Biochemistry Flashcards
Detail the bond strength of molecules form strongest to weakest
covalent, ionic, hydrophobic interaction (non-polar, polar) van der waals forces
What are the oxidation states of carbon?
Alkane(fats), alcohol(carbs), aldehyde, carboxylic acid, carbon dioxide (final product)
What do proteins and peptides consist of?
Amino acids
what are some lipids?
triglycerides, phopholipids and steroids
Nucleic acids?
DNA and RNA
What are some carbohydrates?
mono, di, and poly saccharides
give an example of a Monosaccarides?
glucose but can be present as multiple structures
What is the struture of lactose?
disaccharides
Give an example of a polysaccaride
cellulose, glycogen
What is the first law of thermodynamics
Energy is neither created nor destroyed
What is the second law of thermodynamics?
When energy gets converted from one form into another some of that energy is not available to do work
What equals the change in free energy?
energy of products - energy of reactants
When does negative free energy occur?
exergonic so it occurs spontaneously
When does positive free energy occur?
endergonic ( can not occur spontaneously and therefore requires energy)
How is free energy related to point of equilibrium?
Delta G (free energy) is nar zero means the reaction is readily reversible
What does entropy equal
loss of usable energy
Detail the four different structures of proteins
Primary - sequence of amino acids
secondary - formation of backbone (poly peptide)
tertiary - 3d structure
quaternary - spatial arrangement of multiple subunits (disulphide bonds holds proteins together)
Where are collagen triple helixes present?
Abundant in connective tissue
What do SMR release?
steroid hormones, lipids, phospholipids - involved in testes, ovaries and skin oil glands
rough ER?
synthesises polypeptides
What is the mitochondria?
powerhouse of the cell
What does the golgi apparatus do?
receives material from ER and distributes to cell, it can also modify proteins
ribosomes
RNA is translated into proteins
prokaryote
microscopic single cell organism that does not have a defined nucleus
eukaryote
normal cell with nucleus
What is a nucleoside?
base + sugar
nucleotide?
nucleoside + phosphate
Purines
adenine and guanine
pyrimidines
uracil, thymine and cytosine
Where does phosphodiester bonds lie between?
3’ OH group and 5’ triphosphate
What is the basic base pairing of DNA
guanine - cytosine
adenine - thymine
What are the main points in DNA replication?
always in 5’ to 3’ direction
catalysed by DNA polymerase
RNA primer is required for DNA replication
leading strand - always has free 3’ end
lagging strand - replicated in short fragments called okazaki fragments
helicase unwinds the DNA
What does RNA contain?
it is only single stranded but contains a stem loop
What are the three types of RNA?
tRNA - transfer RNA take amino acids to ribosomes
anticodons consist of 3 nucleotides
rRNA - they are integral parts of the ribosome (combine with protiens)
mRNA - take genetic information to the protein
What are the different types RNA polymerases?
prokayote has 1 type
eukaryote has 3 types (1,2 and 3)
What does polymerase 2 synthesise
all mRNA
Detail the whole process of transcription
RNA polymerase binding - detects initiation sites on DNA (promoters) but requires transcription factors
DNA chain separation - unwinding of DNA
transcription initiation - selection of first nucleotide of growing RNA, requires other general transcription factors
elongation - addition of further nucleotides to RNA chain - RNA synthesised in 5’ to 3’ direction
Termination - release of finished RNA
When is transcription factor 2 D used?
required for all pol 2 transcribed genes
What are are exons and introns? How are they separated?
exons coding regions, introns - non coding regions
separated by splicing which splices out the introns
How many combinations are there if 20 amino acids are present?
64 possible combinations
What are the components involved in translation?
amino acid, tRNA’s, aminoacyl-tRNA synthetases, protein factors, ATP/GTP, ribosomes and mRNA
What is the start codon ?
AUG
Describe the process of initiation of translation
initiation - GTP provides energy, ribosomal subunit binds to 5’ end of mRNA, moves along until start codon is found
initiator tRNA pairs to start codon
large subunit joins assembly and initiator tRNA is located in p site
elongation
elongation factor brings aminoacyl -tNRA to A site, GTP and second elongation factor regenerates the first to pick up next aminoacyl-tRNA
When is peptidyl transferase useful?
catalyses peptide bond formation between amino acids in P and A sites
Describe the process of termination:
Occurs when A site of ribosome encounters a stop codon
finished proteins cleaves off tRNA
what are the 3 tRNA binding sites?
exit, peptidyl and aminoacyl
what are post translation ribosomes?
free ribosomes in cytosol proteins (nucleus, mitochondria)
What are co - translational ribosomes
bound ribosomes on the rough endoplasmic reticulum
What are the two different types of genetic code?
degenerate - many amino acids have more than one code
unambiguous - each codon codes only for one amino acid
What is a biological catalyst
Speeds up the rate a reaction reaches equilibrium but doesn’t change the position of equilibrium
lowers activation energy and stabilises the transition state
What are apo enzymes and what are holoenzymes?
apo = without cofactor holo = with co factor
What is induced fit?
binding of substrate induces a conformational change in the shape of the enzyme resulting in a complementary fit
How is phosphorylation carried out?
through the use of protein kinases
Define Vmax, Km and why lineweaver burk plots are used over hyperboles
Vmax = maximal rate of reaction at unlimited substrate concentration
Km = michaelis constant = 50% Vmax
used because it is easier to read Vmax and Km - Vmax s the interation of the straight line with the Y axis
Km is the line’s intersection with the X axis
What are the two different types of enzyme inhibition?
competitive - binds to active site, Vmax remains the same and Km varies
Non-competitive - bind to site other than active, Km stays the same and Vmax varies
What relationship do enzymes have with allosteric control?
sigmoidal relationship
Why is cholesterol important?
present in cell membranes, component of myelin sheath
precursor molecule for - steriod hormones, Vit D and Bile acids
Why are triglycerides important?
Present in all cell membranes - lipid bilayer
highly concentrated energy stores
What is enthalpy?
heat content
What does metabolism consist of?
Anabolism (requires energy - endergonic and reductive) catabolism ( breakdown of molecules to yield energy - exergonic and oxidative)
WHy is ATP less stable than ADP
negative charges close together in ATP put a strain ( electrostatic repulsion) on the molecule
What is a hydrogen bond?
polarised bond allow the hydrogen to interact with unshared electrons from another electroneagive atom
What are the shape of hydrogen bonds?
tend to be linear(in a straight line)
what is the structure of a micelle?
head group in contact with water and tail group sequestered from water
What is the structure of a peptide bond?
partial double bond character
planar
peptide bonds are strong and rigid
What defines an acid?
proton donators
What are zwitterions?
amino acids without charged side groups
What is central dogma?
DNA - RNA to protein (transcrption, translocation)
What is the product of glucose oxidation?
CO2 and water
How does glucose get into the cell?
Glucose transporters (GLUT) by facilitated diffusion
What is the initial pathway of conversion of glucose to pyruvate? -
glycolysis
What is the net gain of ATP in glycolysis?
Net gain of 2 ATP (uses 2 ATP but creates 4 ATP)
Describe glycolysis
Glucose is converted into fructose 1-6-bisphosphate (using 2 ATP)
then it turns inot 2 triose phosphates then into 2 pyruvate generating 4 ATP and 2 NADH + 2H+
What does hexokinase do?
phosphorylates glucose
What does phosphofructokinase do?
phosphorylates fructose 6 phosphate
How is NAD+ regenerated?
oxiadtive metaboism of pyruvate
What are the two outcomes of pyruvate?
anaerobic - lactic acid, alcoholic fermentation
aerobic - further oxidised in TCA
What is the structure of a mitochondira?
contain inner membrane proteins, outer membranes, central matrix and contain crisae folds
Detail the aerobic metabolism of pyruvate
Enters mitochondrial matrix, converted to acetyl CoA (catalysed by PDC)
condenses with 4C compound to form 6C compound
6C compound decarboxylated twice - yields CO2
4 oxidation reactions, ( yields NADH + H+ and FADH2
GTP formed
4C compound recreated
Where are the enzymes found int he TCA cycle?
matrix, apart from succinate dehydrogenase ( integrated into mitochondrial membrane)
What are the products of the TCA cycle
3 NADH + H+
1 FADH2
1 GTP
2 CO2
What is phosphoryl transfer potential
Free energy change for ATP hydrolysis
How is electron transfer potential measured?
redox potential of a compound
What is the standard redox potential - negative and positive
A measure of how readily it donates an electron
negative - reduced form og X has lower affinity for electrons than hydrogen
positive - reduced form of X has higher affinity for electrons than hydrogen
What are the 2 stages of oxidative phosphorylation
coupling of respiration to ATP synthesis
electron transport and ATP synthesis:
What happens during the electron transport chain?
respiratory chain, Electrons from NADH enter at complex 1, elections from FADH2 enter at complex 2 (TCA cycle)
electrons are handed down from higher to lower redox potentials - transferred onto O2 from H2O
Transfer of electrons through resp chain is coupled to H+ transport from mito matrix to intermembrane space
electochemical gradient - more protons in inter-membranous space than matrix, matrix side more negative, protons attracted to matrix - coupled to ATP synthesis
How is oxidative phosphylation inhibited?
Cyanide, axzide, adn CO inhibit electrons to O2
no proton gradient formed therefore no ATP generated
Why is oxidative phosphorylation important?
electrons form NADH and FADH2 used to reduce O2 and H20
energy used to pump protons from mitochondiral matrix to intermembrane space
protons flow back across membrane
energy of proton flow is used to phosphorylate ADP to ATP
What is the final balance of this whole cycle?
glycolysis = 2 ATP TCA (2 GTP) = 2 ATP 10 NADH + H+ = 25 ATP TCA cycle (2FADH2) - 3 ATP 1 glucose molecule yields = 30-32ATP molecules
What are isozymes?
Isozymes are like isomers – they catalyse the same reaction but have
different structures and chemical properties.
What is a zymogen?
A zymogen is an inert substance
which can be chemically converted into an enzyme.
What does negative enthalpy equal?
exothermic reaction
What does negative gibbs energy equal?
The reaction is carried out spontaneously
What is an accurate description of hydrogen bonds?
They usually lie in a straight line
Production of ATP is required to produce the basic currency of energy for all cellular processes - why do rapidly contracting human muscle cells start producing lactic acid?
The cells have to convert NADH into NAD+
