IB biology 2: molecular biology

Credit to Bioninja for much of this information.

Valency

The property of an element that dictates how many bonds it can form

Why are water molecules polar?

They have a 'bent' shape and therefore positive and negative poles

Catabolism

Breakdown in living organisms of more complex substances into simpler ones together with release of energy

Anabolism

The synthesis in living organisms of more complex substances from simpler ones together with the storage of energy

Metabolism

the sum of organic processes/ reactions that are necessary for life

What is the charge on a hydrogen atom within water?

Slightly positive/ delta positive

What is the charge on an oxygen atom within water?

Slightly negative/ delta negative

Cohesion

The property of water that means individual water molecules 'stick' to each other

Adhesion

The property of water that means water molecules 'stick' to other surfaces such as the side of a glass

Monosaccharide

A single-unit sugar (includes glucose, fructose and galactose)

All monosaccharides are reducing agents

Disaccharide

A two-unit sugar

Includes sucrose, lactose and maltose

Polysaccharide

A many-unit sugar

Includes starch, cellulose and glycogen

Reducing agent

A substance that causes another substance to be reduced by removing oxygen OR donating hydrogen and/or electrons

What does the acronym SHIPS represent in terms of the roles of fatty substances (ie. lipids)?

Storage of energy for long-term use (e.g. triglycerides)
Hormonal roles (e.g. steroids such as oestrogen and testosterone)
Insulation – both thermal (triglycerides) and electrical (sphingolipids)
Protection of internal organs (e.g. triglycerides and waxes)
Structural components of cells (e.g. phospholipids and cholesterol)

What do "saturated" and "unsaturated" mean in the context of fatty acids?

Saturated- no double bond

Unsaturated- contains a double covalent bond between two of the carbon molecules (can be monounsaturated or polyunsaturated)

Are saturated or unsaturated fats more likely to be solid at room temperature?

Saturated

What is a trans isomer of a fatty acid?

When the hydrogens either side of the C=C double bond are on opposite sides of the molecule

What is a cis isomer of a fatty acid?

When both the hydrogens either side of the C=C double bond are on the same side of the molecule

Which two functional groups do fatty acid chains contain?

Methyl/ CH3 group and Carboxyl/Carboxylic acid/ COOH group(=acid 'head')

What is an ester bond?

-An ester bond forms when a hydroxyl (-OH) group from the glycerol bonds with the carboxyl (-COOH) group of the fatty acid.
-It is the joining of two carbons via one oxygen (-O-)
-A molecule of water is produced alongside every ester bond

Describe the structure of cellulose

-A polysaccharide

-A linear molecule made of beta-glucose subunits bound in a 1-4 arrangement

What are the two forms of starch?

-Amylose and amylopectin

-Amylose is harder to digest and less soluble, however, as it takes up less space, is the preferred storage form in plants

Describe the structure of amylose

-Amylose is a linear (helical) polysaccharide molecule

-It is made up of α-glucose subunits (bound in a 1-4 arrangement)

Describe the structure of amylopectin

-It is made up of α-glucose subunits (bound in a 1-4 arrangement)

-Contains additional branching (1-6 linkages)

Structure of glycogen

-Energy storage polysaccharide formed in the liver in animals
-Composed of α-glucose subunits linked together by both 1-4 linkages and 1-6 linkages (branching)

The function of starch

-Energy storage in plants
-Preferred store as it is compact/takes up lace space

Function of glycogen

-Energy storage in animals

Function of cellulose

-Gives plant cell walls their structure

What is meant by "amphoteric" in reference to amino acids?

-They are both acidic and basic simultaneously

Which four elements do amino acids always contain?

C, H, O and N

Which two groups do amino acids contain?

COOH (/carboxyl) and NH2(/amino)

In amino acids, which group can gain an H+ ion in acidic solution?

NH2 can gain an additional H+ (nb. that Nitrogen can sometimes have a valency of 4)

In amino acids, which group can lose an H+ ion in alkaline solution?

COOH can lose an H+ (H+ is lost from the OH)

What is the name of the covalent bond between amino acids?

Peptide bond

What does a condensation reaction between two amino acids form?

A dipeptide and water

What are the two common secondary structures that amino acids can form?

Alpha helices and beta- pleated sheets (when no secondary structure exists, the polypeptide chain will form a random coil)

What type of bond is responsible for the secondary structure of a polypeptide chain?

Hydrogen bonds

What are prosthetic groups?

The non-amino acid component that is part of the quaternary structure of conjugated proteins

What types of bonds are responsible for the primary structure of amino acids?

The tertiary structure of a polypeptide chain will be determined by the interactions between the variable side chains
These interactions may include hydrogen bonds, disulphide bridges, ionic interactions, polar associations, etc.

Give an example of a protein with a quaternary structure

Haemoglobin is composed of four polypeptide chains (two alpha chains and two beta chains)
It is also composed of iron-containing haeme groups (prosthetic groups responsible for binding oxygen)

Amino acids are zwitterions. What are zwitterions?

Neutral molecules possessing both negatively (COO–) and positively (NH3+) charged regions

What are the differences between fibrous and globular proteins?

Fibrous: long/narrow shape, usually structural proteins, repetitive amino acid sequence (eg. keratin)

Globular: round shape, usually functional proteins, irregular amino acid sequence (eg. amino acids)

What is meant by the proteome?

The totality of proteins expressed within a cell/organism/etc at a given time

What are the main roles of proteins in an organism (SHITS ME)

Structure – e.g. collagen, spider silk
Hormones – e.g. insulin, glucagon
Immunity – e.g. immunoglobulins
Transport – e.g. haemoglobin
Sensation – e.g. rhodopsin
Movement – e.g. actin, myosin
Enzymes – e.g. Rubisco, catalase

Give three examples of enzymes used in industry

Proteases and lipases (used in biological detergents), pectinase (fruit juice production) and lactase (lactose-free milk for lactose intolerant humans and cats)

What is the allosteric site?

Any site on an enzyme that isn't the active site

What characterises a competitive enzyme inhibitor?

-Enzyme inhibitors are substances that interfere with the normal functioning of an enzyme
-Competitive inhibitors must bind TO THE ACTIVE SITE of an enzyme on a TEMPORARY basis

Give an example of a practical use of enzyme inhibition.

-Competitive inhibition of alcohol dehydrogenase (the enzyme that converts ethylene into oxalic acid) by ethanol
-Used to treat alcoholics who have consumed antifreeze

How is urea synthesised artificially?

Exothermic reaction of ammonia and carbon dioxide

What is the structure of urea?

CO(NH2)2

Structure of urea

CO(NH2)2

What are amylose and amylopectin?

-They are both forms of starch
-Amylose is a linear (helical) molecule while amylopectin is branched (contains additional 1-6 linkages)
-Amylose is harder to digest and less soluble, however, as it takes up less space, is the preferred storage form in plants

What is the supernatant?

The liquid component lying above a solid residue when a substance has been centrifuged etc.

What are the three components of a DNA molecule and how are they represented?

* 5-carbon pentose sugar (pentagon)
* Phosphate group (circle)
* Nitrogenous base (rectangle)

What are the two structural differences between DNA and RNA?

\-The pentose sugar in DNA is deoxyribose, in RNA it is ribose

\-The nitrogenous bases in DNA can be A,C,G,T; in RNA they are A,C,G,U

What name is given to the individual DNA units?

\-The monomer units are called nucleotides

How many hydrogen bonds form between C and G in DNA?

3

How many hydrogen bonds form between A and T in DNA?

2

Describe the bonds between the DNA monomers

\-Called phosphodiester bonds

\-Form between carbon 3 of one nucleotide and carbon 5 of the next

What are the full names of A, C, G and T in DNA?

Adenine, Guanine, Thymine and Cytosine

Which two DNA bases are purines and which two are pyrimidines?

-A and G are purines, C and T are pyrimidines (nb. Uracil is also a pyrimidine in RNA)

-Only a purine can bond with a pyrimidine!

What is the difference in structure between a purine and a pyrimidine?

Pyrimidines are made up of a single ring of six members while purines are made up of a six-member ring and a five-member ring

What are the three main types of RNA?

Messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA)

What is the role of messenger RNA?

A transcript copy of the gene which can encode a specific polypeptide?

What is the role of transfer RNA?

Carries the polypeptide subunits (amino acids) to the organelle responsible for synthesis (ribosome)

What is the role of ribosomal RNA?

A primary component of the ribosome responsible for its catalytic activity

What is the name of the enzyme responsible for ‘unzipping‘ DNA?

Helicase

What is the name of the enzyme responsible for DNA replication?

DNA polymerase

How does DNA replicate (conservative, semi-conservative or dispersive)?

Semi-conservative (ie. each new DNA molecule contains one strand from the parent molecule and one is totally new)

Who experimented in 1958 to find out how DNA replicates?

Meselsohn and Stahl

What are the stages of aerobic respiration in order?

Glycolysis, the link reaction, the krebs cycle and the electron transport chain

How many molecules of ATP are produced per glucose in anaerobic respiration?

2

How many molecules of ATP are produced per glucose in aerobic respiration?

30-40

ATP

A nucleotide triphosphate that is a common source of energy in cells

Cristae

Invaginations of the inner mitochondrial membrane

Glycolysis

A metabolic pathway that breaks down glucose to pyruvate

Krebs cycle

Link reaction

A decarboxylic reaction that occurs in the mitochondria between glycolysis and the Krebs cycle

Electron transport chain

A group of proteins that accept and donate electrons in series

Phosphorylation

The addition of a phosphate group to a molecule

Reduced NAD

The energy rich form of the hydrogen carrier

Genomics: definition

The study of the whole sets of genetic information (genomes) in the form of base sequences

What is TAQ polymerase?

Taq polymerase is the heat-stable (thermostable) DNA polymerase extracted from the thermophilic bacteria Thermus aquaticus.

What are the three stages involved in PCR?

1. *Denaturation* – DNA sample is heated (\~90ºC) to separate the two strands
2. *Annealing* – Sample is cooled (\~55ºC) to allow primers to anneal (primers designate sequence to be copied)
3. *Elongation* – Sample is heated to the optimal temperature for a heat-tolerant polymerase (Taq) to function (\~75ºC)

What are the uses of PCR?

Used to amplify large quantities of a specific sequence of DNA from an initial minute sample

Each reaction doubles the amount of DNA – a standard PCR sequence of 30 cycles creates over 1 billion copies (230)

COVID testing and other diseases like sickle cell anemia

What is meant by a ‘codon‘?

A triplet of bases. Each one codes for one amino acid.

What is the difference between aerobic and anaerobic respiration?

* Anaerobic respiration involves the partial breakdown of glucose in the cytosol for a small yield of ATP
* Aerobic respiration utilises oxygen to completely break down glucose in the mitochondria for a larger ATP yield

What are the four stages involved in aerobic respiration?

Glycolysis, link reaction, Krebs cycle and the electron transport chain

What are the stages of glycolysis?

Phosphorylation (addition of a phosphate group from ATP), hydrolysis (addition of water) and oxidation (glucose is oxidised)

Outline what happens in glycolysis

What are the products of glycolysis per glucose molecule?

2 pyruvate, 2 NAD and 2 ATP (net gain of 2x ATP)

Fill the blanks: in the link reaction, … passes from the … into the … Here it is completely oxidised forming … and ….

Pyruvate, cytoplasm, mitochondria, water and carbon dioxide

What is the overall equation for the link reaction?

pyruvate+NAD+coA goes to acetyl coA+CO2+reduced NAD

What are the products per glucose molecule in the link reaction?

2 acetyl coA(into Krebs cycle), 2 reduced NAD(into electron transport chain), 2 carbon dioxide (waste)

What does the acronym DODO POO represent in relation to the Kreb cycle?

D- decarboxylation

O- oxidation

P- phosphorylation

In anaerobic respiration in animals, what is pyruvate converted to?

Lactic acid

In anaerobic respiration in plants and yeast, what is pyruvate converted to?

Carbon dioxide and ethanol

What are two applications of the fermentation process of yeast for humans?

• Bread – Carbon dioxide causes dough to rise (leavening), the ethanol evaporates during baking

• Alcohol – Ethanol is the intoxicating agent in alcoholic beverages