Chapter Notes Flashcards
Lysosomes
Small, irregularly shaped organelles in which intracellular digestion occurs, releasing nutrients from food particles and breaking down uwanted molecules for recycling or excretion
Peroxisomes
small, membrane enclosed vesicles that provide a contained environment for reactions in which H2O2, a dangerously active chemical, is generated and degraded.
Continual exchange of materials takes place between what organelles
The ER, golgi apparatus, lysosomes, and the outside of the cell.
What mediates the exchange of materials from the ER to the outside of the cell?
Vesicles. They pinch off from the membrane of one organelle and fuse with another
Most hormones, neurotransmitters, and other signaling molecules are secreted from cells by _____
Exocytosis
True or false. There are no molecules in the cytosol.
False. The cytosol contains a host of large and small molecules crowded together so closely that it behaves more like a gel-like substance
Glycolysis takes place in the ________.
Cytosol
The cytoskeleton is responsible for ________.
Directed cell movement
True of false: Plant cells possess a cytoskeleton
True. The cytoskeleton provides tracks for the transportation of organelles like the mitochondra throughout the cell.
Eukaryotes may have originated from _______
predator cells. The nucleus might have been develop to help guard the genome from the constant capturing of other cells.
Endosymbiosis Theory
Theory now accepted that states that the mitochondria was once a bacterial cell that was engulfed by the animal cell when Earth’s atmosphere first became oxygen rich.
What has research in E.coli revealed?
research has revealed that the basic processes such as DNA replication and decoding of genes occur in essentially the same way in our own cells as they do in E.coli.
Bond Strength
Measured by the amount of energy that must be supplied to break a bond
Covalent bonds
They are strong bonds resistant to being pulled apart by thermal motions (heating) and are usually torn apart only during specific chemical reactions
Sugars, besides having a central role in the production and storage of cellular energy, also play a role in ______
Structural Support
Cellulose
The most abundant organic molecule on earth. Forms plant cell walls-is a polysaccharide of glucose
Glycoproteins
Smaller oligosaccharides can be covalently linked to proteins. These commonly decorate the membranes of cells. These sugar chains are often recognized by other cells. Differences in the types of cell surface sugars form the molecular basis for different human blood groups.
Fatty acids are stored in the cell cytoplasm in the form of droplets of ______
Triacylglycerol
Unsaturated fatty acids are _______ in composition.
Softer (margarine)
Triacyglycerol
When a cell needs energy, the fatty acids chains can be released
Describe the components of a phospholipid molecule
Lipids
Fatty acids and their derivatives including triacylglycerol. These molecules are insoluble in water and soluble in fat and organic solvents
What is the most important function of fatty acids in the cell
The formation of membranes. These membranes are composed of phospholipids. Unlike triacylglycerols, the third site is instead attached to a hydrophilic phosphate group. Phospholipids are amphipathic. Triacylglycerols are predominantly hydrophobic.
Glycolipids
Another type of lipid found in the membrane. Contains one or more sugar groups instead of a phosphate group. These molecules play an important role in cell signaling, along with glycoproteins
Peptide Bond
The covalent linkage that links two or more amino acids together. Formed by a condensation reaction reaction that links one amino acid to the next.
True or false: D-amino acids not observed in any organism.
False. D-amino acids occur as part of bacterial cell walls and in some antibiotics.
What are the subunits of DNA and RNA?
Nucleotides
Nucleoside
A molecule made up of a nitrogenous base linked to a five carbon sugar (either ribose or deoxyribose)
Nucleotide
A nucleoside that also contains a phosphate group
Why are the nitrogenous rings of nucleotides/sides considered bases?
Under acidic conditions, they can each bind to a H+ (proton) and thereby increase the concentration of -OH ions in the solution.
Purine compounds
Adenosine and Guanine. These bear a second five membered ring fused to a six membered ring.
Pyrimidines
Cytosine, Uracil and Thymine. All contain a six membered ring
Besides their role in genetic synthesis, what other roles do nucleotides play in cellular activity?
Nucleotides can act as short-term carriers of chemical energy. ATP, for example, participates in the transfer of energy in hundreds of cellular reactions.
ATP
Formed through oxidation of foods. The three phosphates are linked together by two phosphoanhydride bonds. Rupture of these bonds releases large amounts of useful energy.
What is the most fundamental role of nucleotides in the cell?
Storage and retrieval of biological information. They serve as building blocks for the construction of nucleic acids (long polymers in which nucleotide subunits are covalently linked by the formation of a phosphodiester bond
What is the backbone of DNA composed of?
A sugar-phosphate backbone
How are nucelic acid chains synthesized?
From energy rich nucletide triphosphates by a condensation reaction that releases inroganic pyrophosphates during the phosphodiester bond formation
RNS is ________stranded
Single stranded polynucleotide chain.
DNA
Double stranded. Antiparallel strands are held together through hydrogen bonds between the bases of the two chains
How do cells benefit from catalysis?
It allows them to control their metabolism. The product of one reaction becomes the substrate for the upcoming on. This is what sets up the metabolic pathways.
How is biological order maintained?
Biologica
Electrostatic Interactions
Weak in water. This is becase charged, or partially charged, polar groups are shielded by their interactions with water molecules or with other salts present in the aqueous solution
Van der Waals Interactions
A weak bond formed by electrical attraction caused by fluctuating electric charge that arise whenever two atoms come within a very short distance of each other
Do cells defy the second law of thermodynamics?
No. Although cells appear to defy this law by creating order. In the course of performing the chemical reactions that generate order, chemical bond energy is converted into heat and released into the extracellular environment, thereby increasing the disorder of the surrounding.The amount of heat released by a cell must be great enough that the order created inside the cell is more than compensated by the decrease in order in the environment.
How does food provide organisms with energy?
Energy is stored on the chemical bonds of organic molecules of food stuff.
Why do plants need energy from sunlight?
Photosynthetic organisms-plants. algae, and some bacteria- are able to obtain all the atoms they need from the surroundings. (carbon from CO2, etc) They need the energy from sunglight to form chemical bonds between these atoms, linking them into small chemical bonds to form amino acids, sugars, and nucleotides
How many stages does Photosynthesis consists of?
Photosynthesis consists of two stages. One depends on light and the other does not. The first is the light dependent stage while the second is light independent. In this first stage, oxygen is derived from the splitting of water molecules. The second stage involved carbon fixation
Sugars are manufactured in the ______ stage of photosynthesis.
Sugars are made in the second, light independent stage of photosynthesis. This stage is often called carbon-fixation stage. Sugars are derived from carbon sioxide gas and water. PLants also use sugars as source of materials to make many other small and large macromolecules that are essential to the plant cell.
Can enzymes cause energetically unfavored reactions to occur?
No. Not by themselves. Enzymes speed up the rate of reaction for energetically **favored **reactions.
How does disorder increase?
Disorder increases when useful energy that could be harnessed to do work is dissipated into heat.
What does increasing the concentration of the reactants do to the free energy of the system
It decreases the free energy of the system. As the ratio of Y/X increases, the delta gibbs free energy becomes more negative and favors one side of the reaction
Delta G depends on the concentrations of the molecules in the reaction mixture
a) never
b) At any given time
c) it has no impact
At any given time. Since this occurs, de
Why do cells not reach a state of equilibrium?
The ration from reactant to product increases as more product is being created. But equilibrium is never reached because products are often being carried off to do some function. Products are often substrates for other reactions.
Free Energy
Energy that could be used to do work. In living cells, this is done at constant temperature
Do enzymes alter the standard free energy of a reaction?
NO. They lower the transition state free energy (activation energy) of a reaction and thus increase rate, but they do not change the standard free energy
What must you do to predict the outcome of a reaction?
You must measure its standard free energy change
When can reactions be coupled?
If it follows the first and they share one or more intermediates
Vmax
At this point, the acitive sites of all enzyme molecules in the sample are fully occupied by substrate, and the rate of product formation depends only on how fast the substrate molecule can be processed.
Km
An enzyme’s Km is the concentration of substrate at which the enzyme works at half its maximum speed.
What does a low value of Km signify?
A low value of Km means that the enzyme binds to the substrate very tightly.
What does a high value for Km signify?
It means that there is weak binding between the substrate and the enzyme
The formation of an activated carrier is coupled to an energetically ________ reaction.
FAVORABLE
ATP and phosphorylation
Some favorable ATP hydrolysis reactions often involve the transfer of the terminal phosphate of ATP to another molecule
NADPH
Participates in anabolic (biosynthetic) reactions
NADH
participates in catabolic pathways
S-adnosylmethionine
Another carrier molecule that specializes in the transfer of methyl groups
An alpha helix has hydrogen bonds every ______ amino acid
fourth. It also involves the amino group and the carbonyl group
Neruominidase binding sites are
two non-identical binding sites next to one another
Keratin structure consists of a/n ________
Coiled coiled regions with capped ends by globular domains containing binding sites that allow them to assemble into rope like intermediate filaments, which are a component of the cytoskeleton and create a structural scaffold for the cell’s interior
The most abundant fibrous protein in animals
Collagen
Collagen contains what amino acid every ______ position
Contains glycine at every third position
Elastin
Formed from relatively loose and unstructured polypeptide chains that are covalently cross linked into a rubberlike mesh
Disulfide bonds are catalyzed in the __________
Endoplasmic reticulum
Do di-sulfide bonds change the conformation of a protein?
No. They act as molecular staples
The loops in an immunoglobulin
amino acid sequence of this loops can be altered by mutation without altering the basic structure of the antibody. An enourmous variety of of antigen binding sites can be generated by changing only the length and amino acid sequence of the loops
Antibodies are only produced in ________ animals
Vertebrate
Why doesn’t a pure polysaccharide get cleaved when seated in water?
There is an activation energy that must be overcomed in order to perform the cleavage reaction done by Lysozyme. The polysaccharide molecule has to be distorted
Which two amino acid chains participate in the cleavage reaction of lysozyme?
Aspartate 52 and glutamic 35
Which amino acid first attacks in the lysozyme cleaving mechanism?
Aspartate 52
What gives blood its red color?
The heme prosthetic group attached to each domain in hemoglobin
Retinal
The light sensitive part of rhodopsin
Give an example of positive regulation
When a product in one branch of the metabolic pathway maze stimulates the activity of an enzyme in another pathway. The accummulation of ADP activates several enzymes to begin oxidation of sugar molecules and make ATP
Are phosphotases specific for an individual protein?
Some are highly specific and only remove phosphates from only one or a few set of proteins. Others can act on a broad range of proteins
How many molecules of ATP are hydrolized per phosphorylation.
One
GTP binding proteins are in their acitve state when GTP is _______
bound. The protein itself hydrolyzes GTP to GDP-releasing phosphate- and turns into an inactive state
Many GTP binding proteins function as
Molecular switches
What happens to EF-tu when GTP is hydrolized?
Hydrolysis of GTP releases a latch within the protein that creates a major change in the conformation and causes tRNA to be released
ATP hydrolysis allows motor proteins to walk along the tracks unidirectionally or back and forth?
Unidirectionally. ATP helps motor proteins move forward upon hydrolysis to ADP
Myosin
Muscle motor protein that “runs” along actin filaments and generates muscle contractions
Kinesin
Motor protein involved in chromosomal movements at mitosis
Chromosomes contain both
DNA and protein
What do chromosomes constist of?
A enourmously long linear DNA molecule associated with proteins that pack the fine thread of DNA into a more compact structure
Chromatic
The complex of DNA and protein
Is Gemsa staining done on chromosomes that are compacted to go into mitosis?
No. Gemsa stains chromosomes that are compact, but not so heavily compacted as during mitosis
True or False. The more complex the organism, the more chromosomes it has.
False. Although gene number is roughly correlated with species complexity, there is no simple relationship between gene number, chromosome number, and total genome size
Interphase
When chromosomes are duplicated
M phase
When the cell cycle reaches this phase, DNA coils up, becoming very condensed
Centromere
Allows one copy of each duplicated chromosome to be apportioned to each daughter cell
Nucleolus
Where parts of the different chromosomes carrying genes for ribosomal RNA cluster together. The most obvious example pf chromosome organization. Here, ribosomal RNA’s are synthesized and combined with proteins to form ribosomes
Nucleosomes
The basic unit of eukaryotic chromosome structure
Chromatin
The histone and DNA complex
Which two amino acids are seen in histones
Lysine and arginine. Their positive charge allows the histones to bind tightly to the negatively charged sugar phosphate backbone
H1
Packing of the nucleosomes into the 30 nm fiber depends on this fifth histone. This histone is thought to pull the nucleosomes together. “linker histone” changes the path the DNA takes as it exits the nucleosome core
Chromatin remodeling complexes
One way in which cells adjust the structure of their chromatin. Uses ATP hydrolysis to change the position of the DNA warpped around nucleosomes
Lysine residue 9 in histone H3
methylation of this lysine residue aids the formation of heterochromatin. this attracts a set of heterochromatin specific proteins, which then induce the same histone tail modification in adjacent nucleosomes
