Biology SL - Topic 2, Molecular Biology (2.1-2.5)

what does molecular bio explain

living processes in terms of the chemical substances involved

why are carbon atoms the unit of life?

carbon atoms can form covalent bonds with 4 other atoms, practical, allowing a diversity of stable compounds to exist

what exist as carbon compounds?

carbohydrates, lipids, proteins, nucleic acids (life)

what is metabolism?

the web of all the enzyme-catalyzed reactions in a cell or organism

what is anabolism?

the synthesis of complex molecules from simple molecules including the formation of macromolecules from monomers by condensation reactions (CONDENSATION = - H2O)

what is catabolism?

the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers (HYDROLYSIS = + H2O)

what is an example of a compound that is produced by living organisms and can be artificially synthesized?

urea

how did the artificial synthesis of urea falsify vitalism?

vitalism: the theory that the origin of life is dependent on a force or principle distinct/different to chemical or physical forces.

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The synthesis of urea proved that organic matter from living organisms could be produced simply from the basic building blocks of non-living things (chemical compounds)

molecular diagram of glucose

molecular diagram of ribose

molecular diagram of a saturated fatty acid

molecular diagram of a generalized amino acid

how to identify sugars in a molecular drawing

C H O, ring shape (lots of OH, C, H)

how to identify lipids in a molecular drawing

linear shape, C H O, carboxyl group, (no N or amine group)

how to identify amino acids from molecular drawings

star shape, amine group, R variable group, carboxyl group, C H O N

describe water molecules

they are polar and hydrogen bonds form between them

what are the properties of water?

cohesive, adhesive, thermal, and solvent

how can the properties of water be explained

due to water’s hydrogen bonds and its polarity (can repel or attract other molecules because of charge. between the 2 atoms, one of them is attracting electrons more than the other)

why are water molecules polar?

2 hydrogen bonds are bonded covalently with an oxygen atom. the o atom is larger (contains more (+) protons) the protons attract more electrons than those in h atoms. The o “end” of the molecule is negatively charged, while the h “end” is SLIGHTLY positively charged. = water is polar

what does hydrophobic mean

REPELS water (doesn’t like it) - insoluble (NON-POLAR)

what does hydrophillic mean

ATTRACTS water (likes it) - soluble (POLAR)

how does water’s thermal property compare to that of methane?

water is polar and can form hydrogen bonds between its atoms. methane is non-polar and can only form weak dispersion forces between its atoms.

* Water has a significantly higher melting and boiling point
* Water has a higher specific heat capacity (energy required to raise the temperature of 1 g of substance by 1ºC)
* Water has a higher heat of vaporization (energy absorbed per gram as it changes from a liquid to a gas / vapor)
* Water as a higher heat of fusion (energy required to be lost to change 1 g of liquid to 1 g of solid at 0ºC)

how is water used as a coolant? (automobile radiators)

due to its high specific heat, water can absorb heat from other bodies very easily.

* it has a HIGH SPECIFIC HEAT TOLERANCE/CAPACITY
* it’s cheap
* it can be mixed with anticorrosion inhibitors and antifreeze = perfect !

substances insoluble in water are … and therefore…

1. hydrophobic 2. non-polar

substances soluble in water are… and therefore…

1. Hydrophilic 2. polar

carbohydrates

CHO, make up cellulose, important for storage of energy (cells) important in all biological functions.

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monosaccharide subunits (eg glucose) can make up disaccharide/polysaccharide links by condensation reactions (removing h2o so the O can bond the 2 molecules can bond)

unsaturated fatty acids

(can fit more hydrogen) - have an unlinear molecular shape. they can be trans(bad. hydrogens on different sides) or cis (good. hydrogens on the same side)

how are triglycerides formed?

condensation reactions. (3 fatty acids and 1 glycerol)

structure and function of cellulose and starch in plants + glycogen in humans

starch is the main storage carbohydrate source in plants whereas cellulose is the main structural component of the cell wall of plants and glycogen is the main storage carbohydrate energy source of fungi and animals.

heatlth risks of trans and saturated fats

* Saturated fats increase LDL levels within the body, raising blood cholesterol levels
* *Trans* fats increase LDL levels **and** decrease HDL levels within the body, significantly raising blood cholesterol levels
* Unsaturated (*cis*) fats increase HDL levels within the body, lowering blood cholesterol levels

lipids are more suitable for long-term energy storage than carbohydrates, true or false?

true

BMI

can be calculated or measured using a nonogram

2 main health claims:

* Diets rich in saturated fats and *trans* fats increase the risk of CHD
* Diets rich in monounsaturated and polyunsaturated (*cis*) fats decrease the risk of CHD

how have they been tested?

* Epidemiological studies comparing different population groups
* Intervention studies that monitor cohorts following dietary modifications
* Experimental designs utilising animal models or data based on autopsies

evidence supporting health claims

* A positive correlation has been found between the intake of saturated fats and the incidence of CHD in human populations
* Intervention studies have shown that lowering dietary intakes of saturated fats reduces factors associated with the development of CHD (e.g. blood cholesterol levels, blood pressure, etc.)
* n patients who died from CHD, fatty deposits in diseased arteries were found to contain high concentrations of *trans* fats

evidence against health claims

* *Counter:* Certain populations do not fit this trend (e.g. the Maasai tribe in Africa have a fat-rich diet but very low rates of CHD)
* *Counter:* Validity of intervention studies is dependent on size and composition of cohort, as well as the duration of the study
* *Counter:* Genetic factors may play a role (e.g. blood cholesterol levels only show a weak association to dietary levels)

Proportion of saturated and *trans* fats in Western diets has decreased over the last 50 years, but incidence of CHD has risen

* *Counter:* Increased carbohydrate intake may cause detrimental health effects associated with CHD (e.g. diabetes, obesity)
* *Counter:* Incidence of CHD dependent on a myriad of factors besides dietary intake (e.g. exercise, access to health care, etc.) 

use of molecular visualization software to compare cellulose starch and glycogen

starch (amylopectin) - plants

* is branched every 30 glucose, helical shape
* polymer of beta glucose
* branches allow quick unloading of glucose

glycogen - animals

* branched every 8-12 glucoe,
* polymer of alpha glucose

mammals use it to store glucose in liver

cellulose - plant cells, cell walls

* straight unbranched (linear)
* polymer of beta glucose
* forms cross-links with hydrogen bonds
* very strong (makes cell wall)

generalized amino acid structure

the formation of polypeptides (including peptide bond and condensation reaction)

amino acids are held linked by.. to form…

1. condensation reactions 2. polypeptides

what is the amount of different amino acids in polypeptides synthesized on ribosomes?

20

why are polypeptides diverse?

amino acids chains can be linked together in any sequence; therefore there is a huge variety in possibility

how is the amino acid sequence of a specific polypeptide decided?

genetic code (on the genes)

what can a protein consist of?

a single polypeptide or more than 1 polypeptide linked together

what does the amino acid sequence determine for a protein?

its three-dimensional conformation (configuration) eg primary, secondary, tertiary, quaternary

living organisms synthesize…

many different proteins with a wide range of functions

everyone has an individual proteome, true or false?

true

rubisco

globular, used in photosynthesis by catalyzing oxygen

spider silk

fibrous, used for making webs, ligament, surgical sutures because it holds things together with strength

Insulin

globular, used to regulate blood sugar levels in the pancreas

immunoglobin

globular, defense against infectious disease, antibodies attack antigens on pathogens

rhodoposin

globular, used in light-sensitive pigments in rod cells of the eye

collagen

fibrous, structural helps prevents cracks in teeth and bones, builds up the framework of cells/tissues

fibrous vs globular proteins

fibrous = IS SOMETHING

globular = DOES SOMETHING

What causes the denaturation of proteins

deviation from the optimum pH and temp for a certain protein (which is dependent on where it’s meant to function)

what do enzymes control?

the metabolism

enzyme definition

a globular protein that acts as a catalyst for reactions (increases the rate of reaction) by lowering the activation energy threshold

metabolism definition

a web of all the enzyme-catalyzed reactions in a cell or organism

enzyme structure

active site to which specific substrates bind

what does enzyme catalysis involve?

molecular motion and the collision of substrates with the active site.

what 3 things affect the rate of enzyme activity?

temperature, pH, and substrate concentration

if temp/substrate conc/pH diverge from the optimum, what happens?

the enzyme is denatured

what are immobilized enzymes?

enzymes that are fixed to a static surface so they don’t move, in order to increase the efficiency of the reaction (used in industry)

advantages of immobilized enzymes?

* continuous flow of products formed
* enzymes can constantly be reused (cheaper)
* to not get the enzyme in the product (could have adverse negative effects)

examples of enzymes used in industry

* detergents (lipase, fat stain removal)
* textiles (amylase, digest starch. cellulase, metabolize cellulose)
* food processing (amylase, making more glucose from starch, xtra sweetness)
* pulp and paper (cellulase, breaks down cellulose, catalase, bleaching)

how is lactose free milk produced?

by reacting it with lactase enzyme.

advantages of lactose free milk?

* for lactose intolerant people
* increase sweetness without the need for added sweeteners
* reducing the crystallization of ice creams
* reduce production time for cheese + yogurts