Organic Chemistry Flashcards
What type of bond in Nucleic acids in nucleotides
Phosphodiester
Alcohol
Hydroxyl
Cell Wall
- gives, cell shape / strength / support;
- prevents bursting (when water enters cell by osmosis);
- fully permeable;
The bond that joins the two molecules to form a disaccharide
Glycosidic
Carboxyl
Esters
Esters are a combination of a carboxylic acid and an alcohol where the O-H from the carboxylic acid and the H from the alcohol combine to form water
Termination of Free Radical
Amino
Amines
Chloroplast
Cell Wall
Vacuole
DNA
- deoxyribose (sugar)
- phosphate (group);
- nitrogenous / purine or pyrimidine) base
- Adenine
- Guanine
- Cytosine
- Thymine
Hex-
6C
What type of bonds in Monosaccharides units in sugar
Glycosidic
Active Site
The area on enzyme to which a substrate binds
A - Glycoprotein - Interegal Protein: carrier molecule
B - Phospholipid Bilayer - waterproofing
C - Carbohydrate - receptor
D - Cholesterol: Provide structure, regulate fluidity
Oct-
8C
Initiation of Free Radical
plasma (cell surface) membrane
- controls exchange between cell and environment / selectively permeable; R water
- receptors for, cell recognition / attachment;
- fluid to allow, endocytosis / exocytosis;
Nucleic Acid
Sugar/base/phosphate
Metaphase
The chromosomes align on the equator of the spindle
CoFactor
The general name given to a non-protein helper which helps an enzyme to function
Induced fit hypothesis
The model of enzyme-substrate binding whereby an enzyme adjusts to fit the substrate
Golgi Apparatus
processes, molecules / proteins; AW
use in secretion
lysosome formation
Competitive Inhibitor
- substrate and inhibitor are a similar shape
- able to, bind / fit into / block, active site;
- (shape) complementary to active site
Tertiary Amine
3H have been replaced by R Groups
Mitochondria
- formation ATP / suitable energy ref.;
- aerobic respiration;
A - Golgi apparatus/body
B - Centriole
C - Nucleolus
D - Nuclear Membrane or Nucleus
E - Mitochondrion
F - Rough Endoplasmic Reticulum
Cholesterol
lipids / cholesterol, hydrophobic / non-polar
They share an O and lose 2H and O
Its a condensation reaction resulting in 3 H2O
Ester bond
U - Amino
V - Carboxylic Acid
Tissue
collection / group, of cells (of one or more types); [1]
(cells), working together OR with, common / same, function; [1]
Vacuole
- reservoir of, salts / sugars / waste / pigment / other e.g.;
- ref. to, turgor / support / controlling Ψ (Water Potential)
Halo
Halogen-hydrocarbons
Geometric Isomer
Nucleus / DNA
- controls, activities of cell / transcription / named activity / cell division;
- contains genetic information that can be transmitted to next generation;
Structural Isomer
Formation of Primary Structure of Protein
Amino acid monomers join to form a dipeptide [1]
Process involves removal of water and is a condensation reaction [1]
A carboxyl group from amino acid (OH) is removed together with an H atom from another acid [1]
But -
4C
Protein Production in Rough ER
- Proteins are pinched off vesicles in the Rough Endoplasmic Reticulum/RER
- Proteins are transported in vesicles to the Golgi Apparatus
- Proteins are modified in the Golgi Apparatus/Have carbohydrates added to the proteins
- Modified proteins are placed into vesicles
- Modified proteins are released from the plasma membrane/Exocytosis
Primary Amine
Replace 1 H with an R group
RNA
- ribose (sugar);
- uracil instead thymine
- single stranded
- 3 forms (RNA, mRNA, tRNA)
Carboxyl
Carboxylic Acids
What type of bond in Fatty acids to glycerol in triacylglycerols
Ester
Prosthetic Group
The name given to an ion which is permanently attached to an enzyme so that it may carry out its function
• cytoplasm
• site of chemical reaction(s)
J - Channel protein
K - Receptor, Recognition site, helps to adhere one to the other
M - Cholresterol - Adds structure
L - Phospholipid bilayer - waterproof barrier
Double Bond
Various Unsaturated
Nucleolus
Produces, ribosomes / rRNA
A - Smooth Endoplasmic Reticulum
B - Nuclear envelope
C - Mitochondia
D - Nucleolus
E - Lysosome
F - Rough Endoplasmic Reticulum
The Krebs Cycle
- Acetyl co-enzyme A combines with oxaloacetate to from citrate
- Citrate is decarboxylated and dehyrogenated to yield carbon dioxide (waste gas) and hydrogen (combines with carriers NAD and FAD)
- 5 carbon molecules is created which is decarboxylated and dehydrogenated c
- Reduced FAD and 4 carbon molecule is created
- This is converted to another 4 carbon molecule and ATP is released
- This 4 carbon molecule is dehydrogenated
- Another 4 carbon molecule is created and redFAD
- Dehyrogenated occurs, reduced NAD is created
- Oxaloacetate is regenerated
Alkoxy
Ethers
Thiol
Thiols
The Link Reaction
- Pyruvate has carbon dioxide removed/decarboxylated
- It also has hydrogen removed- dehydrogenated
- It combines with Co-Enzyme A to give acetyl co-enzyme A
Proteins
Amino Acids
A - beta - Glucose
B - 1,4 glycosidic beta link
Reaction
- condensation/removal of water
Function of cellulose
- Cell wall of plants
Rough ER / ribosomes
• protein synthesis
Cellulose
ß-glucose
Chloroplast
- photosynthesis
- chlorophyll / pigment, absorbs light
Temperature and Enzymes
High
- (enzyme) increases in kinetic energy or ‘too much kinetic energy’
- enzyme vibrates too much;
- breaks bonds;
- changes, tertiary/3-D, structure/shape, of enzyme;
- active site changes, shape
- substrate will not fit/no enzyme-substrate complex formed;
- enzyme denatured;
- will, decrease rate/stop reaction;
Low
- not enough kinetic energy
- inactive
Hept-
7C
Propogation of Free Radicals
Fats
Fatty acids, gycerol
Prop -
3 C
Glycolysis (Formation of Pyruvate)
- Glucose is phosphorylated/has a phosphate added
- Using a molecules of ATP
- Creates hexose phosphate
- Second ATP molecule is attached to create hexose bisphosphate
- Hexose bisphosphate breaks down to produce two molecules of triose phosphate
- Triose phosphates are phosphorylated
- Using free Pi ions
- Hydrogen is removed from each triose phosphate/triose phosphate is dehydrogenated
- The H+ ions are transferred to carrier molecules NAD and are used later
- This yields 2 molecules of pyruvate
Anaphase
The chromatids separate and move to the poles
What type of bond in Amino acids in proteins
Peptide Bond
Trans
Formation of the Tertiary Structure of a Protein
Proteins fold to form coiled coils [1]
The tertiary structure is the way the regions of secondary structure fold to form the 3-D shape i.e. a-Helices and b-Pleated sheets [1]
4 possible create the tertiary structure; Disulphide bridges, Ionic Bonds, Hydrogen bonds, Hydrophobic Interactions [1]
Smooth ER
Makes / transports, lipids / steroids / hormones; A named plant e.g.
Non-
9C
Glycogen
a-glucose
Dec-
10C
Lysosome
- hydrolytic / digestive, enzymes
- breakdown, organelles / cell / ingested material
Amide
Amides
Carbonyl
Aldehydes
Boiling Points of Alkanes
0 at 4C
Goes up by approx 30-36 degrees per Carbon
The boiling point increases with increase in molecular formula of carbon atoms/chain length
Because more intermolecular forces/electrons/surface area/ Weak intermolecular forces (van der waals)
Formation of Quaternary Structure of a Protein
The quaternary structure is the association of more than one polypeptide chain [1] •
Haemoglobin is made of 4 polypeptide chains stabilised by inter- & intramolecular bonds [1]
Network of non-covalent interactions [1]
Eth -
2 Carbons
Meth -
1 Carbon
Non-Competitive Inhibitor
- reduces reaction rate;
- fits into, allosteric site / site other than active site;
- alters, shape / charge, of active site;
- so substrate cannot, fit to active site / bind to active site / form ESC;
- increasing substrate concentration has no effect (on the rate);
DNA Replication
- The double helix untwists
- Is then unzipped by the breaking of the H bonds via DNA helicase
- Free nucleotides are attracted to their complementary bases
- C to G (3 H Bonds) and A to T (2 H bonds)
- Hydrogen bonds reform
- Sugar phosphate back bone forms using covalent/phosphodiester bonds using DNA Polymerase
Molecular Structure of Glycogen
- polymer/polysaccharide/described;
- (made of) α-glucose; joined by 1,4 links;
- (chain is) branched;
- 1,6 glycosidic links where branches attach; compact
Oxidative Phosphorylation and Chemiosis
(The Electron Transport Chain)
- Hydrogens are split from FAD (at complex II) and NAD (at complex I)
- Hydrogen is broken into H+ and an electron.
- The electron is transferred along the electron transport chain
- H+ ions are pumped across Complexes I, III and IV into the intermembranal space
- H+ ions diffuse through ATP synthase from the intermembranal space into the mitochondrial matrix
- ATP is created
Telophase
The nuclear membrane reforms and cytokinesis follows.
Carbonyl
Ketones
Formation of Secondary Structure of a Protein
a -Helices – Forms H bond between the C=O group of one amino acid and the N-H group of an another amino acid [1]
ß-Sheet – From interactions between adjacent chains, held in close association by H bonds between C=O and N-H groups on the different strands [1]
Essential Fatty Acids (2)
Fatty acids that cannot be synthesised by the body [1]
They must be supplied/taken in by the diet [1]
Omega-3 anti-inflammatory
Omega-6 pro-inflammatory
Pent-
5C
Secondary Amine
Replace 2 H with R group
Rough ER
• transport of proteins
Prophase
The chromosomes become stainable and the spindle starts to form
Cis
A. phospholipid layer/bilayer
B Cholesterol
C Glycolipid
D Carbohydrate
Outline how haemoglobin acts as a pH buffer in the presence of carbon dioxide.
- Carbon dioxide combines with water to form carbonic acid
- H2O + CO2 –> H2CO3
- Carbonic acid splits into hydrogen ions (H+ ) and hydrogen carbonate ions (HCO3- )
- H+ and HCO3 –
- The reaction is catalysed by carbonic anhydrase
- The hydrogen ions produced combine with haemoglobin to from haemoglobinic acid
- This causes it to release its oxygen which diffuses into respiratory tissue
- Hb is acting as a buffer, helping to keep the pH of blood around 7.4
