Biochemistry Flashcards
Bond strengths in order. Strongest to weakest?
Covalent Ionic Hydrogen Hydrophobic interactions VDW's
Oxidation states of carbon?
Alkane (in fats) Alcohol (in carbs) Aldehyde Carboxylic acid Carbon dioxide
4 major classes of biomolecules and what they consist of?
Proteins/peptides= amino acids
Lipids= triglycerides, phospholipids, steroids
Nucleic acids= DNA/RNA
Carbs= Mono, di, poly saccharides
Example of monosaccharide?
Glucose
Examples of disaccharides?
Lactose
Examples of polysaccharides?
Cellulose
Glycogen
1st law of thermodynamics?
Energy can neither be created nor destroyed
2nd law of thermodynamics?
When energy is converted from one form to another some of that energy becomes unavailable to do work
What type of reaction is it if the change in free energy is negative?
Exergonic (can occur spontaneously)
What type of reaction is it if delta G is positive?
Endergonic (cannot occur spontaneously)
Entropy?
Loss of useable energy
Primary protein structure?
Sequence of amino acids
Secondary protein structure?
Formation of backbone
Tertiary protein structure?
3D structure
Quaternary protein structure?
Spatial arrangement of multiple subunits
What holds proteins together?
Disulphide bonds
5 elements of a cell?
SER RER Mitochondria Golgi apparatus Ribosomes
Role of SER?
Synthesis of steroid hormones
Role of RER?
Synthesizes polypeptides
Role of mitochondria?
Powerhouse of cell can multiply independently
Role of golgi apparatus?
Receives materials from ER and distributes, also modifies proteins
Role of ribosome?
Where RNA is translated into protein
Prokaryote?
Microscopic single cell organism that does not have a defined nucleus
Eukaryote?
Normal cell with normal nucleus
Structure of DNA?
Nucleoside = base + sugar Nucleotide = nucleoside + phosphate
Examples of purines?
Adenine and guanine
What is collective term for base A&G?
Purines
Collective term for C, T & U?
Pyrimidines
Examples of pyramidines?
Cytosine
Thymine
Uracil
What direction is DNA replication?
Always in 5’->3’ direction
What type of primer is required for DNA repication?
RNA primer
DNA replication is catalysed by DNA polymerases. True or false?
True
Which strand always has a free 3’ end?
Leading strand
What unwinds DNA in DNA replication?
DNA helicase
How are okazaki fragments made?
Lagging strand is replicated in short fragments
What are the short replicated fragments of the lagging strand in DNA called?
Okazaki fragments
What does RNA contain?
Stem loop
3 types of RNA?
rRNA (ribosomal)
mRNA (messanger)
tRNA (transfer)
Role of rRNA?
Combines with proteins to from ribosomes where protein synthesis takes place
Role of tRNA?
Carries amino acids to be incorporated into protein
Role of mRNA?
Carries genetic information for protein synthesis
How many nucleotides do anticodons consist of?
3
How many types of RNA polymerases do
- prokaryotic cells have
- Eukaryotic cells have?
- 1 type for pro
- 3 types for eu
Types of RNA polymerase in a eukaryote?
Pol i, ii, iii
Which RNA polymerase synthesizes all mRNA?
Pol ii
Stages of transcription?
- RNA polymerase binding
- DNA chain separation
- Transcription initiation
- Elongation
- Termination
What happens in first stage of transcription?
RNA polymerase binding
- Detects initiation sites on DNA
- Requires transcription factors
What does first stage of transcription require?
Transcription factors
2nd stage of transcription?
Unwinding of DNA
3rd stage of transcription?
Transcription initiation
- Selection of 1st nucleotide of growing RNA
- Required additional general transcription factors
4th stage of transcirption?
Elongation
- Addition of further nucleotides to RNA chain
- RNA Synthesized in 5’ -> 3’ direction
What direction is RNA synthesized in?
5->3
5th stage of transcription?
Termination
-release of finished RNA
What is TFIID?
General transcription factor required for Pol ii transcribed genes
Difference between exons and introns?
Exons= coding regions Introns= non-coding regions
What happens to introns before translation?
They are transcribed together with exons but then removed by splicing before translation into the protein
What do anticodons from tRNA form with codons of mRNA?
How many possible combinations?
Base pairs
64
Number of possible amino acid types?
20
What is the start codon in translation?
AUG
Components of translation?
- Amino acids
- tRNAs
- Aminoacyl tRNA synthetases
- Protein factors
- ATP/GTP
- Ribosomes
- mRNA
Stages of Translation?
Initiation
Elongation
Termination
What happens in initiation of translation?
- GTP provides energy
- Ribosomal sub-unit binds to 5’ end of mRNA and moves along until it finds start codon
- Initiator tRNA pairs to start codon
- Large sub-unit joins assembly and initiator tRNA is locked in P site
What happens in elongation stage of translation?
- Elongation factor brings aminoacyl - tRNA to A site
- GTP
- Second elongation factor regenerates the 1st to pick up next aminoacyl tRNA
- Peptidyl transferase catalyses peptide bond formation between the amino acids in P and A site
What happens in termination stage of translation?
- Occurs when A site of ribosome encounters a stop codon (UAA, UAG, UGA)
- Finished protein cleaves off tRNA
How many tRNA binding sites and their names?
3 sites
E, Aminoacyl (A), Peptidyl (P)
What does degenerate mean?
Many amino acids have more than one codon
What does unambiguous mean?
Each codon codes only for one amino acid
What does an enzyme do?
Speed up the rate at which a reaction reaches equilibrium however does NOT affect position of equilibrium.
-They lower activation energy and stabilise the transition state
What are enzymes without a cofactor?
Apoenzymes
What are holoenzymes?
Enzymes with a cofactor
Induced fit model?
Binding of substrate to active site induces a conformational change in the shape of the enzyme resulting in a complimentary fit
What type of reaction do protein kinases carry out?
Phosphorylation
What is Vmax?
Maximal rate of reaction at UNLIMITED substrate concentration
What is Km?
Michaelis constant = 50% Vmax
Which types of graphs are used to show enzyme kinetics and why?
Lineweaver Burk Plots
- Instead of hyperboles because it is easier to read Vmax and Km
What is Vmax in a lineweaver burk plot?
Intersection of the straight line with the Y axis
What is Km in a lineweaver burk plot?
Lines intersection with the x axis
Competitive enzyme inhibition?
- Binds to active site
- Vmax remains the same
- Km varies
What happens to Vmax in competitive inhibition?
Remains the same
KM varies
Non-competitive enzyme inhibition?
Binds to site other than active site
- Vmax varies
- Km stays the same
What happens to Vmax in Non-competitive inhibition?
Varies
Michaelis Menten control shown in a diagram looks like?
Like a right angle sort of curve.
Steep and not gradual curve
Allosteric regulation in a diagram looks like?
Much less curved, gradual rise (sort of a loose S shape)
Functions of cholesterol?
Present in cell membranes
Component of myelin sheath
Precursor molecule for- steroids, vit D & Bile acids
Where are triglycerides present in cell membrane?
Lipid bilayer
Role of triglycerides?
Highly concentrated energy stores
Anabolism?
Requires energy
reductive
Endergonic
Catabolism?
Breakdown of molecules to yield energy
Exergonic and oxidative
How does glucose get into cell?
Via Glucose transporters GLUT by facilitated diffusion
What is the initial pathway for conversion of glucose to pyruvate?
Glycolysis
Net gain per glucose during glycolysis?
+ 2 ATP
Process of glycolysis?
Glucose | Fructose-1,6-biphosphate | Triose phosphate x2 | Pyruvate
What phosphorylates glucose in glycolysis?
Hexokinase
What phosphorylates fructose-6-biphosphate?
Phosphofructokinase
What converts triose phosphate to pyruvate?
Pyruvate kinase
How is NAD+ regenerated in glycolysis?
Through oxidative metabolism of pyruvate
What happens to pyruvate in anaerobic conditions?
Alcoholic fermentation
Lactic acid formation in humans
What happens to pyruvate in aerobic conditions?
Further oxidized in krebs cycle
Make up of mitochondria?
Inner membrane
Outer membrane
Central matrix (contains enzymes of krebs cycle)
Cristae folds
Aerobic metabolism of pyruvate happens where?
Mitochondrial matrix
What happens in metabolism of pyruvate?
- Converted to acetyl-CoA
-Condenses with 4C compiund to form 6C citric acid
-Citric acid is decarboxylated twice (yields CO2 x2)
-
What is the conversion of pyruvate to acetyl-CoA catalyzed by?
Pyruvate dehydrogenase complex (PDC)
How many oxidation reactions happen in Krebs cycle?
4
Yields 3 NADH + H+ and 1 FADH2
What compound is recreated in Krebs cycle?
Oxaloacetate (4C)
Which enzyme involved in the Krebs cycle is NOT in the mitochondrial matrix and were is it?
Succinate Dehydrogenase
Integrated into the inner mitochondrial membrane
How may pairs of electrons are transferred in NADH+ H+ reaction?
3 pairs
and 1 pair in FADH2
Products from each acetyl CoA in Krebs cycle?
3 NADH + H+
1 FADH2
1 GTP
2 CO2
What is the standard redox potential of a substance?
Measure of how readily substance donates electrons
Phosphoryl transfer potential?
Free energy change for ATP hydrolysis
Electron transfer potential?
Measured by redox potential of a compound
What does a negative standard redox potential mean?
Reduced form of X has lower affinity for electrons than hydrogen
What does a positive standard redox potential mean?
Reduced form of X has a higher affinity for electrons than hydrogen
What is oxidative phosphorylation?
Coupling of respiration to ATP synthesis
How many stages of oxidative phosphorylation?
2 stages
- electron transport
- ATP synthesis
What happens in electron transport chain?
Electrons passed down from high to low redox potentials and transferred onto O2 to make H20
What is coupled in the electron chain transport process?
H+ transport from mitochondrial matrix to intermembrane space
What are protons attracted to in the ETC?
The matrix because the matrix side is more negative, there are more protons in the intermembranous space than in the matrix
How to inhibit oxidative phosphorlation?
Cyanide, Azide, CO= all inhibit transfer of electrons to O2
No proton gradient formed, no ATP synthesized
What happens in Oxidative phosphorylation?
- Electrons from NADH/FADH2 are used to reduced O2 to H20
- Their energy is used to pump protons from mitochondrial matrix to intermembrane space and hen protons flow back across membrane
- Energy of proton flow is used to phosphorylate ADP to ATP
One glucose molecule yields?
30-32 molecules of ATP
Amount of NADH + H+ created?
3 in Krebs 2 in Glycolysis 2 in link = 10 NADH + H+
How many FADH2 produced?
2 in krebs
Calculations for ATP produced from NADH + H= AND FADH2?
10 x 2.5= 25 ATP
2 x 1.5= 3 ATP
=
28 ATP
Overall ATP?
28 ATP from NADH/FADH 2 from glycolysis 2 from Krebs cycle (GTP) = 32 ATP
