Biochemistry from Principles Collated Flashcards
Bond strengths in order. Strongest to weakest?
Covalnt Ionic Hydrogen Hydrophobic interactions VDW's
Oxidation states of carbon?
Alkane (in fats) Alcohol (in carbs) Aldehyde Carboxylic acid Carbon dioxide
What is the function of micelle
helps in the absorption of large lipid molecules, once inside an enterocyte, these lipids are processed and packaged via the rough and smooth endoplasmic reticulum and the Golgi body into a chylomicron for absorption into the lymphatic system.
What forms the outer shell of micelles?
Bile salts and a single phospholipid layer
Micelles have an important role in aiding the absorption of large lipid compounds in the small intestine. They are formed from an outer shell of bile salts, which act as a surfactant to emulsify fat droplets, and a single phospholipid layer, which provides the amphiphilic property (i.e., both hydrophilic heads and hydrophobic tails). The core of the micelles contain long-chain free fatty acids, monoglycerides, and cholesterol, as well as fat-soluble vitamins
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?
Relative orientation of one polypeptide to another
polypeptide in a multisubunit protein.
Spatial arrangement of multiple subunits.
What holds proteins together?
Disulphide bonds (Peptide bonds form the primary structure of protein molecules. Function of this disulphide bond is to stabilize the secondary and tertiary structure of proteins.)
5 elements of a cell?
SER RER Mitochondria Golgi apparatus Ribosomes
Structure of DNA?
Nucleoside = base + sugar Nucleotide = nucleoside + phosphate
Examples of purines?
Adenine and guanine
What is the collective term for the nitrogenous bases adenine and guanine (A&G) found in DNA and RNA?
Purines
Examples of pyramidines?
Cytosine
Thymine
Uracil
What is the central dogma?
DNA is transcribed to RNA, which is translated into protein
A nucleoside has…
5C sugar + organic base
A nucleotide has…
5C sugar + organic base + phosphate group(s)
Pol II synthesises only stable RNA. True/False?
False
Pol II synthesises all RNA. Pol I and III synthesise only stable RNA
DNA polymerase has 3 important characteristics
Can only add to existing nucleic acids
Cannot start synthesis on its own
Requires an RNA primer to start replication
To which “end” of the RNA strand are more nucleotides added during transcription?
3’ end
What is the catalyst for DNA replication?
DNA polymerase
What is required to commence DNA synthesis and replication?
An RNA primer
(DNA polymerase can take over after this)
In which two ways is DNA formed and why?
Continously or discontinuously
Continuously - DNA is built up from the 5’ to the 3’ end easily - this is the leading strand
Discontinuously - the other strand is built from 3’ to 5’ as it is orientated the other way around - this is the lagging strand
The lagging stand in DNA formation must utilise which type of fragments to enable 5’ to 3’ directional growth?
Okazaki
Which enzyme is reponsible for unwinding DNA?
DNA helicase
Which enzyme is reponsible for synthesising an RNA primer to initiate replication on the lagging strand?
Primase
Describe how Okazaki fragments aid the growth of the lagging strand
Short newly synthesised DNA fragments - Okazaki fragments are added at intervals from the open DNA strands downwards
This allows nucleotides to be sythesised in the “correct” direction by essentially filling in the gaps the Okazaki fragments created
Each time DNA helicase opens up the strand a little more, a new Okazaki fragment can jump in and allow synthesis back down the chain
Which enzyme is key in proofreading?
DNA polymerase
What are the three differences between DNA and RNA?
Single vs double stranded
DNA - thymine, RNA - uracil
RNA - ribose sugar, DNA - deoxyribose sugar
Which enzymes are responsible for RNA production?
RNA polymerases
Which variation of RNA polymerase will synthesise mRNA?
Pol II
Where will RNA polymerase bind on a section of DNA?
Sections of DNA called promotors
What is characteristic about promotor regions on DNA?
They all have the TATA box sequence which marks the beginning of the relevant gene
What are enhancers?
Short regions of DNA that can be bound by protein activators to increase the liklihood of transcription
How can enhancers have an influence if they are far from the promotor sequences?
Looping of the strand allows them to come into contact
Which is why mRNA form a stem loops.
Q
Enzymes can affect the equilibrium position of a reaction. True/False?
False
but it reduce the time to reach equilibrium
How do enzymes lower the activation energy of a reaction?
Bind to and stablise the transition state and provide alternative reaction pathways
How do enzymes lower the activation energy of a reaction?
Bind to and stablise the transition state and provide alternative reaction pathways
Enzyme with a cofactor is called a…
Holoenzyme
Induced fit model describes enzyme-substrate interaction by…
Binding of substrate induces a conformational change in the enzyme, resulting in complementary fit
Trypsin and chymotrypsin work in the ____ and have an optimum pH of _
Small intestine, 7
What are isozymes?
Catalyse same reactions as enzymes but have different properties and structure
CK is an isozyme. The M form is produced in ____ and the B form is produced in the ___. MB form is produced in the ___
Skeletal muscle, brain, heart
Which enzymes carry out phosphorylation?
Kinases
What are zymogens?
Inactive precursors of an enzyme
Where are trypsinogen and chymotrypsinogen formed? Why is it important they are produced inactive?
Pancreas
They would digest the pancreas if active
Which enzyme activates trypsinogen? Where does this occur?
Enteropeptidase
Small intestine
How many nucleotides do anticodons consist of?
3 E P and A
What is TFIID?
General transcription factor required for Pol ii transcribed genes
What do anticodons from tRNA form with codons of mRNA?
How many possible combinations?
Base pairs
64
Number of possible amino acid types?
v
What is the start codon in translation?
AUG
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 sit
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 do the terms “degenerate” and “unambiguous” mean in the context of the genetic code?
Degenerate: More than one codon can code for the same amino acid.
Unambiguous: Each codon codes for only one amino acid.
Induced fit model describes enzyme-substrate interaction by…
Binding of substrate induces a conformational change in the enzyme, resulting in complementary fit
Vmax is?
The maximal rate of reaction at unlimited substrate concn
Km is?
The concn of substrate which gives 50% maximal rate, i.e. 0.5Vmax
A low Km means…
An enzyme only needs a little substrate to work at 0.5Vmax (it has high affinity)
Vmax can be obtained from a Lineweaver-Burk plot by looking at the interesection with the X axis. True/False?
False
Intersection with X axis is Km; intersection with Y axis is Vmax
In non-competitive inhibition, Vmax is ___ and Km is ___
Decreased, stays the same
enzymes are stabilised intermediate that are formed as substitutes are converted to products True /false
True
enzymes catalyse the transition state to avoid the loss of free energy True/False
True
prosthetic group
its tightly bound coenzymes