Biochemistry Flashcards
What are the major classifications of carbohydrates?
Monosaccharides (one carbohydrate group), disaccharides (two carbohydrate groups), polysaccharides (many carbohydrate groups)
What are the first and second laws of thermodynamics ?
First = energy is neither created or destroyed just converted from one form to another Second = when energy is converted from one form to another, some of the energy becomes unavailable to work.
What is entropy?
A measure of the amount of disorder in a system
Describe free energy
= energy of of products - energy of reactants
Reactions in which the free energy change is negative can occur spontaneously (exergonic)
Reactions in which the free energy change is positive cannot happen spontaneously and so an input of energy is needed to proceed. (Endergonic)
The closer delta G is to zero the more likely the reaction is reversible
Which is less stable of ATP and ADP?
The negative charges close together in ATP put a strain on the molecule and make it less stable than ADP. The strain is relieved partially by removing one or more phosphate groups. (Anhydride bonds are high energy)
What is catabolism?
Breaking down complex molecules into smaller ones and releasing energy
What is anabolism ?
Synthesising complex molecules out of smaller ones in energy consuming reactions
What is a nucleoside ?
Base + sugar
What is a nucleotide ?
Base + sugar + phosphate group(s)
What are the differences between DNA and RNA?
DNA
-ATGC, 2-deoxyribose sugar, double stranded, building blocks = dATP, dCTP, dGTP, dTTP
RNA
-AUGC, ribose sugar, single stranded, building blocks = ATP, CTP, GTP, UTP
What are the names of the bases when they are converted to nucleosides?
Adenosine, cytidine, guanosine, thymidine, uridine
Describe polymerisation.
Nucleotides with 3 phosphates attached are added to the 3’ end when the -OH group is. The pyrophosphate ion (2 phosphates) is released and the bond is broken releasing energy to drive the action.
Which end of the DNA strand are new nucleotides are added to?
The 3’ end
Describe the structure of DNA
Double helix, four bases ATGC, two antiparallel strands (5’ to 3’ and 3’ to 5’), sugar-phosphate backbone on the outside and base pairs of the inside.
A joins to T with two hydrogen bonds and G joins to C with three hydrogen bonds
What is DNA replication?
Replicating DNA before cell division so that daughter cells have a complete complement of the genome.
It is semi-conservative (half of the original strand is not used during replication)
It is catalysed by DNA polymerase but cannot start DNA synthesis on their own (requires RNA primer)
Describe eukaryotic DNAs origins of replication?
Eukaryotic genomes have many origins of replication and it can start simultaneously at several pony’s in the genome (bidirectional, ensures replication is reasonably quick)
What happens during DNA replication on the leading and lagging strand.
Leading strand is continuous 3’ to 5’
Lagging strand is in segments (Okazaki fragments) 5’ to 3’
What unwinds the DNA before replication?
Helicase
How can DNA be proofread/ repaired ?
DNA polymerase has 3’ to 5’ exonuclease activity which removed incorrect nucleotides and improves the error rate.
Describe RNA
- Single stranded, has U instead of T
- can contain stretches of intramolecular base pairing (stem loops)
- rRNA combines with proteins to form ribosomes
- tRNA carries amino acids to make proteins
- mRNA carries genetic info for protein synthesis
Describe tRNA
Have anticodon consisting of three nucleotides . Specific amino acids are attached to the 3’ end.
All tRNA molecules have a 3D structure
Describe RNA polymerase
- makes RNA
- eukaryotic cells have three types Pol 1, Pol 2, Pol 3
- Pol 2 synthesises all mRNA
How can unfavourable cellular processes take place?
By coupling them with a highly favourable process
What are the types of amino acid?
- non polar/hydrophobic
- polar / uncharged
- acidic
- basic
What are polypeptides made up of?
20 different L amino acids. D and L refers to the stereochemistry of the amino acid.
Which direction are polypeptides synthesised?
From the n terminus to the c terminus
They have partial double bond character due to electrons from the n and c terminus contributing to the bond
What is pH?
A measure of the amount of protons in a solution
What is cationic and anionic ?
Cationic = positive amino acid Anionic = negative amino acid
What are zwitterons?
Amino acids without charged side groups in neutral solutions.
What is the isoelectric point?
The pH at which a molecule has no net charge.
How can polypeptides rotate?
Amino acids are planar but polypeptides can rotate around angle between the alpha carbon and the amino group/ carboxyl groups
Describe secondary structure of poly peptides.
-stabilised by H bonding
Three types - alpha helixes, beta sheets and turns, and collagen triple helixes
Describe alpha helixes
One rod-like polypeptide chain
Mostly right handed , co group forms hydrogen bonds with NH group 4 residues away.
Describe beta sheets and turns
Polypeptide backbone almost entirely extended.
Hydrogen bonds between neighbouring groups
Can involve parallel and antiparallel chains + turns
Repeating zigzag structure
Describe the collagen triple helix
Composed of bone and connective tissues
Has water insoluble fibres
Three left handed helical chains twisted around each other
Repeated sequence X-Y-gly in all strands
what are fibrous proteins ?
polypeptide chains organised approximately parallel along a single axis (long, mechanically strong, insoluble in water, fibres)
what are globular proteins?
proteins folded into a spherical shape (soluble in water, polar side chains, non-polar inside)
what are the forces stabilising tertiary structures?
covalent disulphide bonds, salt bridges, hydrophobic interactions, hydrogen bonds, complex formations with metal ions
what can disrupt protein structures?
heat, extreme pH, detergents, urea, reducing agents
what is the central dogma?
the process of DNA>RNA>proteins
where does DNA replication, transcription and splicing occur?
nucleus
where does translation occur?
ribosome
what are nucleotides and nucleosides?
nucleotides = base, sugar and phosphate nucleosides = base and sugar
what happens in DNA polymerisation?
nucleotides with 3 phosphates attached are added to the 3’ end of the DNA strand and attached to the -OH group. the pyrophosphate ion is released and the bond is broken releasing energy.
what does it mean that DNA replication is semi-conservative?
This means that the two parental strands separate and each makes a new copy of itself. it is catalysed by DNA polymerase. It requires an RNA primer to start.
what do the names of bases become when its in nucleosides?
adenosine cytidine guanosine thymidine uridine
what are the DNA and RNA building blocks?
dATP, dTTP. dGTP, dCTP
ATP, TTP, GTP, CTP
Describe RNA / RNA polymerases
made up of RNA polymerases which is a multi-subunit complex
eukaryotic cells have 3 types of RNA polymerase pol 1, pol 2 and pol 3.
pol 2 is used in the synthesis of all mRNA
what do TATA boxes?
The TATA box is present about 25 nucleotides before the initiation site. The TATA box binding protein (TBP) is part of the TF2D general transcription factor which recognises the TATA box and introduces a kink in the DNA to determine start and direction. it also provides a landing platform for other transcription factors and RNA polymerase.
what do promoters do?
RNA polymerases bind promoters which initiates transcription. The promoter is not a protein it is a DNA sequence marking the start of a gene.
what is transcription elongation/ what happened?
A transcription bubble moves in one direction aiding the DNA, the DNA is unwound in front of the polymerase and rewound behind it.
what happens in termination of transcription?
newly synthesised RNA makes a stem loop structure followed by a stretch of U’s and a specific enzyme cleaves the RNA
what do transcription factors do?
transcription requires specific transcription factors to bind to DNA. these contain two functional domains (DNA binding domain and transcriptional activation domain). They regulate transcription positively or negatively.
how are the ends of mRNA transcripts processed?
GTP ‘cap’ added to the 5’
poly A tail added to 3’ end
what does DNA being degenerative mean?
amino acids can have more than on codon
what does DNA being unambiguous mean?
each codon codes for only one amino acid
what does DNA being nearly universal mean?
all organisms DNA is mostly the same
what do aminoacyl-tRNA synthetases do?
bind amino acids to their corresponding tRNA molecules. uses ATP.
describe ribosomes
they contain four rRNA molecules. they have three tRNA binding sites. E=exit, P=peptidyl, A=aminoactyl
describe initiation
requires initiation factors
GTP is hydrolysed for energy
ribosome binds to the 5’ end of mRNA
moves along mRNA until START codon is found
special ‘initiator’ tRNA base pairs with the START codon
The polypeptide is assembled and initiator tRNA is now located in P site
what are cholesterols functions in health?
- maintains fluidity and structure in plasma membrane
- forms lipid ‘rafts’ that form bridges between receptor proteins and second messengers.
- precursor molecules for bile/ bile acids, vitamin D and steroid hormones.
what is triglycerides functions in health?
-highly concentrated in energy stores.
how are lipids carried around the body?
- they require specialised proteins to carry them called lipoproteins.
what are the different types of lipoproteins?
- VLDL (very low density lipoproteins)
- IDL (intermediate)
- LDL (low density)
- HDL (high density - carries cholesterol back from tissues to liver)
what role does cholesterol play in atherosclerosis?
cholesterol is transported away from the tissues (VLDL, IDL, LDL) and towards them (HDL). the two exist in balance and if transport away from tissues is more then cholesterol accumulates in vessels leading to atherosclerosis.
What happens in the blood vessels in atherosclerosis?
inflammation > increased endothelial permeability > fatty streaks form (initially leukocytes and lipid, then later smooth muscle) >progresses to intermediate and advanced lesions > forms fibrous cap that walls off lesion from lumen > rupture or ulceration of fibrous plaque leads to thrombosis.
what do statins do?
- lower cholesterol and reduce risk of atherosclerosis
- much more
