Biological molecules I

Question 1

Marcomolecules:

Answer 1

composed of molecular subunits (monomers)

Question 2

Supramolecular Complexes:

Answer 2

Assembly of macromolecules

Question 3

Cells and organelles:

Answer 3

Comprised of supramolecular complexes

Question 4

Biomacromolecules:

Answer 4

Natural polymers (MW > 5000) are assembled from monomers with MW < 500, usually

Question 5

There are 4 main types of biomacromolecules,

Answer 5

each built using specific “building blocks”

Question 6

4 types of Biomacromolecules:

Answer 6

Aminoacids > Proteins
Fatty acids > Phopholipids
Carbohydrates > Polysaccharides
Nucleobases > Nucleis acids (DNA/RNA)

Question 7

Biomacromolecules interact with one another and self-assemble into cellular structures in very specific and highly regulated ways.

Answer 7

The macromolecules are then responsible for fundamental cellular functions but their interactions are often weak and reversible and reliant on their three-dimensional shape.

Question 8

Biomacromolecules: Important Information

Answer 8

Most of their constituents (natural building blocks) are chiral molecules which exist as single enantiomers

Interactions between bio(macro)molecules are stereospecific: they require specific configurations in the interacting molecules

The environment in which bio(macro)molecules interact is mainly constituted by water: water is the solvent of all biochemical processes, and it often acts also as a reactant in biochemical reactions

Question 9

Carbohydrates

Answer 9

Carbon (C), Hydrogen (H), Oxygen (O) atoms
Monosaccharide Molecular Formula: Cm(H2O)n
Empirical Formula (most simple sugars): C(H2O)

An exception: Deoxyribose (sugar in DNA)
Has a different molecular formula – Missing one OH group

Question 10

Fischer Projections

Answer 10

Useful for showing molecules with multiple stereogenic centres (start at most oxidised end)

Question 11

Carbohydrate

Answer 11

Monosaccharides (simple sugars): carbohydrates cannot be hydrolysed to more simple compounds

Question 12

Disaccharides

Answer 12

sugar that can be hydrolysed to two monosaccharides

Question 13

Polysaccharides

Answer 13

carbohydrates that can be hydrolysed to many monosaccharides

Question 14

Monosaccharides: Classification

Answer 14

1) the number of carbon atoms in the carbon chain
triose (3C), tetrose (4C), pentose (5C)

2) Whether the sugar contains a ketone or an aldehyde group (aldoses or ketoses)

3) The stereochemical configuration of the asymmetric carbon atom farthest from the carbonyl group

Question 15

Epimers:

Answer 15

diastereomers that differ only in the stereochemistry at a single carbon

Question 16

Carbohydrate Chemistry:

Answer 16

the FGs of aldehyde to hemiacetal is important in carbohydrate chemistry:

reactions catalysed by a trace of strong acid

Hemiacetals and hemiketals - generally unstable

Nucleophilic addition to C=O

Question 17

Carbohydrate Chemistry

Answer 17

Step 1: Protonation of the carbonyl group

Step 2: The OH group acts as a nucleophile

Step 3: Deprotonation gives a cyclic hemiacetal

Note: 5- and 6-membered cyclic hemiacetals are stable

Question 18

Aldohexoses (glucose):

Answer 18

the equilibrium favours six-membrane rings with a hemiacetal linkage between the aldehyde carbon and the hydroxy group on C5

Question 19

Aldopentoses and ketohexoses (fructose) form…

Answer 19

five-membered rings

Question 20

OH group at C1 hemiacetal form can be up and down

Answer 20

Diastereomeric products = anomers
C1 = anomeric carbon

Question 21

Reactions of Carbohydrates

Answer 21

1. Reduction
2. Oxidation; monosaccharides are reducing sugar, act as a reducing agent because have a free aldehyde group or a free ketone group
3. Glycoside formation (conversion to an acetal)
4. Alkylation to give ethers and acylation to give esters

Question 22

Disaccharides

Answer 22

Maltose: An alffa 1-4, Glucosidic Linkage

Cellobiose: A beta 1-4C, Glucosidic Linkage

Lactose: A beta 1-4C Galactsoidic linkage

Gentiobiose: An beta 1-6C Glucodidic Linkage

Question 23

Sucrose:

Answer 23

alpha-D-glucopyranosyl-B-D-fructofuranoside (or B-D-frutofuranosyl-a-D-glucopyranoside)

Question 24

Polysaccharides (glycans):

Answer 24

crbohydrates contain many monosaccharide units joined

Question 25

What kind of bonds are polysaccharides joined by?

Answer 25

glycosidic bonds

Question 26

Oligosaccharides;

Answer 26

smaller polysaccharides, containing 3-10 monosaccharide units

Question 27

all anomeric carbon atoms of polysaccharides (except for units at end of chains) are invokved in what kind of links/bonds?

Answer 27

acetal glycosidic links

Cellulose, glycogen, amylose, amylopectin

Question 28

Cellulose

Answer 28

Polysaccharide of many D-glucose, monomers

Important in human nutrition
> low fibre intake is associated with constipation and some gut disease such as bowel cancer
> high fibre intake can help reduce cholesterol, reduce risk of diabetes and protect against overweight

Question 29

What are the 3 main functions of Polysaccharide?

Answer 29

Intracellular energy storage e.g. starch, glycogen, polymers of glucose

Confer a rigid structure to cell walls e.g. cellulose

Extra/intra cellular signalling (poly or oligosaccharides attached to membranes, proteins or lipids)

Question 30

Where we “See” Carbohydrates

Answer 30

sweeteners in drinks, aspartame

Question 31

“see” lactulose; A beta 1-4 Glucosidic Linkage

Answer 31

an osmotic laxative

not naturally occurring sugar, manufactured synthetically

causes water to accumulate in colon - softens stool

e.g. of drug with unusual mode of action - no ‘target’

Question 32

“cardiac glycosides”

Answer 32

Digitalis lantana - source of the CV drug digoxin

Foxgloves

Digoxin - used for HF and other CV conditions

Question 33

Glucosamine

Answer 33

simple amino sugar

Supplement for joint health

No evidence to support any medicinal benefit

Gentamicin - carbohydrate drug (antibiotic)

phase 2 metabolism, drugs are conjugated with glucuronic acid in liver

Question 34

Important mediators of cellular communication (cell-cell antibody)

Answer 34

e.g. AB0 Blood groups in red blood cells (RBC)

Question 35

DNA and RNA

Answer 35

repositories of genetic information

DNA - carrier of genetic information
RNA - use of information to make all the biomolecules and components of cells

Question 36

building blocks of DNA

Answer 36

Nucleoside = base + sugar
Nucleotide = base + sugar + phosphate

Question 37

What kind of nucleotides in DNA made out of?

Answer 37

deoxyribonucleotides

Question 38

What kind of nucleotides is RNA made out of?

Answer 38

ribonucleotides

Question 39

DNA and RNA: Primary Structure

Answer 39

in polynucloetide chain, phosphodiester bonds link two consectutive nucleotide units:

rotation of phospho (deoxy)ribose backbone is

restricted: sugar can adopt four puckered conformations, with 4 atoms nearly in single plane, and 5th atom (C2 or C3) in same endo/ opposite side of plane of C5

Question 40

DNA and RNA: Secondary Structure

Answer 40

2 chains of DNA or RNA in opposite directions, form double-stranded structures (backbone outside bases inside), held together by base-pairing, follows a specific H-bonding pattern