bio test unit 1 biochemistry Flashcards
1
Q
elements for foundation for living things
A
Carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur
2
Q
Isotopes
A
- Isotopes are atoms of the same element that differ in the number of their neutrons
- Electrons remain the same outside the nucleus, only the atomic mass of the atom changes.
-Radioisotopes: Isotopes can become unstable, which means that their nucleus decays by emitting radiation in the form of subatomic particles or electromagnetic waves. - Isotopes are commonly used in medical diagnostics called isotope tracing where doctors inject radioactive material into a patient and trace its movement in the body
- Cancerous tissues in the body are characterized by a much higher level of activity than healthy tissue. They tend to consume more glucose because they have rapid uncontrolled cell division.
- Thus, injecting a patient with radioactive glucose, doctors can observe which cells consume glucose faster (positron emission tomography – PET scan)
3
Q
Molecules
A
substance composed of two or more non-metal atoms that are covalently bonded together. This means that the atoms share electrons with each other
Many of the molecules of life are organic compounds
4
Q
Organic compounds
A
carbon-containing molecule in which carbon atoms are nearly always bonded to each other and to hydrogen
5
Q
Biochemistry
A
the study of the activity and properties of biologically important molecules
6
Q
Covalent Bonding
A
- Formed between compounds of relatively similar electronegativity, non-metal – non-metal
- This occurs as a result of a balance between the attraction of electrons to the nucleus of an atom and a repulsion of electrons with respect to each other.
- This “sharing” occurs when the orbitals of two atoms overlap resulting in the formation of a new “Hybridized” orbital with lower energy levels then the original orbitals
6
Q
Ions
A
- atoms or groups of atoms (polyatomic) that have gained or lost one or more electrons, giving it a positive or negative charge.
- Certain compounds such as NaCl are hydrophilic and dissolve in water and separate into Na+ and Cl- ions. Sodium is an important ion for biological function and neurotransmission
- Some molecules, non-polar molecules, will tend to bond to each other and form clumps in water because they are hydrophobic.
- General rule: “like dissolves like”
7
Q
Intramolecular force
A
the force occurring between atoms within a molecule
Ionic
polar covalent
non-polar covalent
8
Q
Intermolecular force
A
the force occurring between molecules
Hydrogen bonding
ion dipole
dipole dipole
London dispersion
8
Q
Acyclic
A
(Fischer) structure: a sugar in chain form, split at the #1 carbon and oxygen in the chain, with hydrogen and hydroxyl (-OH) groups are presented as horizontal groups
8
Q
Polar bonds
A
- unequal sharing of the electrons. One area of the molecule ends up being more negative, and the other more positive
- Polar bonds are determined by looking at the electronegativity of the atoms
- Polar bonds have characteristics of both ionic and non-polar bonds
- The electron is pulled more strongly to the more electronegative element and so spends more time at one end of the bond.
- This results in partial charges, capable of attracting and repelling each other
9
Q
Macromolecule
A
a large, complex molecules usually composed of repeating units of smaller molecules covalently linked together
9
Q
Hydrophobic
A
non-polar molecules that do not have attraction interactions with water molecules.
Ex: Fats/oils tend to be hydrophobic
9
Q
Hydrophilic
A
polar molecules that have attractive interactions with water molecules.
Ex: Glucose is hydrophilic
10
Q
Cyclic
A
(Haworth) structure: the sugar exists in ring form, with hydrogen and hydroxyl groups above or below the plane of the ring
10
Q
Functional Groups
A
- atoms or groups of atoms attached to a molecule that gives the molecule particular chemical and physical properties. They contain oxygen, nitrogen, phosphorus, and/or sulfur.
- The presence of a carboxyl or hydroxyl group will make a molecule polar
- Carboxyl functional groups will make a molecule acidic
10
Q
Organic molecules
A
ALL MOLECULES ARE ORGANIC MOLECULES
made up of only carbon and hydrogen atoms called hydrocarbons. These molecules are non-polar and release lots of energy when broken apart
11
Q
Polysaccharides
A
- a carbohydrate polymer composed of many monosaccharides joined together by covalent bonds
- The three common types are starch, glycogen, and cellulose, all composed of glucose.
- The different ways that the glucose units are linked together results in molecules having quite different three dimensional shapes.
11
Q
polymer
A
a large structure composed of repeating units of smaller molecules (monomers)
12
Q
Carbohydrates
A
- a biological macromolecule that contains carbon, hydrogen, and oxygen in a 1:2:1 ratio (CH2O).
- Sugars and starches store chemical energy in a way that is easily accessible to the body
- The high number of hydroxyl and carbonyl groups make most carbohydrates polar molecules
- They provide short- and long-term energy storage for living organisms depending on their structure
13
Q
Isomer
A
a molecule containing all the same atoms in the same numbers, but different structural arrangements.
13
Q
Monosaccharides
A
- One Sugar
– a carbohydrate composed of between three and seven carbon atoms. - “They are “simple” sugars such as glucose, fructose, and galactose
- Glucose, fructose, and galactose are isomers of each other
14
Q
Why 2 shapes/projections?
A
- Different molecules have different optical ability
- That is, they affect how light is absorbed and reflected
- It matters if even 1 of those OH groups are pointed in the wrong direction. Changing a molecules 3D shape can have vastly different effects on the molecules function in our bodies
- This is a matter of life and death in pharmaceutical research and drug manufacturing
- For example, enzymes can only bind to molecules with certain conformations (3D shapes)
14
Q
Disaccharides
A
- a carbohydrate composed of two monosaccharides joined by a covalent bond.
- The two monosaccharides are covalently bonded by a glycosidic linkage
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Sucrose
Glucose and fructose
alpha
Disaccharide
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Glycosidic Bond
- The bond linking each monosaccharide to another
- Forms between the 1-Carbon of one sugar, and the 4 or 6-Carbon of the second
- The 1-Carbon is to the right of the oxygen in the ring
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Lactose
Glucose and galactose
beta
Disaccharide
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Maltose
Glucose and glucose
alpha
Disaccharide
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Triglycerides
lipids for energy storage
- a lipid molecule composed of a glycerol molecule and three fatty acids linked by ester bonds
- Humans cannot synthesize polyunsaturated fats, thus, these essential fats must be consumed in our diet.
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starch
Polysaccharide
- Is responsible for energy storage in plants
- Long chain of glucose subunits
- More linear
- Provides short term energy storage
- Ex. Potatoes
- short energy
- long time to metabolize
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Lipids
- a biological macromolecule composed of carbon, hydrogen, and oxygen atoms, with a high proportion of non-polar carbon-hydrogen bonds.
- Unlike carbohydrates, there are fewer oxygen atoms present
- Lipids are hydrophobic, given their non-polar nature. - The presence of many energy-rich C-H bonds makes lipids efficient energy storage molecules
- provide long term energy, however, they are not as easily accessible as carbohydrates, and are only used when carbohydrates run out
- Lipids are essential in mammals as they provide insulation from colder temperatures
- They help protect and cushion the organs of the body from external damage
- In non-human organisms, lipids provide water-repelling coatings for fur, feathers, and leaves
- Many of the membrane properties can be explained by the functioning of lipids
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Glycogen
Polysaccharide
- Responsible for energy storage in animals.
- Animals and humans when consuming glucose break it down and convert it into glycogen where it is stored in the liver.
- Has a larger amount of branching than starch in order to pack more glucose units into a single cell.
- Too much glycogen can result in Glycogen Storage disease, which is usually hereditary
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Cellulose
Polysaccharide
- Used by plants to build walls
- Structural molecule as it protects and supports the plant
- Principal component of wood
- Stores a lot of energy but only a few bacterial species produce the digestive chemicals to break it down into glucose units and release energy
- Animals must have these bacteria in their gut in order to obtains nutrients from grass and leaves
- Mammals and humans do not have the bacteria.
WHEN DIGESTED
- swells up when comes interacted with water
- attaches itself to other stuff
- shows up in feces b/c can't be digested
PROVIDES
- nutrients
- water
- vitamins
- fiber
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fatty acid
- a hydrocarbon chain ending in a carboxyl group
- Fatty Acids with double bonds in their structure are called unsaturated fatty acids
–0 double bonds = saturated
–1 double bond = monounsaturated (Cis or Trans)
–2 or more double bonds = polyunsaturated (Cis or Trans)
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Glycerol
a ‘triol’ – molecule that contains 3 hydroxyl groups
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Saturated Fats
- Saturated with Hydrogens
- No double bonds between carbon atoms
- Fairly straight, pack tightly together
- Solid at room temperature (higher melting point)
- E.g. Stearic acid (18C), butter, cheese
- intermolecular force
- London dispersion
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Monounsaturated Fatty Acid
one double bond
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Unsaturated/Polyunsaturated Fats
- One or more double bonds between carbon atoms, reduces the amount of Hydrogens
Cis Double bonds
- cause kinks in molecules
- At the double bond, both sides of the chain bend the same way
- Cannot pack tightly–Liquid @ room temperature
- E.g. Oleic acid (18C), vegetable oil, peanut oil
Trans Double bonds
- do NOT cause kinks/bends in molecules and thus resemble a linear structure
- At the double bond, both sides of the chain bend opposite ways
- Mimic Saturated Fats and thus pack tightly
- Semi-solid @ room temperature
- Trans fats are associated with increased risk of heart disease.
- Both saturated fats and cis-unsaturated fats are natural. We produce the necessary enzymes to metabolize these. However, there is no evidence that we produce the enzymes to metabolize trans-fatty acids
- trans fats hang on to other trans fats, which block
- foods that are trans fats always look the same, they never rot
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Phospholipids
- Is a lipid composed of a glycerol molecule bonded to two fatty acids and a phosphate group with an R group
- *The difference is that a phosphate group replaces the third fatty acid of a triglyceride.
- *The “head” of the phospholipid molecule is polar, while the lower “tail” portion has only non-polar C-C and C-H bond.*Thus the head is hydrophilic, and the tail is hydrophobic.
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Hydrogenating unsaturated vegetable oils
- adds hydrogen atoms to double bonds, making the fatty acid straighter, making them semi-solids such as margarine
- causes the fatty acid chain to become straighter, packs more tightly together and form a solid at room temp
- Hydrogenation: unsaturated bond + break it + hydrogen to where double bonds would be = convenience, to get fatty acid chain to become straighter, so that you don't need to add anything additional like oil. this is not as healthy. this is a semisolid and is chemically modified
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High Density Lipoprotein
good
- aids in moving cholesterol through blood stream
- Removes cholesterol/trans fats by transporting to the liver
- too much is bad, as it can overwork the liver
- to get more hdl, eat more polyunsaturated cis fats
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Polyunsaturated fatty acid
many double bonds
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R group
a group of atoms that varies in composition
25
Steroids
- Lipids composed of four attached rings - commonly seen in hormones in our bodies
- Cholesterol is a common member of this group and is a precursor to other important steroids such as testosterone and estrogen.
- Steroids are prescribed as an anti-inflammatory in medicine
- Estradiol (estrogen), testosterone, and progesterone are the sex hormones and control development of sex traits
- Cortisol regulates blood pressure and metabolism
- Aldosterone plays a role in blood pressure and re-absorption of ions/water in kidneys
25
Cholesterol
- Component of cell membranes
- High cholesterol can restrict blood flow as it builds up in veins/arteries forming plaque - heart disease, high blood pressure
- Cells convert cholesterol into compounds such as Vitamin D (bones and teeth) and bile salts (digestion of fats)
- Adds structural support to the cell membrane whilst allowing for it to bend and be flexible (Important for keeping cell membrane fluid, not rigid)
25
Lipid bilayer
- a structure with hydrophilic “heads” of phospholipids directed toward the aqueous environment and hydrophobic “tails” directed toward the center, interacting with each other.
- This keeps water out
- Allows the cell to be ‘selective’ of what goes in and out
- Forms as the fatty, hydrophobic chains orient away from water molecules
- When added to water, phospholipids also form spheres, called micelles.
- This forms a single layer membrane, with a hydrophobic interior
- Detergents
- Micellular water is used to remove makeup because these capsules can dissolve the makeup (like dissolves like) and they break down both polar and non-polar molecules
- Micelles are also used for pharmaceutical purposes because they can be in polar and non-polar drugs. The non-polar drugs wouldn't interact with blood in the body, which is why they are in the interior of micelles so that they are protected by the exterior (polar). The same thing can happen when capsules are flipped, which can happen when micelles are put in oils/fats
- Hydrophilic (polar) head attracted to water and the hydrophobic tails mix with one another in centre of sphere.
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Lipoproteins
Carry and transport lipid molecules (cholesterol) in the blood stream
protein + lipids
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Low Density Lipoprotein
bad
- Deposits cholesterol onto vessel wall
- Causing blockages
- makes fats stickier
- to get more ldl, eat more polyunsaturated trans fats
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Waxes
- Lipids containing long-chain fatty acids linked to alcohols or carbon rings
- Hydrophobic
- Firm, pliable consistency
- Used as waterproof (hydrophobic) coating on plants and animals
- E.g. Plants cuticle on leaves, birds feathers, beeswax for honeycombs
28
Why are complex carbohydrates better for long term energy than sugary snacks, like candy or chocolate?
- It takes longer for our body to break it down, so it doesn't caus a spike in blood sugar
- Complex poly sugars
- simple sugars
29
What property of the carbohydrate molecule contributes to it’s strength as a polymer polysaccharide?
- Hydrogen bonding and intermolecular force between the polymers which create hydrogen bond
30
Hand creams often contain waxes and lipid-based materials. What property of fatty acids makes this product useful as a hand cream?
- they are hydrophobic, meaning they will stay on the surface of the skin because they are non-polar while the skin is polar
31
Peptide bonds
- Amide bond
- In order to form a protein, amino acids are joined by covalent bonds called peptide bonds
- This results in the formation of long polymer chains
- A peptide bond forms between the carboxyl group of one amino acid and the amino group on another
- The link is formed by removing a water molecule
31
Describe the properties of the phospholipid bilayer that allow it to create a barrier around the cell
- the duo-polarity, where the non-polar tails link as "like dissolves like"
32
Polypeptide
- a polymer composed of many amino acids linked together by covalent bonds
- There are many different combinations of possible sequences given the 20 possible amino acids present in the human body.
*8 of 20 amino acids cannot be synthesized by the body and must be obtained from our diets – essential amino acids
- The number of possibilities of peptide chains is greater than the number of atoms making up the Earth and everything on it! (20n possibilities)
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Proteins
- A macromolecule composed of amino acid monomers
- They are a diverse group of macromolecules as they vary in shape and size. Thousands of proteins perform thousands of functions, such as:
*Catalyze chemical reactions
*Provide structural support
*Transport substances in the body
*Enable organisms to move
*Regulate cellular processes
*Provide defense from disease
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Amino Acids
- monomers
- A protein is composed of amino acids assembled in various ways
- An amino acid is an organic molecule composed of a central carbon atom bonded to:
*a hydrogen atom
*an amino group
*a carboxyl group
*and a variable R group.
- All amino acids are somewhat polar, due to the polar C=O, C-O, C-N, and N-H bonds
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Protein organization
- Intermolecular forces are responsible for protein folding
- There are 4 stages of protein folding, which will be studied in further detail in the future
- Since amino acids are polar, the possibility of hydrogen bonding exists between the N-H portion, and the C=O portion
- Hydrogen bonds form between polar atoms and a highly polarized hydrogen (H) atom
- Hydrogen must be bound to N or O (F is not found in the body)
Primary (1°) Structure
- The primary structure of a protein is the polypeptide chain, formed by covalent peptide bonds
- The chain ‘starts’ at the N-terminal of amino acid 1
- linear
- not functional
- Only intramolecular forces
Secondary (2°) Structure
- The polypeptide chain begins to fold and interact with itself due to hydrogen bonding
- It has been observed to form 2 possible orientations
*An alpha helix (a coil)
*A Beta pleated sheet (a paper fan-like sheet)
- Both alpha and beta can be together, which is hydrogen bonding
Tertiary (3°) Structure
- Forms due to hydrophobic and hydrophilic interactions within the cellular environment
- Alpha helixes and beta sheets will fold and re-orient themselves
- Hydrophilic groups will direct towards water
- Hydrophobic groups will be directed to the interior of the folded protein, to avoid interaction with water
- After that, it will be functional
- Proteins pay attention to their surroundings, either hydrophilic or hydrophobic
- Can be functional when there's only 1 subunit
Quaternary (4°) Structure
- Some proteins are made of several polypeptide chains not directly linked by covalent bonds
- When these different 3° structure group together and interact, they form a large 4° structure
- Interactions are mediated mainly through hydrogen bonds, dipole interactions, and hydrophobic/-philic interactions
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The R-group
- The R-group is what gives the amino acid its specific properties.
- There are 3 classes of R-groups
*Polar
*Nonpolar
*Electrically charged (acidic or basic)
- An R group can be ANYTHING, however we study the 20 most common to our body
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Nucleic Acids
- Composed of nucleotide monomers
- The two types are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
- DNA is composed of nucleotides containing the sugar deoxyribose
- RNA is composed of nucleotides containing the sugar ribose.
- DNA is the genetic material of living organisms that carry hereditary information and instructions for the organism to carry out
- DNA and RNA are made of thousands of repeating nucleotides which are composed of a sugar bonded to a phosphate group and a nitrogen containing base.
- DNA is composed of four different types of nitrogenous bases: Adenine (A), Thymine (T), guanine (G), and cytosine (C).
- In RNA, uracil (U) is used in place of Thymine (T)
- The nucleic acids bond with each other to form the double helix structure of DNA
- Adenine (A) pairs with Thymine (T)
*2 hydrogen bonds hold them together
*Guanine (G) binds with Cytosine (C)
*3 hydrogen bonds hold them together
*Stronger bond due to more interactions
Strands
- A polymer of the nucleotide is known as a strand
- A strand is made up of the monomer nucleic acids
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Denaturation
- Under certain conditions, proteins will unfold due to breaking of bonding interactions with R-groups
- The protein can no longer function normally at this point
- break down nature of protein until it's at primary
- Caused by:
*Changes in temperature
*Change in pH of the environment
*Exposure to harmful chemicals
*Salt concentration
35
phosphodiester bond
- covalent bond between 2 nucleic acids
- A bond between the phosphate group of one nucleic acid and the sugar or the next
- this connects one strand, while hydrogen bonding connects two strands together
36
What are the healthiest to unhealthiest types of fat?
1. polyunsaturated cis fats
2. Monounsaturated cis fats
3. saturated fats
4. Monosaturated trans fats
5. Polyunsaturated trans fats
37
What is a reaction?
A process that leads to the transformation of one set of substances to another
38
Types of reactions in the body
Neutralization Reaction
- Reactants: Acid and Base
- Products: Salt and Water
Reduction-Oxidation Reaction (Redox)
- One substance gains electrons (reduced)
- Another substance loses electrons (oxidize)
Condensation Reaction
- 2 reactants are joined
- A water molecule is removed
Hydrolysis Reaction
- A water molecule is added to a larger molecule
- A bond is broken
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pH Scale
- The concentrations of acids and bases are often very low.
- We use the pH scale in order to more effectively convey the concentration of H+ in our solution.
- The pH scale is 0-14.
- An acid has a pH of 0-7
- A base has a pH of 7-14
- Neutral chemicals have a pH of 7.
- The normal pH range of human blood is from 7.35-7.45 (slightly alkaline)
- A pH greater than 7.8 or less an 7.0 can be fatal
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Neutralization
- Acid – a substance that produces hydrogen ions, H+, when dissolved in water.
- Base – a substance that produces hydroxide ion, OH-, when dissolved in water.
- we can classify a solution using a pH scale, 0-14, to determine how acidic or how basic a substance is
Acid Base Neutralization Reaction
- A chemical reaction between an acid and a base, producing water and a salt
Acid + Base = Water + Salt
Ex: HCl+ NaOH = H2O + NaCl
40
Alkalosis
If the pH increases to 7.5, this could be the result of breathing too quickly at high altitudes, feeling anxious, too many antacids, the person can feel dizzy and agitated
41
Acidosis
the pH falls between 7.1-7.3 and symptoms include disorientation and fatigue and can result from severe vomiting, brain damage, and kidney disease
41
Condensation Reaction
- synthesis
- A chemical reaction that results in the formation of a covalent bond between two molecules with the production of a water molecule
- An H atom is removed from a functional group of one molecule, and an OH group is removed from another molecule which combine to form water and condense.
- Carbohydrates, lipids, proteins, and nucleic acids are assembled by condensation reactions among their monomers to form a polymer
42
Buffer
- Organisms require buffers to maintain optimal pH ranges
- a buffer is a substance that minimizes changes in pH by donating or accepting hydrogen ions as needed.
- Buffers tend to exist as a specific pair of acids and bases
- In the human body, carbonic acid H2CO3 (aq) and hydrogen carbonate ion, HCO3-
- The reaction takes place between the two substances
- If blood becomes too basic, carbon dioxide and water react to produce carbonic acid which dissociates into hydrogen carbonate and hydrogen ions and increases the acidity of the blood Maintain optimum pH Ranges
42
Oxidation-Reduction Reactions
- Oxidation – the process involving the loss of electrons
*oxidation agents = reduced = forming bonds with electrons
- Reduction – the process involving the gain of electrons
*reduced agents = oxidized = breaking bond and losing electrons
- Redox reaction – the chemical reaction that involves the transfer of electrons from one substance to another.
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Enzymes
- Enzymes are catalysts – these are chemicals that speed up a chemical reaction without being used up in the process
- Most biological processes involve the successful collision between reactant molecules in order for products to form
- To ensure the success of such collisions, enzymes need to become involved
- The molecule that the enzyme acts on is called the substrate molecule.
- Enzymes are very specific for the substance to which they bind
- The site where the enzyme binds to the substrate is called the active site
- The notch in the protein is compatible with the shape of the substrate, such they fit together
- When the two are attached, this creates the enzyme-substrate complex
- Some enzymes require the presence of certain substances before they can work properly – these behave like “switches” that turn an enzyme on and off.
- Enzymes can be inorganic (cofactors) or organic (coenzymes). Vitamins and minerals tend to be inorganic because they are human made. Calcium is also inorganic as calcium is added on. Calcium can be organic if body breaks it down from bones
- organic means it's made in the body, while inorganic means it must be digested
- cofactors help enzymes
- Enzymes prepare substrates for reaction by changing the substrate, its environment, or both in some way
- Enzymes reduce the activation energy required for a reaction to begin.
- Less energy needed for reactions to occur
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Hydrolysis Reaction
- A chemical reaction that results in cleavage of a covalent bond with the addition of a water molecule.
- An H atom from water is added to one monomer, and an OH group is added to the monomer beside that one.
- The covalent bond between the monomers breaks and the larger molecule splits into two smaller molecules.
- Polymers are broken down by hydrolysis reactions to form monomers
44
inhibitor
Molecules that bind to the allosteric or active site of an enzyme and causes a decrease in the activity of that enzyme
45
Allosteric site
a site on an enzyme that is not the active site, where other molecules can interact with and regulate the activity of the enzyme
45
Competitive inhibition
interferes with the active site of the enzyme so substrate cannot bind
46
Factors affecting enzyme activity
- An enzyme is a protein.
- If it becomes denatured, it will not function to catalyze the reaction properly.
3 important factors affecting activity:
- Temperature
- pH
- substrate concentration
Temperature
- As temperatures increase, so does the vibrational energy of each atom
- This causes the intermolecular forces holding the protein together, to break.
- The result is a denatured protein. In this case, an inefficient enzyme.
- Likewise if the temperature is too low
pH
- Some enzymes function best in acidic environments, others basic ones.
- Example: pepsin thrives in the stomach - pH =2
- Trypsin thrives in small intestines
- pH =8
- As pH changes, the enzyme’s amino acid R-groups gain or lose protons (H+), which change their shape.
- this is due to differing intermolecular forces
Substrate Concentration
- If there are more molecules present in solution, there is a higher chance that one will interact with the enzyme
- At a certain point (x), there are not enough enzyme molecules to catalyze all of the substrate molecules.
- The enzyme becomes the limiting factor
46
Non-competitive inhibition
changes the shape of the enzyme so it cannot bind to substrate.
46
Activator
- Non competitive activation
- Molecules can also bind to an allosteric site
- It is a molecule that keeps an enzyme active or causes an increase in the activity of that enzyme
46
Eukaryotic cells
- Animals, plants, fungi, and protists are all composed of eukaryotic cells.
- Genetic material is within the nucleus
- A cell membrane, a phospholipid bilayer separates interior cell contents from the rest of the organism
- The cell interior has a jelly like cytoplasm
- 80% water, also contains salts and protein
- The Surface Area:Volume ratio is very important for a cell
- As it grows, the cell’s volume becomes too large for the membrane to hold, and the ratio decreases
- It is fixed by cell division and folding of the organelle
47
Cell membrane
- Separates contents of the cell from the extracellular environment
- A phospholipid bilayer, 0.006nm thick
- Fatty acid tails (hydrophobic) point inwards
- Polar head groups (hydrophilic) face inside and outside environment of cell (mostly water)
- Many of the membrane properties can be explained by the functioning of lipids
- Phospholipids are held together by weak intermolecular forces NOT covalent bonds
- Molecules embedded in the membrane can move around freely without breaking structure
- Push phospholipids out of the way
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Selectively permeable
only certain molecules can pass freely in and out
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Fluid
- varies its shape due weak intermolecular attractive forces, not covalent bonds
- Flexible
- A small tear is quickly fixed by lipids rearranging themselves
Factors affecting Fluidity
- Temperature: change in state
- Double bonds: create kinks and affects ability to pack tightly
- Fatty Acid Tail length: more molecules increase intermolecular attraction
Temperature
- As temperature increases, molecules gain more energy
- Intermolecular forces begin to break
- Fluidity increases
- Summary: As temperature increases, so does fluidity, but intermolecular decreases. As temperature decreases, so does fluidity, but intermolecular increases
Double bonds
- A double bond in the fatty acid tail creates bends in the chain, or ‘kinks’
- The more kinks a chain has, to lower its ability to pack tightly
- Less tightly packed molecules have lower intermolecular interactions, therefore HIGHER fluidity
- Summary: More double bonds, lower intermolecular forces, higher fluidity. Less double bonds, higher intermolecular forces, lower fluidity
Tail Length
- The longer a fatty acid tail is, the more C/H atoms there are compared to a shorter tail
- Intermolecular forces increase as the number of atoms increase
- Summary: As chain length increases, fluidity DECREASES, as chain length decreases, fluidity INCREASE
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Mosaic
- a variety of macromolecules make up the membrane inside and surface
- Proteins, glycoproteins, cholesterol
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Cholesterol
- like gum
- Large chains of lipids
- Carbon ring structure
- Increases the amount of intermolecular forces in the membrane
- At room temperature or higher (23°C +), cholesterol keeps membrane tightly packed (decreasing fluidity)
- At lower temperatures, it prevents the lipids from packing as a gel, which increases fluidity
- low fluidity, high intermolecular, more sticky, high temperature
- high fluidity, low intermolecular, less sticky, low temperature
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membrane proteins
- Integral membrane proteins are embedded, with hydrophobic ends within the membrane
- all channel proteins are integral proteins, but not all integral proteins are channel proteins
- Peripheral membrane proteins are loosely bound to the surface, and they have a polar surface
- Regulate transport of substances
- Reaction catalysis
- Cell recognition: proteins recognize certain carbohydrate chains. Help differentiate from foreign cells
- Signal reception and transduction: bind hormones and initiate a cellular response
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Passive Transport
- The movement of ions or molecules across a cell membrane from a region of higher concentration to a region of lower concentration, without the input of energy.
- The ions or molecules move as a result of a concentration gradient
- A difference in concentration between one side of a membrane and the other
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Diffusion
- The random motion causes a net movement of these substances from regions of higher concentration to low concentration.
- But how does ions and molecules pass if the interior of the lipid bilayer is hydrophobic? Only non-polar molecules can move through the bilayer easily
What affects diffusion?
- Molecule size – larger molecules are difficult to transport
- Molecule polarity – highly polar molecules have difficulty passing through
- Molecule or ion charge – cannot generally pass through a lipid bilayer
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Osmosis
- The movement of water from an area of higher concentration to an area of lower concentration, across a semi-permeable membrane
- Water moves in or out of a cell, along their concentration gradient until their concentrations on both sides of the membranes are equal
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solutions
- Hypertonic – [solute in solution] > [solute inside] cell
SOLUTE IN THE SOLUTION HIGHER THEN INSIDE THE CELL
- Hypotonic -[solute in solution] < [solute inside] cell
SOLUTE IN THE SOLUTION LOWER THEN INSIDE THE CELL
- Isotonic – both solutions have the same solute concentration
Lysis – in a hypotonic solution the osmotic pressure inside the cell is so great it burst
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Channel Proteins
- Facilitated diffusion – protein membranes help aid diffusion without the use of energy
- Channel proteins – forms a channel across a cell membrane, which allows specific ions or molecules to cross the membrane along the concentration gradient
- The shape and size of the hole will determine which ions/ molecules will pass through
- Channel proteins allow substances such as Na+ and K
- all channel proteins are integral proteins, but not all integral proteins are channel proteins
- they can have the interior be polar or non-polar, depending on the lining. The substance coming in needs to be the same polar type as the lining in order to pass through channel protein
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Carrier Proteins
- binds to specific molecules, transport them across the membrane, and then release them on the other side. Thus, the proteins carry the molecules across
- Channel proteins can transport ions or small polar molecules
- The exterior of a carrier protein is usually composed of non-polar amino acids that interact with the non-polar interior of the membrane
- The interior of the carrier protein is lined with amino acids that can bind to the particle to be transported
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Active transport
- The transport of a solute across a membrane against its gradient
- This occurs usually with the aid of ATP (adenosine triphosphate), the main source of energy for cells
- With the aid of water, ATP undergoes hydrolysis to create ADP which releases energy for the cell
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Endocytosis
- Process by which a cell engulfs material by folding the cell membrane around it and then pinching off to form a vesicle inside the cell
1.Phagocytosis – involves solid particles
2.Pinocytosis – involves liquid particles
3.Receptor-mediated endocytosis – use of receptor proteins on a portion of a cell that bind with specific molecules outside the cell
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Exocytosis
- Transport method in which a vacuole fuses with the cell membrane and released its contents outside the cell.
- This is important in plants to construct cell walls
- In animal cells provides a mechanism for secreting and releasing many hormones, neurotransmitters, digestive enzymes, and other substances
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eukaryotic cells
animals, plants, fungi, and protists
- all e cells have genetic material (DNA) that is contained within a membrane-bound nucleus
- the cell membrane is comprised of a phospholipid bilayer (double layer) and the embedded proteins separate the cell's contents from its surroundings
- The cell interior is a jelly-like cytoplasm. It consists of everything outside the nucleus and within the cell membrane.
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Nucleus
- stores and replicates the genetic information of a cell
- Each molecule of DNA in the nucleus combines with an equal mass of protein to form a chromosome. Humans have 23 pairs of them.
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Nucleoplasm
thick fluid that fills the nucleus
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Nuclear matric
network of protein fibres that provide internal structure and support
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vacuole
a large membrane-bound sac in plant cells and some other cells that stores water, ions, macromolecules, sugars, and amino acids
- also contains enzymes that determine the turgor pressure (internal pressure) of the plant cell. A vacuole presses against the cell wall, increasing turgor pressure and causing the plant cell to be rigid. This pressure is the source of the rigidity in the flexible stems of herbaceous plants.
- Without enough water, a vacuole will shrink and pull away from the cell wall, which will make it wilt as the turgor pressure in the cells decrease
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Nucleolus
within the nucleus
a denser region containing RNA, protein, and chromatic
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Nuclear envelope
-surrounds nucleus
- a double membrane consisting of two phospholipid bilayers, which separate the nucleus from the rest of the cell
- studded with thousands of nuclear pore complexes
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Lumen
the narrow space between bilayers
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nuclear pore complexes
groups of proteins that form openings in the nuclear envelope. Small particles such as water and ions travel freely through these openings, but the passage of macromolecules such as RNA is controlled by the nuclear pores
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Endoplasmic reticulum
- nuclear envelope is connected to and a part of a complex of membrane-bound tubules and sacs (er)
ROUGH
- the er furface regions devoted to the synthesis of proteins are studded with ribosomes
- proteins that are part of membranes or intended for export from the cell are assembled by rough er ribosomes
SMOOTH
- the regions of er that have no bound ribosomes
- synthesizes lipids and lipid-containing molecules like phospholipids that make up membranes
- preformes other functions depending on type of cell
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ribosomes
molecular aggregates of proteins and RNA
- are different in eukaryotic cells than prokaryotic cells (that's why antibiotics kill bacteria of prokaryots than eukaryotes
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endomembrane system
- contains nuclear envelope, endoplasmic reticulum, golgi apparatus, and vesicles
- the transportation and product-processing section of the cell
- helps to make sure cell's functions are at a restricted to specific regions
- The organelles that are a part of the system are connected to one another either directly or by transport vesicles
1. surface of the rough er, polypeptides are produced by bound ribosomes and extruded into lumen, rather than being released into the cytosol
2. polypeptides travel through lumen to the smooth er, where they are stored and processed. When proteins are ready for transport, pieces of the smooth er pinch off to form vesicles containing the protein
3. vesicles from smooth er travel across cell to the cis face of the golgi apparatus. the vesicles merge with the membrane of the golgi apparatus and release their contents into the interior. In ga, some proteins are stored and others are modified further.
4. when the modified proteins are ready for transport, pieces of the golgi apparatus pinch off from the trans face to form vesicles. the vesicles transport the proteins to the cell membrane r to other destinations within the cell
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golgi apparatus
stack of curved membrane sacs that packages, processes, sorts, and distributes proteins, lipids, and other substances within the cell. Its like the post office for the cell
- in animal cells, ga also produces lysosomes
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Peroxisomes
- membrane-enclosed sacs containing enzymes
- form by budding off from the endoplasmic reticulum
- enzymes are oxidases that catalyze redox reactions
- break down many biological molecules and some toxic molecules
- liver cells contain many peroxisomes b/c they have many toxic molecules
- many reactions produce toxic hydrogen peroxide, so all peroxisomes contain an enzyme known as catalase that breaks down hydrogen peroxide into water and oxygen gas
- can synthesize molecules
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vesicles
a membrane-enclosed sac used for transport and storage
- form by pinching off from the cell membranes and organelle membranes
- can fuse with cell's membranes and organelle membranes to release their contents
- plants don't contain it, instead they have a vacuole
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chloroplasts
cells of eukaryotic organisms that carry out photosynthesis typically have one to many of them
- contain photosynthetic pigment, chlorophyll, which absrobes light energy as part of the provess that converts carbon dioxide and water, through redox, into energy-rich organic molecules
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lysosomes
- a membrane-bound vesicle containing enzymes that catalyze hydrolysis reactions, breaking down macromolecules
- contain more than 40 enzymes that catalyze hydrolysis reactions, breaking down parts of the cell that are old or no longer needed
- also break down bacteria and other foreign particles that have been ingested by the cell
- enzymes in lysosomes function best at an acidic pH of around 5
- Since the cytosol of a cell has a pH of about 7.2, this difference in pH acts as a safeguard for the cell. even if lysosome breaks, spilling its enzymes into the cell won't break down the parts of the living cell
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mitochondion
break down high-energy organic molecules to convert stored energy to usable energy
- have a smooth outer membrane and a folded inner membrane. the folds are called cristae, and the fluid-filled space in the inner membrane is called the matrix
- mitochondria and chloroplasts have their own DNA, which encodes some. but not all, f their own proteins
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cytoskeleton
all cells contain an internal network of protein fibres
- the fibres of it extend throughout the cytoplasm, providing structure and anchoring the cell membrane and organelles in place
- vesicles and other organelles move along these fibres, which act like tracks that lead from one part of the cell to another
- in some cells, it forms appendages that enable the cell to propel itself through the fluid surrounding it
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cilia and flagella
- appendages that develop on the outside of some eukaryotic cells.
- If there are just one or two longer appendages, they are called flagella.
- If many shorter appendages are present, they are referred to as cilia
- these structures are composed of an internal shaft made of microtubules, covered with an outer membrane that is a continuation of the cell membrane
- flagella are like tails, and their whip-like movements propels cells
- in unicellular protists such as paramecia, the wave-like motion of cilia enables the organisms to move
