biochem review

Question 1

Molecular Biology

Answer 1

Explains living processes in terms of the chemical substances involved

Question 2

Valence E

Answer 2

• The electrons in the outermost shell of an atom
• Determine how reactive an element is
• Chemical bonds occur when atoms gain, lose or share e-
• Atoms bond with each other in order to completely fill their outermost (valence) energy level/shell.
• Once the outer shell is full, the atom is stable. This is often referred to as the octet rule since most biologically important elements have outer shells that hold 8 electrons

Question 3

Intramolecular forces

Answer 3

The forces that hold atoms together within a molecule are intramolecular forces
- 2 Types: Ionic bonds and Covalent bonds
- covalent bonds: Covalent bonds are formed when non-metallic atoms SHARE electrons
2 Types: Polar covalent bond
Non polar covalent bonds
- Atoms on the periodic table have different abilities to attract electrons called electronegativity
- Non-polar Covalent: e- in the bond are shared equally between the atoms
- Polar Covalent: e- are NOT shared equally. e- spend more time around the more electronegative atom, giving it a slightly negative charge

Question 4

Intermolecular forces

Answer 4

There are also forces between molecules called intermolecular forces. Much weaker than intramolecular interactions. Determine how molecules interact.
- Hydrogen bond: A weak association b/w an atom with a partial negative charge and a H atom with a partial positive charge. Represented with a dashed line
- Like dissolves like
- Hydrophobic – water fearing (non-polar molecules that do not have attractive interactions with water)
- Hydrophilic – water loving (polar molecules with attractive interactions with water)
- Hydrophobic Effect – the natural clumping together of non polar molecules in water (e.g. oil in water)

Question 5

Biochemistry

Answer 5

The study of the activty and properties of biologically important molecules. Essential to undertsanding their functions in teh cell and in other living systems

Question 6

Monomer and Polymer

Answer 6

Monomer: indivdual molecules or subunits –> very small, mainly soluble in water, pass in and out of cells easily
Polymer: large molecules made up of smaller molecules joined together. do not enter and leave cells freely by diffusion

Question 7

Metabolism

Answer 7

The sum of all reactions that occur in an organism
Anabolism: reactions that build larger molecules from smaller ones
Catabolism: reactions that break down larger molecules into smaller ones

Question 8

Carbon containing molecules

Answer 8

• Carbon is 15th most abundant element on earth. It can form up to four covalent bonds, which allows for making many different and complex molecules
• Functional groups are groups of atoms that confer specific chemical properties on organic molecules
• R groups are “the rest of the molecule”

Question 9

Different functional groups:

Answer 9

• Hydroxyl: R – OH (characterized by the hydroxyl group) (polar, example is ethanol and is found in all macromolecules)
• Carbonyl group: C–O (double bond) Ketone is when DB O in middle and aldehyde is DB O at the end (polar, example is acetaldehyde and is found in carbs and nucleic acids)
• Carboxyl: OH-C–O (c DB o and SB oh –> COOH non ionized and COO- ionized (polar acidic, example acetic acid and found in proteins and lipids)
• Amino: R-NH2 non ionized and R-NH3 ionized (polar, basic, example alanine and found in proteins and nucleic acids)
• Sulfhydryl: also called thiol R-S-H found in proteins (slightly polar, example is cysteine and found in proteins)
• Phosphate group: o–P-o-o-o (P single bonded with 3 o and double bond with one o) (polar negatively charged, glycerol phosphate and found in nucleic acids)

Question 10

Macromolecules

Answer 10

carbohydrates, lipids, proteins and nucleic acids –> they are 4 main classes of carbon compounds in living things

Question 11

Organic vs Inorganic

Answer 11

Organic molecules
- contain carbon (and usually H and O).
- proteins, carbohydrates, lipids, and nucleic acids (like DNA and RNA).

Inorganic molecules
- don’t contain carbon. Many inorganic molecules are essential to life as well.
- Water, vitamins, minerals

we are mainly made of O, C, H, and N

Question 12

Water

Answer 12

“covalent” molecule “intramolecular” bonds result from a sharing of electrons between the oxygen and hydrogen atoms.
- Note that the unpaired electrons on oxygen repel the bonding electrons, thus giving the water molecule a bent shape.
- Oxygen is more “electronegative” than hydrogen
and will pull bonding electrons closer to itself. H2O molecule is a partially negative pole while the other is partially positive
- Structure and polarity of the water molecule allows for many remarkable properties:
- Hydrogen Bonding strong form of “intermolecular attraction” occurs between water molecules due to the polarity of the covalent bond Partially +ve H is attracted to partially –ve O

Question 13

Water Properties

Answer 13

• Cohesion: the tendency of like molecules to stick to each other. Without strong cohesion, water couldn’t be drawn up the xylem of a plant. Cohesion also results in water’s high “surface tension”, which actually allows some insects to walk on water.
• Adhesion: the tendency of like molecules to cling to surrounding materials and surfaces. allows water to be drawn through vessels like the xylem (plant’s water transport system)

Thermal Properties:
- High Specific Heat Capacity: a relatively large amount of energy is needed to substantially increase water’s temperature. Why? Because a large amt of E is needed to break water’s many hydrogen bonds excellent for temperature regulation!
- High Heat of Vaporization: requires a lot of energy for evaporation of the liquid to occur. Therefore it also has a high boiling point (Note that water’s boiling temperature of 100 degrees C is relatively high for a liquid). In order for sweat to evaporate, it must absorb a great deal of heat from your body, thus cooling you down.

Solvent properties:
- Water’s polarity makes it ideal for dissolving other polar or ionic compounds.
- Consider that many important nutrients and biomolecules must exist in solution.
- This also explains the hydrophilic (water loving)and hydrophobic (water hating) nature of various molecules.

Density:
Water solidifies (freezes) in a form that is less dense than the liquid form. Therefore, ice floats on water.
While the surface of water freezes, liquid water is insulated beneath, maintaining aquatic ecosystems.
Why?
H-bonds don’t break when frozen, so they form a lattice → less dense

Question 14

Carbohydrates

Answer 14

• source of energy and necessary to build different molecules
• Carbohydrates contain elements C, H and O in a 1:2:1 ratio –> General formula (CH2O)n –>name often ends in –ose
• functional groups are carbonyl and hydroxyl
• functions are source of energy, used as building materials and cell surface markers for cell-to-cell identification and communication

Question 15

monosaccharide

Answer 15

-simple surgar (mono=1 and saccharide = sugar)
- examples include glucose (produced during photosynthesis), galactose (in milk) and fructose (in fruit)
- all have c6h1206 formula, galactose has oh’s on same side as ch2oh and fructose has pentagon shape
- all are isomer- same formula but different arrangement of atoms so therefore diff shapes and physical and chemical properties
- 2 forms of glucose alpha which oh is downwards and beta which oh is upwards
- ribose is a 5c surgar (ribose has oh on c2 but deoxyribose is missing o on c2)

Question 16

disaccharides

Answer 16

• 2 monosaccharides joined by a glycosidic bond
• maltose (glucosex2)
• sucrose (glucose and fructose)
• lactose (glucose and galactose)
• condensation reaction or dehyration synthesis is when h2o is removed or is a byproduct of the linakge between two monosaccharides

Question 17

polysaccharide

Answer 17

• Complex Carbohydrates –> Many glucose molecules (hundreds to thousands) joined by glycosidic bonds
• The variety of linkages in the glucose chains give different shapes and different functions
• Two important functions in living cells: Energy storage and Structural support
• energy storage polysaccharide: starch which is a polymer of alpha glucose in plants and glycogen which is a polymer of alpha glucose in animals
• structural polysaccharides: cellulose is a polymer of beta glcose in plant cell walls and chitin is similar to cellulose but has modified glucose units with n containing funtioanl group (in insect exoskeletons)

Question 18

polysaccharides 2

Answer 18

starch: found in plants, alpha 1,4 link, mixture of 2 polysaccharides (amylose which is unbranched and amylopectin which is branched. both types twist into coils making them insoluable in water)
glycogen: found in animals, similar to amylopectin but many more branches and alpha 1,4-link
cellulose: plants only, polymer of beta glucose, 1,4-link (alternating bond orientation and linear), h bonds between cellulose molecules form bundles with high tensile strength
- alpha glucose subunits: starch is chain of alpha glucose subunits and glycogen is branched chain of alpha glucose subunits
- beta glucose subunits: cellulose is a chain of beta glucose subunits (stairs)
chitin: resembles cellulose but is made out of modified glucose units that bear a nitrogen containing functional group. the hard exoskeleton of arthropods is made of chitin. also found in the cell walls of fungi

Question 19

hydrolysis

Answer 19

The opposite of a condensation reaction is hydrolysis, where in the presence of water and an enzyme the “glycosidic linkage” is broken.

Question 20

lipids

Answer 20

• contain c,h and o
• hydrophobic so insoluble in water
• contains hydroxyl and carboxyl
• divided into 4 families (triglycerides, phospholipids, steroids and waxes)

Question 21

triglycerides

Answer 21

• Eg. The fat in adipose tissue in humans, the oil in sunflower seeds
• Fats can be liquid or solids, oils are always liquids
• Used as energy stores, heat insulators
• Composed of one glycerol molecule and three fatty acid molecules
• Fatty acid chains are long C-H chains with carboxyl at one end
• Fatty acid chains are connected to glycerol molecule by ester linkage
• saturated fatty acid has only single bonds between c atoms so has max h atoms and is solid
• unsaturated fatty acid has one or more c-c double bonds (mono is one double bond and poly is more than 1 double bond) and has fewer h atoms
• cis unsaturated fatty acid has h atoms on the same side of the two c that are double bonded so it has a bend in a chain making them unable to pack tightly and therefore are liquids
• trans unsaturated fatty acid has h atoms on the opp sides of c’s that are double bonded so there isn’t a bend in the chain and therefore solid (they only exists as a byproduct of hydrogenation)

Question 22

hydrogenation and esterfication

Answer 22

• hydrogenation: adding h atoms to convert unsaturated fat to saturated fat (trans unsaturated is created through this)
• esterfication: fatty acids are linked to glycerol by a condensation reaction, reaction is between COOH on fatty acid and OH on glycerol this forms an ester linkage

Question 23

phospholipids

Answer 23

• made of 2 fatty acids and a phosphate group
  -amphipathic as there is a polar head(phosphate) and non polar tail (fatty acid)
• phospholipid bilayer makes up cell membranes (polar head facing water and nonpolar tail inwards)

Question 24

steroids

Answer 24

• 4 fused hydrocarbon rings (carbonyl groups)
• includes cholesterol in cell membranes and sex hormones
• cholesterol is complex, testosterone has one double bond and estrogen has benzene

Question 25

waxes

Answer 25

• diversity of structures
• usually long carbon-based chains
• solid at room temp
• in plants: carbuna wax, coats the surface of leaves preventing water loss and repels insects
• in animals: beeswax and earwax, present on the skin, fur and feathers of animals

Question 26

proteins

Answer 26

• 1000s of diff proteins in cells
• DNA codes for their structure
• 3D structure determines their function
• Functions include: Catalyzing chemical rxns, Provide structural support, Transport substances in body, Regulate cellular processes, Provide defense from disease
• Functional groups are amino group and carboxyl group
• monomers: are the amino acids, central c atom with amino groups, carboxyl group and h atom, 20 different side chains (r groups), 8 aa are essential and need to be eaten, can be polar non polar charged(acidic or basic) depending on the nature of their side chain
• polymers: polypeptides, many aa bonded together, formed by condensation reaction and joined by peptide bonds
• peptide bonds: form when oh from the carboxyl of an aa and the h from teh amino of the otehr aa form water
• a protein consists of one or more polypeptides twisted and coiled into a specific shape (shape determined by the order of amino acids)

Question 27

protein organization levels

Answer 27

• primary structure: sequence of aa’s, determined by the nucleotide sequence in dna, this order determines the final protein shape (shape is critical for fucntion)
• secondary structure: folding and coiling of a single polypeptide chain, caused by h bonds forming between nearby aa’s (alpha helix and beta pleated sheet are the 2 types of secondary structure)
• tertiary structure: folding caused by forces of attraction and repulsion between the polypeptide and its environment, usually occur to intereactions and bonds between r groups of aas, gives proetin a 3d structure

intereaction of r groups include hydrophobic effect (aa with nonpolar r groups move in the interior of polypeptide away from water), h-bonds (form between polar side chains), ionic bonds (form between oppositely charged side chains), and disulfide bridges (form between r groups containing sulfur, strong stabalizers of 3 degree structure)

• quaternary structure: 2 or more polypeptides wound together

Question 28

extra prptein info

Answer 28

Proteins with a 3D structure (ie.3degree and 4degree) fall into two main types:
- Globular - form ball-like structures where hydrophobic parts are towards the centre and hydrophilic are towards the edges, which makes them water soluble. Ex: HEMOGLOBIN
- Fibrous - form long fibres and mostly consist of repeated sequences of amino acids which are insoluble in water. Ex: Collagen(skin) and keratin (hair)

shape of protein is also infeucned by: chemical and physical environetal factors (pH and temp) may casue changes in protein shape - called denaturation, protein becomes non-functional as structure determines function. protein can resume shape under normal conditions if priamry structrue is maintaned

Proteome:
- All of the proteins produced by a cell, tissue, or organism = proteome
- Varies → different cells in an organism make different proteins
- Reveals what is happening in the organism (vs. What could happen)
- Proteome of each individual is unique (although there are strong similarities b/w individuals in the same species)

Question 29

enzymes

Answer 29

• Are proteins that work as catalysts
• RECALL: a catalyst speeds up a reaction without being consumed or permanently altered in the process
• Enzyme names often end in ‘ase’
• Found in all living cells
• enzymes are part of our daily lives and they are essential to drive a lot of the functions in our bodies like digestion.
  -If we didn’t have enzymes, a lot of the chemical reactions in our cells just wouldn’t happen.

jello example:
- Specific enzymes in fruits like pineapple and kiwi speed up the hydrolysis reaction that breaks collagen into its individual amino acids.
- These enzymes are proteases, which means they can break apart proteins (specifically the peptide bonds joining together individual amino acids).
- As a result, the Jell-O will never be able to set.
- Certain fruits like pineapples contain enzymes that speed up the hydrolysis reaction that turns collagen into individual amino acids

Question 30

enzymes in everyday life

Answer 30

Meat Tenderizer
- Made from fruits like papayas, which contain papain, or pineapples, which make bromelain.
- Help break down collagen
- Since meat is a bunch of protein, having a protease go to work on it can reduce its toughness.
- The enzymes act to break down collagen, which makes up muscle-associated connective tissue (eg. sinew, tendons, ligaments etc… aka the tougher parts of a cut of meat).
- This is also why pineapple is often paired with tough cuts of meat, to aid in digestion.

Fermentation
- The most familiar type of fermentation is the conversion of sugars and starches to alcohol by enzymes in yeast.
- Enzymes produced by yeast are used to help speed the reaction where sugars and starches are converted to alcohol
- Used to make alcoholic beverages, cheese, and bread

Absence of enzymes in digestive system
- The absence of certain digestive enzymes can cause serious, and severe health problems.
- Recall: Lactose
- Example: Lactose Intolerance
- One digestive enzyme that should be in the body, but is not always present, is lactase.
- Lactase is the enzyme speeds up the hydrolysis reaction that breaks down lactose, the principal carbohydrate in milk, to implement its digestion.
- if a person lacks this enzyme, consuming dairy products may cause diarrhea, bloating, and cramping.
- Such a person is said to be “lactose intolerant,” and if he or she is to consume dairy products at all, they must be in forms that contain lactase.
- For this reason, Lactaid milk is sold in the specialty dairy section of major supermarkets, while many health-food stores sell lactaid tablets.

ex. those who cant digest sucrose or maltose the prnciple carbs in furits and grains have congenital sucrase-isomaltase deficiency so to treat it they take the sacrosidASE medicine

Question 31

chemical reactions

Answer 31

• The laws of thermodynamics define which reactions are spontaneous and which are not
• RECALL: A spontaneous reaction is a reaction that occurs in a given set of conditions without intervention.
• Some spontaneous chemical reactions occur at nearly imperceptibly slow rates
• The rate of many metabolically important chemical reactions is insufficient to sustain life
• enzymes speed up chemical reactions by lowering their activation energy (Activation energy is the initial input of energy needed to start the reaction? Lower activation energy means a faster reaction time) the net change in free energy remains unchanged

Question 32

how enzymes work

Answer 32

substrate: The reactant that an enzyme acts on when it catalyzes a chemical rxn, Enzymes are very specific for the substrate they bind. The location where the substrate binds to the enzyme is the “active site” –> Complementary fit, Lock-and-key fit, induced fit (shaking hands)

ex. hydrolysis of maltose
- the players are substarte (maltose), enzyme (maltase) and there is active sight on malatse
- Substrate binds to enzyme
- enzymes’ conformation changes to better accommodate the substrate (induced fit)
- Glycosidic link is broken (hydrolysis) once water is added with the substrate in the active site
- Conformation of protein changes –> it loses its affinity for the products (2x glucose)
- Releases them
- Active site is now available for another maltose to attach

(Enzymes prepare substrates for reaction by changing the substrate, its environment, or both in some way, and thus lowering the activation energy of the reaction. Depending on the enzyme, this process may occur in a variety of ways. For example, the active site may:
- contain amino acid R groups that end up close to certain chemical bonds in the substrate, causing these bonds to stretch or bend, which makes the bonds weaker and easier to break;
- bring two substrates together in the correct position for a reaction to occur;
- transfer electrons to or from the substrate (that is, reduce or oxidize it), destabilizing it and making it more likely to react;
- add or remove hydrogen ions to or from the substrate (that is, act as an acid or base), destabilizing it and making it more likely to react.)

This cycle is known as the catalytic cycle.
Some enzymes require the presence of additional molecules or ions to catalyze a reaction. Organic molecules that assist an enzyme are called coenzymes.
Some enzymes require the presence of metal ions, such as iron or zinc, which are referred to as cofactors. Your body requires small amounts of minerals and vitamins in order to stay healthy. In many cases, this is because those minerals and vitamins are essential to enzyme activity. Without them, enzymes in your body cells cannot catalyze reactions

Question 33

factors affecting enzyme activty

Answer 33

The rate of an enzyme-catalyzed reaction is dependent upon several factors: Temperature, pH, [Substrate] and [Enzyme]

Temperature
- When a liquid is heated, particles are given more kinetic E. Both enzyme and substrate molecules will move faster at higher temps ∴↑ collisions b/w enzyme & substrate. ∴ ↑ enzyme activity
- When enzymes are heated, bonds in the enzyme vibrate more and the chance of bonds breaking is ↑. An enzyme’s 3D shape is defined by various chemical bonds. Altered enzyme shape compromises activity. “Denaturation”
(When the temperature becomes too low, the bonds that determine enzyme shape are not flexible enough to enable substrate molecules to fit properly. At higher temperatures, the bonds are too weak to maintain the enzyme’s shape.)

pH
- Most enzymes have an optimum pH at which their activity is highest – if the pH is altered, the structure of the enzyme is altered. Beyond a certain pH the structure of the enzyme is irreversibly altered –> denaturation

[Substrate]
- ↑ concentration of substrates, ↑ substrate-active site collisions. At some substrate concentration all of the enzymes’ active sites are bound to substrate. The enzyme is “saturated”. Adding more substrate will not increase the rate

[Enzyme]
- More enzyme, more rxn. Assume that there is excess of substrate.

This is why jello deserts can be made with some fruits. U have to inactivate the enzyme so it cant break down the collagen/gelatin into amino acids (u can boil fruits/denature the enzyme with hgh temp thats whats down with canned fruits or you can change the pH of the jello or use a different substance like agar instead of jello)

Question 34

nucleic acids

Answer 34

• Informational macromolecules
• Used by all organisms to store hereditary information that determines structural and functional characteristics
• functional groups incldue phosphate group, hydroxyl group adn amino group
• monomers: nucleotides, made of 3 subunits –> 1. a nitrogenous base (a,t,g,c or u if rna –> ag have double c ring but u,t,c have single ring) 2. a 5-c (pentose) sugar (deoxyribose or ribose) 3. a phosphate group

Question 35

DNA and RNA

Answer 35

DNA:
- Permanent storage site of genetic info
- Sugar = deoxyribose, a 5C sugar with one less oxygen than ribose of RNA
- 4 nitrogen bases = A,C,T,G
- 2 purines = a and g (double ringed)
- 2 pyrimidines = c and t (single ringed)
- complementary base pairs: a-t and c-g
- bases are held together with hdyrogen bonds (triple bonds between c and g (like GC) and double bonds between a and t
- 2 strands running in opp directions (antiparallel) form an alpha helix (pentagone faces opp direction on other side which is why antiparallel)
- phosphodiester bonds link sides of teh helix
- phosphate groups of one bonds to hydroxyl of sugar on other

RNA
- reads the info in dna and transcribes it into a polypeptide –> because dna cant leace the nucleus
- single strand of nucleotides
- linear shape
- composed of a,u,g and c

• Rna single stranded, dna is double stranded
• Dna has deoxyribose sugar, rna has ribose sugar
• Dna cant leave nucleus but rna can
• Dna contains thymine and rna contains uricil

Question 36

Biochemical reactions

Answer 36

main biochemical reactions include neutralization reactions, oxidation and reducation reactions, condensation reaction and hydrlysis reactions.

The chemical reactions that are associated with biological processes can be grouped into several types. Often, these biochemical reactions involve a combination of more than one type. The four main types of chemical reactions that biological molecules undergo in the cell are neutralization, oxidation-reduction, condensation, and hydrolysis reactions.

Question 37

Neutralization reactions

Answer 37

Acids produce H+ ions when disolved in water and they have a pH lower than 7. Bases produce OH- ions when disolved in water and have a pH higher than 7 (up to 14).

When acid and bases react this is called a neutralization reaction and produces salt and water. As a result of a neutralization reaction, the acid loses its acidic properties and the base loses its basic properties. In other words, their properties have been cancelled out, or neutralized.
Acid + base –> h2o + ionic salt

ex. 2NaOH + H2SO4 → Na2SO4 + 2H2O

Buffer is a substance that maintains constant pH levels when a fluid becomes too acidic or too basic by either taking up or releasing H+ or OH- ions as needed. Ex. it matters that we need to keep our blood at a slightly aklakine pH so we have buffers that help maintain this range

Question 38

Oxidation-reduction reactions

Answer 38

Reduction reaction: a gain of electrons (ex. O + 2e- –> O-2)
Oxidation reaction: a loss of electrons (ex. Mg –> Mg +2 + 2e-)

Electrons are highly reactive and do not exist on their own or free in the cell. Therefore, when one molecule undergoes oxidation, the reverse process must also occur to another molecule.

rmbr LEO says GER

redox reactions: an oxidation and reduction reaction occur at the same time

ex. C6H12O6 + 6O2 → 6CO2 + 6H2O

A common type of redox reaction is a combustion reaction. For example, the combustion of propane, C3H8, in a gas barbecue occurs according the following chemical equation: C3H8 1 5O2 3CO2 1 4H2O The propane is oxidized, and the oxygen is reduced. This reaction also releases a large amount of energy—energy that is used to cook food on the barbecue. Similar types of redox reactions occur in cells. For example, the process of cellular respiration has an overall chemical equation of C6H12O6 1 6O2 6CO2 1 6H2O Sugars such as glucose are oxidized to produce carbon dioxide and water.

Question 39

Condensation and hydrlysis reaction

Answer 39

condensation: two or more monomers join togetehr to form a polymer and water (also known as dehydration synthesis) (In a condensation reaction, an H atom is removed from a functional group on one molecule, and an OH group is removed from another molecule. The two molecules bond to form a larger molecule and water. )

ex. glycine + glycine → dipeptide

hydrolysis: the addition of water breaks a polymer into its monomers ( In a hydrolysis reaction, 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 these monomers breaks and the larger molecule is split into two smaller molecules.)

ex. Sucrose → glucose + fructose

(double arrows in reaction pic indicate reversability?)

Question 40

Enzymes and regulation

Answer 40

Enzymes are a class of protein that increase the rate of a reaction by binding to a specific substrate at the active site and lowering the activation energy of the reaction. Almost all chemical reactions in organisms are facilitated by enzymes. The types of chemical reactions discussed in this section are all catalyzed by enzymes. Is affected by factors like temp, pH, and the intital concentrations of substarrte and enzyme.

Enzyme activty can be also affected by the presence of an inhibitor (Inhibitors are molecules that interact with an enzyme and reduce the activity of the enzyme. They do this by reducing an enzyme’s ability to interact with its substrate) which can interfere with enzyme activty in two possible ways:
- competitve inhibiation: inhibitor binds directly to active site (less enzyme for substrate)
- noncompetitive inhibition: inhibitors that bind to enzymes with allosteric sites (non active site where othe rmolecules can interact with and regulate the activty of the enzyme) alter the overall shape of the enzyme, inclduing the active site

• if enzyems are crucial for activty in all lviing systems and bacteria is a threat to us then it would be great if we had an antibiotic that would disrupt the bactera enyzme atcivty then we could limit their growth limiting the infection to us → if we hurt baterial enzyme activty they cant live . if u target the enzymes of bacteria, that will stop the bacteria from growing since enzymes are important to all living organisms

Activator (a molecule that binds to the allosteric site of an enzyme and keeps an enzyme active or causes an increase in the activity of that enzyme) molecules can also bind to an allosteric site. In this case, the conformation of the enzyme alters in such a way as to cause an increase in enzyme activity. The regulation of enzyme activity by activators and inhibitors binding to allosteric sites is called allosteric regulation.

Question 41

Eukaryotic cells

Answer 41

Animals, plants, fungi, and protists are composed of eukaryotic cells. Cellular organization varies among different organisms, but all eukaryotic cells have these features in common.
- The genetic material—DNA—is contained within a membrane-bound nucleus.
- A cell membrane comprised of a phospholipid bilayer (double layer) and embedded proteins separates the cell’s contents from its surroundings.
- Filling the cell interior is the jelly-like cytoplasm, which consists of everything outside the nucleus but within the cell membrane. This includes the organelles, cytosol, and molecules and ions dissolved or suspended in the cytosol. The cytosol is the fluid itself of the cytoplasm.

important general functions of organelles in eukaryotic cells: Cellular organization, compartmentalization, specialization, conducting life processes, containing biochemical reactions and storage.

Question 42

Cell Functions 1

Answer 42

Nucleus: found inside the cell, near the centre, its the control centre and contains DNA, which stores and replicates the genetic information of the cell (dna combines with protein to form chormosomes and chromatin is the unfoled state of chromsome found in cells), found in both a and p

nuceloplasm/nuclear matrix: A thick fluid called nucleoplasm fills the nucleus, and a network of protein fibres called the nuclear matrix provides internal structure and support.

nucleolus: found inside the nucleus, produce and assemble ribosomes (contains rna, protein and chromatin), found in both p and a

nuclear membrane: found aorund the nucleus, protects the nucleus and lets things in and out of the nucleus (pores), found in both p and a

Cell wall: found in outer layor of cell, protects and supports plant cells and prevents water loss and contains cellulose, found in only p

cell membrane: found around the cell, protects the cell and lets things in and out of it (functions as a selective, dynamic cellular boundary), found in both p and a

mitochondria: found in cytoplasm, makes energy from breaking down organic molecules that were stored and is the powerhosue of the cell, found in both p and a

golgi bodies/apparatus: found in the cytyoplasm, packages and secretes waste, manufacters macromolecules, and produces lysosomes found in both p and a

smooth er: attacthes from the cell membrane to nuclear membrane, transports materials and sends messages to all parts of the cell (doesnt have ribosomes)(lipid synthesis and detoxifies drugs and alcohol), found in both p and a

rough er: attacthes from the cell membrane to nuclear membrane, transports materials and sends messages to all parts of the cell (has ribosomes) (protein synthesis/assembles proteins for export and membrane proteins), found in both p and a

ribosome: found in cytoplasm or attatched to er, makes porteins, found in both p and a

Question 43

cell functions 2

Answer 43

vesicle: membrane-bound sacs used for the transport and storage of substances in the cell. Vesicles form by pinching off from cell membranes and organelle membranes. They can fuse with cell membranes and organelle membranes to release their contents. A typical animal cell contains many small vesicles.
Plant cells contain instead a single large central vesicle, called a vacuole.

Vacuole: found in the cytoplasm, stores food adn water, contains enzymes that break down macromolecules and cell waste, (The quantity of water in the central vacuole determines the turgor pressure, or internal pressure, of the plant cell. A full vacuole presses against the cell wall, increasing turgor pressure and causing the plant cell to be rigid. Without enough water, a vacuole will shrink and pull away from the cell wall) found in both p and a

lysosome: found in the cytoplasm, contains digestive eznymes (breaks down macromolecules), destroys bactera and old cell parts, found in a cells only

centrioles: in cytoplasm, help the cell to divide, found in a cells and some p

cytoplasm: found in cell, gel-like substance that holds all organelles in cell, found in both p and a

chomatin, chromosomes: in nucleus, contains genetic information/traits and found in p and a

cilia: outside of cell, short hair-like projections used for movement, found in a and some p

flagella: outside of cell, long whip like tails used for movement, found in a no p

chloroplast: found in plant cells, traps suns energy and makes food through redox reactions, found in p only

peroxisome: found in cytoplasm, small, membrane-enclosed organelles that contain enzymes involved in a variety of metabolic reactions (catlyze redox reactions. they break down biological molecules and some toxic molecules, also synthesize molecules like cholesterol and bile acids), found in both a and p

cytoskelatin: inside cell, support structure of the cell, anchros the cell membrane and organelles in place and transports materials through the cell (made of microtubules and microfilaments), found in both p and a

plastids: in plant cell, stores extra food, in p only

microtubule: thick fibres, gives shape to cell, helps in cell division and moves organelles in cytoplasm

microfilament: thin fibres, maintain cell shape, involved in msucle contration and assist in cell division

Question 44

endomembrane system

Answer 44

consists of the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, and vesicles. This system acts as the transportation and product-processing section of the cell. The endomembrane system compartmentalizes the cell so that particular functions are restricted to specific regions.
The organelles that make up the endomembrane system are connected to one another either directly or by transport vesicles. It modifes and transports proteins. exmplained below

1. On the surface of the rough ER, polypeptides are produced by bound ribosomes and extruded into the lumen, rather than being released into the cytosol.
2. These polypeptides travel through the lumen to the smooth ER, where they are stored and processed. When proteins are ready for transport, pieces of smooth ER pinch off to form vesicles (a membrane-enclosed sac used for transport and storage) containing the protein.
3. Vesicles from the smooth ER travel across the cell to the cis face of the Golgi apparatus, which is a stack of curved membrane sacs, shown in Figure 2.7. There, the vesicles merge with the membrane of the Golgi apparatus and release their contents into the interior. In the Golgi apparatus, some proteins are stored and others are modified further. For example, some proteins have carbohydrate chains added to them in the Golgi apparatus or in the ER, converting them into glycoproteins, which are important parts of cell membranes. (Note: The Golgi apparatus is called Golgi bodies in some resources.)
4. When the modified proteins are ready for transport, pieces of the Golgi apparatus pinch off from the trans face to form vesicles. These vesicles transport the proteins to the cell membrane, or to other destinations within the cell.

The endomembrane system performs a series of related but separate functions vital to a eukaryotic cell’s survival: the rough ER folds, processes, and packages proteins; the smooth ER synthesizes lipids; and vesicles transport proteins or lipids to the Golgi apparatus, which further modifies, sorts, and packages these molecules. Meanwhile, lysosomes (produced by the Golgi apparatus) break down worn-out cell parts and other materials while keeping the lysosomal enzymes from affecting other cell components. Without the endomembrane system, the functions of the cell would not happen or would not happen in an organized matter.

Question 45

Cell membrane structure

Answer 45

Made of a phospholipid bilayer
Two rows of phospholipid molecules with proteins, lipids, and Carbohydrates scattered throughout
hydrophilic heads face insde and outside of the membrane (the water environemt)
hydrophobic fatty acid tails face each other in the mdidle of the membrane

this is what naturally forms the membrane → barrier from watery enevrinonemnt but also live in one

amphipathic: has both hydrophilic and hydrophobic: allows for natural arrangemnt into bilayer

(visualized proteins inserted into the phospholipid bilayer with their non-polar segments in contact with the non-polar interior of the bilayer and their polar portions protruding from the membrane surface)

Question 46

functions of cell membrane

Answer 46

(selective gatekeeper, forms shape of the cell and acts as barrier)

controsl what enter and leaves the cell (food in and waste out) (the food broken down to monomers by body is done so we can feed our cells → which is why food enetres)

acts as a barrier

Semipermeable: some molecules are allowed to pass freely through the membrane (there is some level of control/filtering of what is allowed to freely pass thrjogg the membrane) –> smalle soluble lipids can pass through, water moves freely across however large molecules do not easily pass through because of how tightly oacked the phospolipids are (u need to have a good balance between allowing some things to go in and out, and then being selective of the larger things)

some molecules require energy to pass through while others dont use enrgy at all (cell membrane has certain areas that will allow larger stuff to come through → there are some openings (small for small things and large openings for large stuff?))

The cell membrane has a crucial role in maintaining the integrity of the cell as it functions as a selective, dynamic cellular boundary. The cell membrane maintains the integrity of the cell of which it is a part by regulating the passage of molecules and ions in and out of the cell. Without this regulation, harmful substances could enter freely and substances may leak out of the cell so the cellular processes could fail and the cell would die without the membrane.

Question 47

fluid mosaic model

Answer 47

this is what the cell membrane looks like –> the appearance of the cell membrane is a fluid mosaic model because is flexible, not rigid, has fluibilty, and it’s position of components is random, no pattern

“FLUID” – Because the parts of the membrane are free to drift around in a fluid motion
“MOSAIC” – Because the position of the many different components is random, with no set pattern

Phospholipid bilayer: Each layer ontains phospholipids embedded with proteins. The hydrophobic “tails” of the phospholipids face each
other while the hydrophilic “heads” face out, toward the cytoplasm or extracellular fluid.

Fluid membrane: Phospholipids can move about freely, thus can rearrange themselves to seal ruptures in the cell membrane.

mosaic of proteins and other moledules: Proteins and other molecules form a floating mosaic on or in the membrane: peripheral proteins are bound to the cytoplasmic or external surface; integral proteins reach through the membrane. Glycolipids and carbohydrate chains are attached to some membrane proteins.

Question 48

Fluidity of membrane

Answer 48

• The fluidity of the bilayer/cell membrane is important to allow the cell to adapt its shape and movement to different conditions. It allows it to be flexible for when we move. It also prevents it from crystallizing.

The main factors that affect fluidity include the following.
- Temperature: With increasing temperature, the bilayer becomes increasingly fluid until it is unable to act as a barrier. At decreasing temperatures, the bilayer eventually solidifies into a gel-like state.
- Presence of double bonds in the fatty acid “tails”: Double bonds form “kinks” in a fatty acid tail. The presence of one or more double bonds causes fatty acids to be less tightly packed and more fluid.
- Fatty acid “tail” length: Longer fatty acid “tails” have more intermolecular attractions and hold together more tightly compared to shorter fatty acid tails, thus reducing fluidity. The most common length of a fatty acid is 16 or 18 carbon atoms.
- The presence of cholesterol in cell membranes also affects fluidity. Many eukaryotic cell membranes contain cholesterol molecules.
At room temperature and higher, the presence of cholesterol increases the intermolecular forces in the membrane and holds it more tightly together, thus reducing fluidity. At lower temperatures, however, cholesterol molecules break up the packing that occurs as phospholipids solidify into a gel. As a result, cholesterol increases the fluidity of the cell membrane at low temperatures.

Question 49

Components of cell membrane

Answer 49

phospohlipds, proteins and cholesterol

Phospholipids: Lipid Bilayer: 2 layers of phospholipids, Phosphate head is polar (water loving), Fatty acid tails non-polar (water fearing), Proteins embedded in membrane

Membrane proteins:
- Functions: Receptor sites for hormones (hormone-binding sites) → like a recognition site, if a hormone need to target a specific organ it has to recognize the organ cells/tissue, it recognizes the cell by the membrane proteins that are receptor sites which tells hormone where to bind (like an address) → are like blinking lights telling them where to bind to do their job. Immobilize enzymes → membrane proteins immobilize enzymes when we don’t need the enzymes anymore (like when they r done their job they signal to them to stop) → if the signal doesnt work then too many enzymes are produced and that may cause a deficiency of something. Cell adhesion- makes tight junctions between cells → membrane proteins allow cells to glue to each other → conducive to cell-to-cell communication. Cell-to-cell communication. Transport of materials: membrane proteins have ways to move larger molecules with or without the use of energy in/out of the cell–> Passive transport and Active transport

Types of proteins: intergeal proteins (span acroos the membrane (transmembrane) and hydrophillic parts tsicking out on iether side of membrane like polar head), peripheral proteins (found on the inner or outer suraface of the memrbane and can be attacthed to intergal protein), glyocoporteins (proteins with a carb attatched and usually involved in cell recognintion, signiling or sites for harmone binding)

protein count (more active the membrane the more proteins, most cell structure have 50% but mitochondira and chlroplast have 75 due to the more work they do (photoysnthesi and cellular respiration) so they need more energy/protein count)

cholesterol: Found in animal cells only, Type of lipid – steroid, Many hydrophobic but has –OH (hydroxyl) group which makes that part hydrophilic (to interact with p-lipid heads), Involved in controlling fluidity of the CM , Disrupts the p-lipid molecules – makes CM more fluid (so not to crystallize)/ but not too fluid so it still has a rigid ring structure, it also reduces permeability of hydrophilic molecules that need to enter the cell (At low temps it will increase the fluidity by preventing the close packing of phospholipids and at high temps cholesterol will reduce fluidity when it becomes to fluid by increasing the intermolecular forces that hold the membrane together)

Question 50

Types of Cell Transport

Answer 50

Passive transport (cell does not use energy): simple diffusion, osmosis and facilitated diffusion (in simple diffusion the substance passes between the membrane but in facilitated diffusion, there are specialized membrane channels that the molecule (charged or polar) will go through))

Active transport (cell uses energy): primary and secondary

membrane assisted transport (cell uses energy from atp): enodcytosis(phagocytosis and pinocytosis), exocytosis

GENERAL:
- Simple diffusion: The random movement of particles from an area of high concentration to an area of low concentration. Continues until all molecules are evenly spaced (equilibrium is reached).
- Facilitated diffusion: Transport of ions or molecules across a membrane by means of a membrane protein along the concentration gradient. The highly specific channels run through the membrane and the structure will determine what particles can travel through. It can be opened or closed in response to signals. Channel proteins are less specific and are transmembrane proteins. Carrier proteins are also transmembrane however are slower because of the extra steps (Bind to specific molecules, Transport them across membrane and release them on other side, Change shape, Lower rates of diffusion compared to channel proteins).
- Osmosis: The diffusion of water through a selectively permeable membrane. Water will move from a high to low water concentration. Some cells will even have water channels called aquaporins which increase the permeability of water. Water will also go from low to high solute concentration (so it will leave or enter the cell based on the conditions).
- Primary active transport: The cell uses ATP energy to directly move the molecules or ions. It actively moves molecules to where they are needed so movement from an area of low concentration to an area of high concentration and is against or up concentration gradient.
- Secondary active transport: Uses an electrochemical gradient (the combination of a concentration gradient and an electric potential (voltage) across a membrane, stores potential e that can be used by the cell) as a source of energy to transport ions or molecules across a cell membrane.
- Membrane-assisted transport: The fluidity of the membrane allows materials to be taken in (endocytosis) and out (exocytosis) of the cell. It is done by vesicles which are small sacs of membrane formed by pinching off of the plasma membrane or membrane-bound organelles like Golgi or ER and move things around the cell.

Question 51

Concentration Gradient

Answer 51

A difference in concentration between one side of membrane and other

Question 52

Passive Tranport 1

Answer 52

• Movement of ions or molecules across a membrane from a region of [higher] to a region of [lower] –> Without the input of E

Simple Diffusion: Random movement of particles from an area of [high] to an area of [low]. Continues until all molecules are evenly spaced (equilibrium is reached). Note: molecules will still move around but stay spread out.

Factors that affect diffusion: - Molecule Size: the larger the molecule, the more difficult it is for it to diffuse across a membrane
- Molecule Polarity: small polar molecules can cross membranes, but their rates of diffusion are generally lower/slower than those of non-polar molecules of the same size
- Molecule or Ion charge – charged molecules and ions cannot diffuse across a membrane(have diff way)
- Temperature - ↑ temp, molecules have more E and move faster (↑ rate of diffusion)
- Pressure - ↑pressure forces molecules across membrane (↑ rate of diffusion)

Question 53

Passive Transport 2

Answer 53

Facilitated diffusion: Transport of ions or molecules across a membrane by means of a membrane protein along the concentration gradient. Facilitated diffusion is the transport of ions and molecules across a membrane by means of a membrane protein along the concentration gradient for that ion or molecule. Ions or polar molecules go through channel proteins and molecules go through carrier proteins.

Channels: Form highly specific channels through the membrane, Structure/shape and size of hole determines which particles can travel through, Channel proteins permit the passage of ions or polar molecules that would not otherwise diffuse through the membrane, Can be open or closed in response to signals from hormones, electric charge, pressure/bp, light (less specific compared to carrier proteins, and transmembrane).EX. potassium channel in axon of neurons. K+ channels are voltage gated in axon. When charges are more “+” outside axon – channel is closed. When charges are more “-” outside axon channel opens temporarily allowing K+ to leave (via diffusion). If voltage difference is great enough channel opens.

Carrier Proteins: carry the molecules across rather than letting them travel, transmembrane, bind to specific molecules, Transport them across membrane and release them on other side, Change shape, Lower rates of diffusion compared to channel proteins

Question 54

Passive Transport 3

Answer 54

Osmosis: diffusion of water through a selectively permeable membrane. Water moves from high to low water concentrations. Water moves from low to high solute concentration (opp of diffusion).
Some cells have water channels called- aquaporins
which increase permeability of water in that cell. Water moves freely through pores.

Osmotic Conditions:
(The cell not being able to control the movement of water in or out wants to bath in solute concentration that is same of the insides (dont want to lose or gain too much water so wanst to bathe in same concentration))
- Hypertonic solutions: fluid surrounding the cell has a higher [solutes] than the cell’s cytoplasm. The solution has a high osmolarity so water diffuses out of teh cell by osmosis (cell shrinks) as the water likes to go to place with high concentration of solute.
- Hypotonic solutions: Fluid surrounding the cell has a LOWER [solute] than the cell’s cytoplasm. Solution with low osmolarity. Water diffuses INTO the the cell by osmosis (cell grows) as it goes to solution with higher solution concentration.
- Isotonic solutions: fluid surrounding the cell has an EQUAL [solutes] as the cell’s cytoplasm. Water diffuses INTO and OUT OF the the cell by osmosis in equal amounts (cell size does not change).

Osmotic conditions general terms: Hypertonic (hyper = more than), Hypotonic (hypo = less than), Isotonic (iso = equal). WATER WILL ALWAYS MOVE TO DILUTE THE SOLUTE

Plant cells and osmosis: in a hypotonic solution water moves into cell and cell becomes turgid(swollen) but doesnt not burst because of cell wall). In a hypertonic solution, water moves out of the cell called plasmolysis (cell membrane pulls away due to lac of water).

Animal cells and osmosis: in a hypotonic solution cells swell and burst - lysis (since the water goes into the cell). In a hypertonic solution cells shrink and shrivel - crenation (because water leaves). This is what happens when someone drinks seawater (seawater is hypertonic so water leaves the cell to dilute the salt and end up dehydrating cells to the point they may not have enough water to perform cellular functions). In a isotonic solution, there is no net movement of water.

• tissues or organs that are going to be used in transplants are bathed in a solution with the same osmolarity as the cytoplasm to prevent osmosis this is because we dont want any net osmosis (change in water motion) so its placed in an isotonic solution.

Question 55

Active Transport

Answer 55

(Active transport is a different way that material is brought in. Active transport of solutes against their concentration gradient via ion pumps, atp with primary active transport or energy of electrochemical gradient in secondary active transport. Generally it requires energy form the cell)

• Primary active transport: The cell uses ATP energy to directly move the molecules or ions. It actively moves molecules to where they are needed so movement from an area of low concentration to an area of high concentration and is against or up concentration gradient. Uses ATP directly to move molecules or ions from one side of a membrane to the other. Ex. Ion pumps are carrier proteins that use ATP to pump ions across the membrane. Eg. Sodium / Potassium Pumps are important in nerve responses.
• Secondary active transport: Uses an electrochemical gradient (the combination of a concentration gradient and an electric potential (voltage) across a membrane, stores potential e that can be used by the cell) as a source of energy to transport ions or molecules across a cell membrane.

Sodium potassium pump: Maintains an electrochemical gradient between the inside of the cell and the outside, with the inside being more negatively charged. Note number of binding sites. 3 Na+ ions leave for every 2 K+ that come in. This electrochemical gradient is used by nerve cells to relay signals. Ex. Neuron (of your nervous system). Made up of Axons. Nerve impulses – how messages are sent down a neuron results in rapid movement of Na and K across the axon’s membrane. INSIDE axon – 3 Na enter and attach to binding sites. ATP- changes the shape. Na+ leave axon and 2 K+ are picked up
Protein changes to original shape and release K+ inside axon.

Question 56

Membrane-assisted transport (bulk transport)

Answer 56

• Fluidity of the membrane allows materials to be taken in (endocytosis) and out (exocytosis) of the cell. Done by “vesicles” (Small sac of membrane, Formed by “pinching” off of the PM or membrane bound organelles (golgi or ER), move things around the cell)

Endocytosis:
- A cell engulfs material by folding the cell membrane around it, pinching off to form a vesicle. (requires energy from the cell and substances are moved against concentration gradient) i.e.: antibodies from mom’s milk, bacteria and viruses (immune system cell)
- Phagocytosis: cell eating, endocytosis involving solid particles
- pinocytosis: cell drinking, endocytosis involving liquid particles
- receptor-mediated endocytosis : cell engulfs specific molecules bound in clathrin-coated pits

Exocytosis:
- Vesicles fuse with cell membrane and empty their contents into extracellular environment
- Macromolecules and other large particles use this method to leave the cell

Question 57

Properties of the molecules that makeup membrane

Answer 57

Q: Explain how the properties of the molecules and macromolecules that comprise biological membranes are important to processes that transport materials in and out of cells.

A: Phospholipids provide a fluid bilayer that allows some small, non-polar molecules to diffuse through its hydrophobic interior. Ions and large molecules need the assistance of membrane proteins (channel proteins, carrier proteins, or pumps) to pass through the hydrophobic interior of the membrane. In general, non-polar amino acids coat the exterior portion of membrane proteins (the portion that interacts with the non-polar interior of the cell membrane). The interior of a membrane protein (the portion that faces the particle being transported) may be of a specific size and shape and may have polar or charged amino acids that interact with the particle being transported. Active transport pumps undergo shape changes in order to move substances across the membrane.

Question 58

Functions of proteins that are found in the membrane

Answer 58

The general functions of membrane proteins are Receptor sites for hormones (hormone binding sites), Immobilize enzymes, Cell adhesion – makes tight junctions between cells, Cell to cell communication, and Transport of materials: Passive transport and Active transport

• Peripheral: Found on the inner or outer surface of the membrane and can be attached to integral protein. Function in support, communication, and molecule transport.
• Integral: Transmembrane, with hydrophilic parts sticking out on either side of the membrane. Function in molecule transport, cell recognition and enzymatic activity.
• Channel: Form specific channels through the membrane and their structure will determine which particles can travel through. Can be open or closed in response to stimuli. Transmembrane
• Carrier: Bind to specific molecules, Transport them across the membrane and release them on other side, Change shape, Lower rates of diffusion compared to channel proteins.

Question 59

General summary of transport mechanisms

Answer 59

Diffusion: no energy needed, movement of susbatnces toward lower concentration, related factor is concentration gradient, examples of transported susbatnces are lipid-soluble molecules, water and gases

Facilitated difusion: no energy needed, movement toward lower concentration, channel proteins or carrier proteins and concentration gradients are related factors and examples of transported susbatcns are sugar and aa

Active transport: requires energy, movement towards higher concentration (against concentration gradient), related factors are carrier protein and energy, examples of transported susbatnces are ions and amino acids

Endocytosis: requires energy, movement towards interior of cell, related fatcor is vesicle formation, transported substances are macromolecules

Exocytosis: requiresz energy, movement towards exterior of cell, related factor is fusion of vesicle with cell membrane, and substances transported are macromolecules