Biochemistry Flashcards
What percentage of any living organism is made of water?
50-95%
The rest of the cell not including water is made of what?
- Nucleic Acid
- Proteins
- Lipids
- Carbohydrates
All living organisms are made of primarily 6 types of atoms
Carbon, Hydrogen, Oxygen, Nitrogen, Sulfur, Phosphorus
What is a covalent Bond
Sharing of Electrons
What is an Ionic Bond
Transfer of Electrons
What is a Polar Covalent Bond
Unequal sharing of Electrons
All organic compounds contain?
Carbon
What is catabolism
chemical reactions that break down compounds into simpler forms
What is anabolism
Chemical reactions that build up substances
What is an element
A pure substance that cannot be broken down using ordinary chemical or physical techniques
What are atoms
Smallest particles of elements that allow elements to differ from each other
What are most organic compounds made of?
Carbon, Hydrogen, Oxygen, as well as Nitrogen
What are 3 subatomic particles
Protons, Electrons, Neutrons
Do atoms have net charges
No, # of neutrons = # of protons
What is the mass number
Sum of protons and neutrons in an atom
What is an isotope
Different neutron containing form of an element
What are intermolecular forces
Bonds in between molecules, weaker relative to other forces: London Dispersion, Dipole-Dipole, Hydrogen bonds
What are intramolecular forces
Bonds in between atoms of a molecule: ionic, covalent, etc.
What are the three types of intermolecular forces
London Dispersion, Dipole-Dipole, hydrogen bonds
What are characteristics of London Dispersion forces
Weakest intermolecular force, increase in strength with bigger molecules, exists between all atoms and molecules, formed by the temporary unequal distribution of electrons as they orbit the nucleus
What are Dipole-Dipole forces
Stronger than london forces, hold polar molecules together, -ve is attracted to +ve of another molecule
What are hydrogen bonds
The strongest intermolecular forces, strongest type of Dipole-Dipole force between an H+ of one molecule and a N, O or F of another molecule
Properties of water
Water is a polar molecule, so hydrogen bonds form between water molecules, known as the universal solvent, dissolves the most substances, small non polar molecules are only slightly soluble in water, large non polar molecules do not dissolve at all
What are acids
Increase the concentration of hydronium ions in water solutions (H3O+)
What are bases
increase the concentration of hydroxide ions in water (OH-)
What is a neutralization reaction
The reaction where an acid and base produce water and a salt
Why was the pH scale created
Easier way to interpret the concentration of H3O+ ions
According to Bronsted-Lowry, what are acids and bases
Acids are proton donors and Bases are proton acceptors
What are buffers
Certain chemicals or combination of chemicals minimize changes in pH by consisting of conjugate acid-base pairs in equlibrium
what do reversible reactions mean for acids
Reversible reactions means the acids are usually weak
What is the smallest hydrocarbon
Methane
What are only ionic or strongly polar
Functional groups
What do carbohydrates supply
Short term energy to cells
What ratio do carbohydrates exist in
1:2:1 (carbon, hydrogen, oxygen)
What is a monosaccharide
simple sugar monomer that bonds with others to create carbohydrates (like glucose)
What is a Disaccharide
Sugars that consist of 2 monosaccharides (like maltose)
How can monosaccharides be distinguished
By their carbonyl group (aldehyde or keytone), as well as the amount of carbon they contain
What do monosaccharides with 5 or more carbons form
Ring structures when dissolved in aqueous environment
What are glucose, fructose, and galactose
isomers (all C6H12O6)
What is another example of a sugar isomer
Alpha and Beta Glucose
What are polysaccharides
Complex carbohydrates that are polymers of monosachharides
What are the three most important polysaccharides
Glycogen (short term energy storage in animal cells), Starch (energy storage in plants and good energy source for humans)
and Cellulose (makes up plant walls, not good source of energy for humans as it is a hard dietary fibre to break down)
What are glycosidic linkages
Covalent bonds holding monosaccharides together where the H from one’s hydroxyl group and the hydroxyl group of another come together
What does a glucose with hydroxyl group down mean
Alpha glucose
What does a glucose with hydroxyl group up mean
Beta Glucose
When a sugar is in the ring form, what is the middle of the ring called
Plane of Ring
Description of starch molecule
1-4 Glycosidic linkage of alpha glucose and humans can break it down for energy
Description of Cellulose molecule
1-4 Linkage of Beta Glucose, humans cannot break down the bonds between Beta glucoses and no energy will be released
What are both carbohydrates and lipids known for
Both have roles of being energy sources
What are roles that carbohydrates play other than energy
Structural support and cell-to-cell communication
What are all biological membranes made of
Lipid molecules
What do lipids provide for nerve cells
Insulation
What is a unique ability for lipids
Waterproofing abilities
What do plants and algae produce alot of every year
millions of tonnes of carbohydrates
What is the most widely known monosaccharide
Glucose
What are the most common monosaccharides
Ones that contain 3 carbons (triose), 5 Carbons (Pentose), or six carbons (Hexose)
What do sugars typically have attached to them
Polar functional groups
What is the relation of sugars and water
Sugars are highly hydrophillic making them soluble in water
What type of sugars are the sweetest
Monosaccharides
What is the relation of disaccharides and water
Because they contain similar polar groups to monosaccharides, they are also soluble in water
What is the most common disaccharide sucrose found in
Table sugar, sugar cane, and sugar beets
What are polysaccharides
hundreds to thousands of monosaccharides linked together
What is polymerization
The process where small sub-units link to form a large molecule
What is the relation of polysaccharides to water
they are very polar, and hydrophilic, however due to size are insoluble in water
How does paper towel work
Uses cellulose fibres to absorb water, but as they are insoluble in water, it does not break down
What are characteristics of lipids
Non Polar compounds made of mostly carbon and hydrogen
Are lipids bigger or smaller than carbohydrates
Lipids are smaller than complex carbs (polysaccharides)
What relation do lipids have with water
Lipids are non polar which means they are insoluble in water, this trait allows them to be present in membranes
What are the 5 main categories of Lipids
Fatty Acids, Fats, Phospholipids, Steroids and Waxes
What are fatty acids
The structural backbones of most lipids, consists of a carboxyl group, and a hydrocarbon chain, as chain length increases water solubility decreases
What are saturated fatty acids
If all carbons are linked with single bonds
What are non saturated fatty acids
Any double bonds means non saturated
Only one double bonds meaning in fatty acid
monounsaturated
More than one double bond in fatty acid
Polyunsaturated
What are fats
Lipids made from fatty acids and glycerol molecule
How many fatty acid chains are joined with a glycerol in a Fat
1-3 fatty acid chains
What are the most well known fats
Triglycerides (3 fatty acid chains attached to one glycerol molecule)
What are saturated fats made of
Saturated fatty acids
What are unsaturated fats made of
Unsaturated fatty acids
Shorter fat chains remain as what at room temperature
Oils at room temperature
What do more saturated fats exist as at room temperature
they get packed together staying solid (butter)
What are fats most commonly used as
Long term energy storage
What are phospholipids
Molecule with a polar end and a non polar end, non polar side consists of glycerol bonded to two fatty acids and a phosphate group
What are Amphipathic molecules
molecules containing both hydrophilic and phobic regions like phospholipids
What do phospholipids make in cells
Lipids bi-layer of cell membranes
What are steroids
A lipid molecule composed of 4 carbon rings used for message transmission (hormones)
What is the most abundant steroid
Sterol, containing a single polar -OH group at one end and a non polar hydrocarbon chain at the other end
What steroid is an important constituent of Plasma membrane around animal cells
Chloresterol
What do high concentrations of cholesterol do
Bad for the body leading to atherosclerosis (plaque build up in blood vessels)
What are waxes
Large lipid molecules formed by long fatty acid chains joined to alcohols or carbon rings
What are characteristics of waxes
Hydrophobic, extremely non polar, soft-solids over a wide range of temperatures
What is used to conserve water and prevent infections in plants
A wax named Cutin
How to birds keep wings dry
secrete a wax
How do bees make honeycombs
Produce beeswax
What is the concentration of energy between Carbs and Lipids
one gram of fat contains more than twice as much energy as carbohydrates or proteins
What type of linkage occurs when glycerol reacts with fatty acids in triglyceries
a dehydration synthesis takes place between carboxyl group of fatty acid and hydroxyl group of glycerol creating a ester linkage via esterification
What are healthier, saturated or unsaturated fats
unsaturated fats (some plant and animal products)
What are proteins
Molecules providing shape and support to cells
How do proteins have functional diversity
function as enzymes, help transport substances across cell membranes (hemoglobin), and chemical messengers (some hormones are proteins)
What are the monomers of proteins
Amino Acids consisting of an amino group, a carboxyl group, single hydrogen up and a remainder group opposite to hydrogen
What makes every one of the 20 amino acids unique?
The Remainder group
What are Dipeptides
two amino acids joined together by dehydration synthesis
What is the polymer of proteins
Polypeptides are the polymer however they are not proteins
What bonds form between amino acids when they link
Peptide bonds
What is the functional group linkage called when amino acids come together
Amide linkage
Howmany amino acids are essential to humans
8 are essential as they are not produced in the body
Howmany levels of protein structure are there
4 Levels: Primary, Secondary, Tertiary, Quarternary
What is a chain of amino acids
A linear polypeptide that is not a functioning protein
What determines the properties of a protein
The final shape of the protein’s 3-D structure
What is the primary structure
The sequence of amino acids
What is the secondary structure
coils up into a alpha helix or Beta pleated sheet via hydrogen bonds
What is the tertiary structure
The helix or sheet folds into a 3-D structure held by covalent disulfide bridges, hydrogen, ionic, and Non Polar bonds (REMEMBER CHIN)
What is the quaternary structure
Many proteins contain two or more folded polypeptides joined together to create a functional protein with 2 R groups and CHIN
What are Nucleic Acids
Polymers of nucleotides where cells contain two types of nucleic acids (DNA and RNA)
What is the main component of hereditary material or genes
DNA
What are nucleotides (monomer) made of
Three subunits: Nitrogen containing base (Adenine, Guanine, Cytosine, Thymine in DNA, or uracil in RNA), a five carbon pentose sugar (Ribose in RNA or Deoxyribose in DNA), and a phosphate group
What are single ringed pyrimidines
Cytosine, Thymine, and Uracil (look for ones containing ‘y’ in name and Uracil in RNA)
What are larger nitrogenous bases
Double ringed purines like Adenine and Guanine (look for ‘nine’)
What do sugar and phosphate groups form in DNA
Outer Backbone (sides of ladder)
What do the bases form in DNA
Rungs of Ladder
Nucleotides are held together by what?
Phosphodiester bonds between the phosphate group of one nucleotide and the sugar of the next (connecting sides of ladder)
Difference between RNA and DNA
RNA is single stranded, DNA is double stranded and strands are antiparallel
What is the form of DNA
Form of double helix and the two strands (left and right side of ladder) are held together by hydrogen bonds that form between a base on one strand and its complementary base on the other strand
What are the complementary base pairs in DNA
Adenine with Thymine (Two H-Bonds)
Guanine with Cytosine (Three H-Bonds)
What is Adenosine Triphosphate (ATP)
a nucleotide derivative that acts as the primary energy transferring molecule in living organisms, three phosphate groups attached to ribose by bonds that are considered as high-energy bonds
Describe the reaction of releasing energy from ATP
Exergonic, catabolic, hydrolysis (ATP -> ADP + Inorganic Phosphate + ENERGY)
Describe the reaction of forming ATP
Endergonic, Anabolic, Dehydration Synthesis
What is the rule for determining if a base is a pyrimidine or purine
No garage or second ring means pyrimidine
What two types of amino acids make up amino acids
Basic Amino acids and acidic amino acids
What is Denaturation
Loss of both protein structure and function due to extreme temperature and/or pH and unfolding of protein
What are the most complex molecules in living organisms
Proteins
What are defensive proteins
Antibodies
What are motile proteins
proteins that allow molecules to move around
What are examples of signal proteins
Hormones and messenger chemicals
What are bigger pyrimidines or purines
Purines as they have a garage
Who is Linus Pauling
A scientist with expertise in Chemistry, Biology, and physics, only person to win 2 Nobel prizes independently
What did pauling establish
Pauling’s rules for understanding crystals, electronegativity scale, 2 fundamental secondary structures of proteins (Alpha helix and Beta Pleated Sheets) started in 1937
What did pauling advocate against
Nuclear arms, which made the US government deem him a communist sympathizer making him a threat and took away his passport. This took away his ability to travel to the UK where a lot more information was available about proteins.
What is an enzyme
A biological catalyst, usually a protein, that speed up a chemical reaction.
Howmany enzymes are in a typical cell
4000 different enzymes
What does Lipase do
Speeds up hydrolysis of Triglycerides
What does Sucrase do
Speeds up hydrolysis of Sucrose into monosaccharides
How is every enzyme unique
They all have different 3-D shapes
How do enzymes work
For any chemical reaction to happen, it has to overcome a specific energy barrier, when an enzyme binds to a specific reactant called a substrate, this lowers the energy barrier
How long do enzymes bind to substrates
In reaction this binding only holds briefly
Howmany reactions can a single enzyme catalyze
One enzyme can only catalyze the reaction of one molecule or one family of molecules which is why there are so many of them
Where does the substrate bind to on the enzyme
This area of binding is the active site
What is the induced fit hypothesis
A model of enzyme activity that describes how an enzyme changes shape to better accommodate a substrate
When an enzyme binds to a substrate what does it form
An enzyme-substrate complex
What is the rate at which a reaction is catalyzed
10 –> 100 million substrate molecules per second
What is a cofactor
A non protein group that binds to an enzyme essential for catalytic activity
What are examples of common cofactors
Metals like Iron, Copper, Zinc, and Manganese
Are cofactors needed for normal enzyme activity
100% NECESSARY JAKE
What are organic cofactors called
Coenzymes
What are coenzymes derived from
Water-soluble vitamins
What conditions or factors effect enzyme activity
Temperature, pH, and substrate concentration and several control mechanisms
What are control mechanisms
mechanisms that adjust reaction rates to meet a cell’s requirements
What does extra substrate mean
Rate of reaction is directly proportional to substrate concentration
What is the limiting factor is these catalytic activities
Amount of enzyme available
What happens when the amount of enzyme is at a constant intermediate concentration
Increasing substrate concentration will increase rate of reaction to a certain point called saturation level
What happens as collision become more frequent
Rate of reaction increases
What are enzyme inhibitors
Molecules that lower the rate at which an enzyme catalyzes a reaction
Where do enzyme inhibitors bind to on the enzyme
Some bind on the active site and some on other critical sites of the enzyme
What is competitive inhibition
When inhibitors bind directly to the active site blocking access from the substrate
What is non competitive inhibition
Where inhibitors bind to a site that is not the active site distorting the 3-D shape of the enzyme and stopping the substrate being able to bind easily to the enzyme
What is reversible inhibition
The inhibitor’s binding is weak and readily reversible and will have the enzyme return to normal activity after reversal
What is irreversible reaction
Some inhibitors bind so strongly via covalent bonds that it disables the enzyme and the only way this can be overcome is by increased enzyme synthesis
What is Allosteric Control of Enzyme Activity
Molecules that naturally regulate enzyme activity in a cell often behaving like a non competitive reversible inhibitor binding to a site that is not the active site called the allosteric site causing a change in the shape of the enzyme
What is Allosteric Regulation
The regulation of one site of a protein by binding to another site of the same protein. This causes stimulation or inhibition of enzyme activity based on situation
What does the binding of an allosteric activator do
Causes the active site to have a high affinity for a substrate
What does the binding of an allosteric inhibitor do
Stabilizes the inactive form of an enzyme by releasing the substrate from its active site
What is feedback inhibition
The regulation of a pathway by one of the products of this pathway preventing the waste of cellular resources in the synthesis of molecules
What is the typical pH for peak enzyme activity
pH of apprx 7
What is the typical temperature for peak enzyme activity
40-50 degrees, above 40 some start to denature
Where are enzymes found in the real world applications
Milk and dairy have lactose and people who are lactose intolerant do not have adequate production of Lactase, cheese relies on Chymasin for production, Industrial food production to break down starch into glucose syrup for food medicine, and vitamins, added to detergents for better stain removal
What are the 4 main types of chemical reactions in biological organisms
Hydrolysis, Dehydration Synthesis, Redox, and Neutralization
Nucleus
Contains most DNA in the cell, Nucleus isolates the DNA and keeps it safe, isolated so that none of the metabolic processes damages it, contains at least one nucleolus, Dense irregularly shaped region where ribosomes are assembled
Nueleolus
Area where ribosomes are made for endoplasmic reticulum, found in the nucleus
Smooth ER
Doesn’t make proteins, proteins from rough ER make it to smooth as enzymes, cells lipids are synthesized which also breaks down carbs, fatty acids, drugs.
Rough ER
They make, store, and secrete lots of proteins. Puts finishing touches on lipids and polypeptides and transports proteins from on organelle to another. (E.g pancreas)
Plasma membrane
Forms a barrier around the cytosol of the cell and maintains and internal environment that enables the organelle to carry its function
Nuclear envelope
Double membrane that consists of two lipid bilateral that are folded together. There are different proteins - some are receptors and transporters. Others collect thing pores that spans the membrane
What are the two properties that make it easy for molecules to make it through plasma membranes
Polarity (preferably non polar or less polar relatively), Size (easier when molecules are small)
What does “LEO the Lion Goes GER” mean?
Losing electrons means oxidation, gaining electrons means reduction. this helps with identifying parts of a redox reaction.
What are organelles
Internal structures that carry specialized functions
What is the advantage of having several organelles
Various tasks can be completed efficiently
What is the difference between cytosol and the cytoplasm
Cytoplasm is all of the internal components of the cell, whereas cytosol is the liquid portion of the cell
What is the gatekeeper of the cell
The plasma membrane as it is a barrier that only lets certain molecules in to the cell
Do all eukaryotic cells have a nucleus
ALMOST all of them do
The nucleus contains most of the cell’s DNA, where else is it kept
Chloroplast (only plant cells) and Mitochondria (both animal and plant cells)
What is the nucleus surrounded by
The nuclear envelope or nuclear membrane
What are golgi bodies
They are fused vesicles that have emptied their contents, looks like stack of membranes, puts finishing touches on polypeptides and lipids
What are transport vesicles
Membrane enclosed sac-like molecules that transport proteins from one organelle to another
What are the mitochondria
The organelle where cellular respiration takes place where glucose is broken down into 36 packets of ATP by reacting with oxygen, this process is the most efficient way to extract energy from organic molecules
What are chloroplasts
Organelles found only in plant cells where photosynthesis takes place which produces glucose (sugar) using light energy, Carbon dioxide gas and water
What are lysosomes
Vesicles that bind with the cell membrane to empty their contents. Contain strong digestive enzymes that help with waste disposal also known as the stomach of the cell
What are peroxisomes
Organelles that inactivate toxins like hydrogen peroxide into water and O2 which are usually by products of broken down fatty acids
What are vacuoles
Liquid filled organelles in plant cells that transport, store and digest substances within a cell and fills up anywhere from 50-90% of the cell
What are ribosomes
Organelles that assemble polypeptide chains used to form proteins, found on the Rough ER
What are centrioles
Organelles that make microtubules for the cytoskeleton and is involved in cell division
What is the endomembrane system
A group of interacting organelles between the nucleus and plasma membrane
What are the 4 main parts of the mitochondria and where are they on the organelle
There is the outer membrane which is the outer wall, the inner membrane, the cristae which is the fold and the matrix which is the internal liquid portion
What cells require alot of mitochondria
Cells that require alot of energy
What are plastids
plastids are membrane enclosed organelles that are used in photosynthesis or storage of molecules and some common examples are chloroplasts, chromoplasts and amyloplasts
What are the main parts of chloroplasts
outer membrane, liquid portion is called the stroma, single pancake is called the thylakoid and the stack of pancakes are called the granum.
What is the cytoskeleton
A dynamic system that provides cell structure, helps with cell division, and enables the cells and organelles to move around
What is the cell membrane made of
A double layer of phospholipid molecules called the phospholipid bilayer
What is the fluid mosaic model
The idea that a biological membrane contains a ‘fluid’ phospholipid bilayer in which proteins are able to move laterally between the two layers
What happens to the lipid bilayer if the temperature drops low enough
the lipid molecules will pack tightly and the membrane will no longer be fluid, results in increased chloresterol
What are integral proteins
Channels that go all the way through the lipid bilayer for bigger molecules to get through the membrane
What is the difference between the head and tail of a phospholipid
The fatty acid tails are hydrophobic and non polar while the head of the molecule are hydrophilic and extremely polar due to the -ve phosphate group
What are Glycolipids and Glycoproteins and what do they do for the cell
Molecules that project into the extracellular space, carbs bound to lipids or proteins and used for recognition of foreign materials
What is the role of cholesterol in the membrane
Cholesterol maintains fluidity and are found between the phospholipids
Peripheral and Integral proteins of the membrane serve 4 main functions which include?
Transport, Communication/Enzymatic Activity (receptor proteins), Attachment/Recognition (cells of immune system), structural support by anchoring themselves to the cytoskeleton
How do you alter membrane fluidity
Alter the cholesterol level as they are the stabalizers
What are characteristics of cell membranes and walls
They are porous allowing water, CO2, O2 and nutrients to pass through easily
What maintains homeostasis in the cells
The cell membrane
What is passive transport
A process that DOES NOT require energy to move molecules from a HIGH to LOW concentration
What are the three types of passive transport
Diffusion, Facilitated Diffusion, Osmosis
What is diffusion
The movement of particles down/along the concentration gradient until equilibrium is reached
What is facilitated diffusion
Movement of larger molecules like glucose through the cell membrane along the concentration gradient from high to low concentration through the protein CHANNELS
What is osmosis
The diffusion of water through a semi-permeable membrane along the concentration gradient from a high concentration to a low concentration
What are hypertonic solutions
High concentration of solute compared to another solution, when cells are placed in this solution, the water % is more in the cell making water diffuse out and shrivel up
What are hypotonic solutions
Low concentration of solute compared to another solution, when cells are placed in this solution, the water % is less in the cell making water diffuse into the cell swelling the cell and sometimes animal cells burst
What are isotonic solutions
The solutions with the same concentration of solute, when a cell is placed in this solution, water diffuses equally both ways, however there is no net water movement
What is Active transport
The movement of molecules against the concentration gradient from Low to High concentration where energy is required to facilitate the movement
What is an example of active transport
Body cells must get rid of CO2 in the vessels however since the vessels are already high in concentration, Energy is required to push the CO2 out via proteins pumps, which are proteins that work as pumps
What is endocytosis
The process in which food is moved into the cell in large volumes
What is exocytosis
the process in which waste is secreted out by the cells in large volumes
What is an example of endocytosis
White blood cells engulf bacteria as food in large volumes
What are common molecules transported by active transport
Na+ and K+ ions that conduct nerve signals in and out of the cells
What vesicle binds to the cell membrane for exocytosis
Transport vesicle releases waste contents outside cell
What happens to the cell membrane during endocytosis
the membrane folds on itself producing a vesicle that brings molecules in to the cell
What are two types of Transport proteins
Channel proteins and Carrier Proteins
The rate of diffusion in facilitated diffusion is based on what
The concentration gradient, efficiency of transport protein and number of transport molecules available
Is facilitated diffusion faster than simple diffusion
It is , however it has a upper limit when all transporters are occupied
