway, although it overcomes the problems of photorespiration, does have a cost
- To produce a single glucose requires 12 additional
ATP compared with the Calvin cycle alone - Cy photosynthesis is advantageous in hot dry climates where photorespiration would remove more than half of the carbon fixed by the usual C3
pathway alone
comparing C4 and CAM photosynthesis
- Both use both C3 and C4 pathways
- C4 - two pathways occur in different cells
- CAM - C4 pathway at night and the C3 pathway during the day
