Biochemistry Flashcards
What are examples of lipids?
Triglycerides, phospholipids, steroids
What is an example of a monosaccharide?
Glucose
Which carbons react with each other in monosaccharides and what do they form?
Carbon 1 and carbon 5 to form a cyclic compound
What type of reaction is combining carbons of the same monosaccharide to form a cyclic compound?
Intermolecular reaction to change the structure of a molecule
What type of bonds can disaccharides be held together with?
Alpha or beta linkages
What is the importance of different types of bonds in disaccharides?
Important in our ability to break bonds apart during metabolism
In disaccharides, which carbons are the alpha or beta linkages between?
1 and 4
What two things do reactions involve a change in?
Entropy and enthalpy
What is the equation for a free energy change in a reaction?
delta G= delta H - T(deltaS)
What are exergonic reactions?
Total free energy of products is less than reactants- delta G is negative and these can occur spontaneously
What are endergonic reactions?
Total free energy of products is more than reactants- delta G is positive and these need energy to occur
What are delta G values of near 0 characteristic of?
Readily reversible reactions
What are examples of unfavourable cellular processes (+ delta G)?
Transport against a gradient or synthesis of large molecules
What are unfavourable cellular processes driven by?
Coupling
What reaction is very favourable and is often coupled?
Formation of ADP + Pi
What causes ATP to be less stable than ADP?
negative charges are very close together
How is the strain on ATP reduced partially?
Removal of a phosphate group
What are anhydride bonds?
High energy bonds
What are reactions with large negative delta G values used for in metabolic reactions?
Control points
What is metabolism?
All reactions taking place in the body
What is catabolism?
Breaking down smaller molecules into complex ones to release energy (favourable)
What is anabolism?
Synthesising complex molecules out of small ones in energy consuming unfavourable reactions
What is an example of a catabolic reaction?
Glycolysis (breakdown of glucose to generate ATP)
What is the net gain of glycolysis?
2 ATP
What is an example of anabolism?
Gluconeogenesis- making new glucose from non-carbohydrate precursors
What is the polarity of water?
Polar
What is the shape of water?
Bent
Water is hydrophilic. What dissolves in it?
Ionic and polar substances
What substances are insoluble in water?
Non-polar substances
How strong are hydrogen bonds compared to covalent ones?
Weaker individually but may be stronger collectively
What are amphipathic molecules?
Both hydrophobic and hydrophilic
What do amphipathic molecules form in water?
Micelles
What does the chiral carbon of an amino acid bind to?
An amino group, carboxyl group, hydrogen and side chain
What are the D and L forms of amino acids?
Stereoisomers
What bonds form between amino acids?
Peptide
What describes an acid?
Donates protons
What describes a base?
Accepts protons
What is the strength of an acid based on?
How readily it dissociates
What is the equation for the dissociation constant of an acid?
Ka= [H+] [A-] / [HA]
What is pH a measure of?
Concentration of protons in a solution
What does the Henderson-Hasselbach equation do?
Connects the Ka of a weak acid with the pH of the solution containing it
What is the Henderson-Hasselbalch equation?
pH= pKa + log ([A-] / [HA])
What is the isoelectric point?
pH at which a molecule has no net charge
How many pKa values do amino acids have?
2
What is primary protein structure?
The amino acid sequence
What is secondary protein structure?
Localised conformation of polypeptide backbone
What is the 3D structure of a polypeptide, including side chains?
Tertiary structure
What is the arrangement of polypeptide chains in a protein with multiple subunits?
Quaternary structure
What type of bonds are involved in secondary structure?
Hydrogen bonds
Secondary structure is localised. What does this mean?
Similar features are kept together
What are types of secondary structure?
Alpha helices, beta sheets, triple helices
What forms hydrogen bonds in secondary structure?
CO group of one amino acid and the NH group of another- 4 amino acids away
What residues break alpha helices?
Proline
How many polypeptide chains are involved in alpha helices?
1
How many polypeptide chains are involved in beta sheets?
Can be more than 1
What two types of bets-sheets are there?
Parallel or anti-parallel
Can different elements of secondary structure occur between the same protein?
Yes
What forms a triple helix?
Collagen
Where is collagen found in the body?
Bone and connective tissue
What is a repeating sequence of an amino acid?
Triple helix
What type of inter-chain bonds are present in triple helices?
Hydrogen
Apart from hydrogen, what other type of bonds are present in triple helices?
Covalent bonds
What are globular proteins?
Proteins folded into a spherical shape
What is an example of a globular protein?
Haemoglobin
What is the solubility of globular proteins like?
Soluble in water and salt solutions
What are fibrous proteins?
Contain polypeptide chains organised approximately parallel along a single axis
What are examples of fibrous proteins?
Keratin, collagen
What is the solubility of fibrous proteins?
Not soluble in water and salt
What are stronger, fibrous or globular proteins?
Fibrous
What are some different bonds involved in tertiary structure?
Hydrogen bonds, hydrophobic interactions, salt bridges, disulfide bridges
What are disulphide bridges?
Covalent bonds between cysteine amino acids
What are proteins which aid the folding process known as?
Chaperones
What conditions can cause denaturation of proteins?
pH, heat, detergents, urea, thiol or reducing agents
What are prosthetic groups?
A type of tertiary structure- proteins which contain another non-protein structure
What is an example of a prosthetic group?
Haem
What is quaternary structure involved in?
Proteins involving more than one polypeptide chain
What happens when one subunit of a protein binds to oxygen and what is this process known as?
Increases the other subunits affinity for oxygen- allosteric regulation
What is the genome?
The total DNA in each cell
What are the sugars in RNA and DNA?
Ribose and deoxyribose
What is a nucleoside?
Base and sugar
What is a nucleotide?
Nucleoside and phosphate group
What bonds are involved in nucleotides?
Phosphodiesterase
What are phosphodiesterase bonds formed between in nucleotide binding?
Free 3’ OH group and 5’ triphosphate
How many high energy bonds does the phosphodiesterase bonding of nucleotides take up?
2
Where are new nucleotides added?
To the free 3’ end only
How many nucleotide strands does DNA contain?
2
What is on the outside of the DNA strand?
Sugar phosphate backbones
What is on the inside of the DNA strand?
Bases
How are base pairs bonded?
Hydrogen bonds
What are the differences in bonds between AT and CG pairs?
AT- double bond
CG- triple bond
What must happen to DNA before cell division?
Replication
DNA replication is semi-conservative and catalysed by what?
RNA polymerase
What is needed to start DNA replication?
RNA primer
Where can DNA be added?
Only to existing nucleotides
Where does DNA replication start?
Simultaneously at multiple points in the genome
How is the lagging strand replicated?
In small short segments known as Okazaki fragments
What does helicase do?
Unwinds the DNA helix and stops it rewinding
What does 3’-5’ exonuclease do?
Removes incorrect nucleotides to improve error rate
What is rRNA?
Combines with proteins to form ribosomes where protein synthesis takes place
What is tRNA?
Carries amino acids to be incorporated into the protein
What is mRNA?
Carries genetic information for protein synthesis
Where does the specific amino acid attach to tRNA?
3’ end
What happens at the RNA polymerase binding stage of transcription?
Detection of initiation sites on DNA, requires transcription factors
What is the 2nd stage of transcription?
DNA chain separation
What is the 3rd stage of transcription?
Transcription initiation
What are the 4th and 5th stages of transcription?
Elongation and termination
Where does transcription start?
Nucleotide +1
What is a TATA box?
A nucleotide sequence which specifies to other molecules where transcription begins
Where is the TATA box found?
About 25 nucleotides infront of the transcriptional start
What does the TATA box binding protein do?
Recognises TATA and introduces a kink into DNA which determines the transcriptional start and direction
What direction is the RNA chain synthesised in?
5’-3’