unit 2 Flashcards
what’s the difference between nucleotides and nucleosides?
- nucleotides are composed of 3 parts: sugar/phosphate/heterocyclic base
- nucleosides are composed of 2 parts: sugar + heterocyclic base
what is the function of nucleic acids?
store genetic information
what’s the difference between DNA & RNA
what types of bases are there
monocyclic pyrimidines: cytosine/thymidine/uracil
bind at n1
aromatic
bicyclic purines: adenine/guanine
bind at n9
aromatic
organize from polymer to smallest monomer
1- nucleotides
2-nucleoside
3-nucleic acids
nucleic acids > nucleotides > nucleosides
what is the function of phosphate in nucleotides?
it is able to form stable bonds between molecules and builds new active molecules upon increasing phosphate bonds
what are the properties of phosphate?
- good leaving groups
- stable anions
why is it that ATP has high reactivity?
because phosphates are stable anions and good leaving groups, thus they are able to be attacked fromhard or soft nucleophiles from the ch2 group
why is DNA so named?
because the 2’ position at the ribose ring is vacant, lacking a hydroxyl group, therefore it is known as 2-deoxyribonucleic acid
why is it that purine must bind to pyrimidine in nucleic acids?
because only the combination of larger purines and smaller pyrimidines bridges the gap between the nucleic acid coils, allowing each nucleotide to recognize its pair
how are purines connected to pyrimidines?
via 2 or 3 hydrogen bonds of two kinds (amine-carbonyl group) or (amine-imine)
why do cells need to extract energy from sources and store it?
- cells needs to move in the environment;
- to build molecules that require, DNA, proteins and enzymes for cells living,
- reproduction and growth and also energy is involved in transport of ions/molecules in/out of cells, for example balance Na/K to keep isotonic (inside=outside) pressure, to take sugars/aminoacids/vitamins (nutrients) inside the cell
what does ATP consist of?
triphosphate, deoxy-ribose (sugar, OH) and adenine (H).
deoxy-ribose (sugar, OH) and adenine (H) are one of 4 basis DNA called “adenosine”. other bases are ___, _______ &_____
guanosine
cytidine
uridine
what are the energy reach compounds
- guanosine triphosphate (GTP)
- cytidine triphosphate (CTP)
- uridine triphosphate (UTP)
what molecule is this
ATP
where is ATP located in the cell?
cytoplasm
in ATP, 5 carbons are bound to oxygen of phosphate to form phosphate ester bond and other bonds are _________
phosphoanhydride bonds
describe bonding in ATP
1 phosphate ester bond formed by linkage between the alpha-phosphoryl group to the 5’-oxygen of ribose and Phosphoanhydride bonds formed by alpha, beta and beta, gamma linkages between phosphoryl groups. Usually present as complexes magnesium cations.
metabolism is divided into two sets of reactions known as:
anabolic (producing molecules)
catabolic (producing energy)
describe the sequence of catabolic and anabolic processes within the cell
- simple sugars go through glycolysis where sugars are broken down and pyruvate is produced and small amount of ATP.
- Pyruvate is then converted in Acetyl Co enzyme A that enters citric acid cycle (Krebes cycle), where CO2 and electrons are produced and the electrones are transported to the oxidative phosphorylation stage, ATP is produced during oxidative phosphorylation.
- Fats are broken down into glycerine that enters the catabolic routes at glycolysis stage, whereas the fatty acids are broken down and they enter catabolism as acetyl Co enzyme A.
- Proteins are broken down in the amino acids and depending on amino acid they enter catabolism in different places.
true or false
anaerobic reactions produce a small amount of ATP whereas aerobic reactions produce w larger amount
true
For most organisms the main supply of energy is by metabolism of glucose and other sugars. what happens when sugar/glucose is depleted?
Metabolism of fats and proteins becomes more important for energy production when the supply of glucose and other sugars is limited.
what is the initial stage of metabolism known as?
glycolysis
- it takes place in the cytoplasm
- it does not require oxygen
- it is not efficient
- the reaction also produces two molecules of NADH (Nicotinamide Adenine Dinucleotide)
what are the types of reactions in glycolysis
Type 1: Phosphoryl transfer
Type 2: Phosphoryl shift
Type 3: Isomerisation
Type 4: Dehydration
Type 5: Aldol cleavage
Type 6: Oxidation
what are the two parts of glycolysis?
- the first reactions with 6 carbon units which requires energy (hexose stage)
- the reactions on the 3 carbon units which provides energy (triose stage)
The end product of glycolysis is _______
Pyruvate.
Pyruvate can have several different fates, what are they?
- conversion to acetyl coenzyme A
- conversion to lactate
- conversion to ethanol.
briefly describe how ATP is generated in glycolysis
During glycolysis, glucose ultimately breaks down into pyruvate and energy; a total of 2 ATP is derived in the process (Glucose + 2 NAD+ + 2 ADP + 2 Pi –> 2 Pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O). The hydroxyl groups allow for phosphorylation. The specific form of glucose used in glycolysis is glucose 6-phosphate
in which reactions is acetyl coA used?
krebs cycle
electron transport chain
where does acetyl coA form?
in the mitochodria
what is pyruvate converted to when fermented?
ethanol
where does the citric acid cycle occur
mitochondria
true or false
citric acid cycle is aerobic
true
•During the citric acid cycle the acetyl CoA is fully oxidised to _______
carbon dioxide and water.
The krebs cycle can be divided into a number of parts
- 6-Carbon atoms
- 5-Carbon atoms
- 4-Carbon atoms
explain what happens in krebs cycle
it’s easier when take it bit by bit, try mnemonics maybe?
there’s plenty on the internet
I really liked this source
(453) KREBS CYCLE MADE SIMPLE - TCA Cycle Carbohydrate Metabolism Made Easy - YouTube
what are the products of krebs cycle?
- 3 molecules of NADH
- 1 molecule of FADH2 (Flavin Adenine Dinucleotide)
- 1 molecule of GTP
what is the product of krebs cycle as a biosynthetic intermediate
- carbs
amino acids
urea
pyrimidine nucleotides
what is oxidative phosphorylation
process by which NAD reacts with FADH2 to produce ATP
each molecule of NAD produces (a) _____ ATP
each molecule of FADH2 produces (b) ________ ATP
during oxidative phosphorylation
a- 3
b- 2
each molecule of glucose gives rise to 36 ATP molecules in which 32 of them are produced during _________
oxidative phosphorylation
where is ADP located within the mitochondria?
in the innermembrane
what is the site of oxidative phosphorylation?
inner membrane of the mitochondria
where is the site of citric acid cycle and fatty acid oxidation
matrix of the mitochondria
protons are pumped out of the membrane creating gradient between inside and outside and this gradient is used by __________ enzyme to perform the synthesis of ATP from ADP.
ATP synthetize
Electrons are transferred from NADH (or FADH2) to _________ by the electron transport chain.
molecular oxygen
what are the four protein complexes of the electron transport chain
- NADH–ubiquinone oxidoreductase (Complex I)
- Succinate-ubiquinone oxidoreductase (Complex II)
- Ubiquinol- cytochrome c oxidoreductase (complex III)
- Cytochrome c oxidase (Complex IV)
what are the two electron carriers of the krebs cycle?
- ubiquinone
- cytochrome c
what are the properties of glycosides? (s-/n-acetals/o-)
increase solubility and permeability through membranes which helps in the expulsion of particles from the cell
bases bind to sugars through a ________ bond at c1 and this bond is often beta
n-glycoside
what’s the difference between alpha and beta glycosidic bonds?
OR bond lies down in alpha
OR bond lies up in beta
what type of bond is phosphate bound at 5’ and 3’ positions?
phosphodiester
define DNA
long unbranched chain of oligonucleotides which are linked via a phosphate group that joins the sugar with the base
what type of bond binds nucleotides together
phosphodiester bond (ester linkage), it links one nucleotide from 5’ to 3’
why is the DNA of some organisms circular?
because the 5’ and 3’ ends bind to each other, thus forming circular DNA
what are the DNA base pairs
A-T
C-G
what are the properties of bases in DNA
they are able to form hydrogen bonds between each other which makes them able to translate, transcribe, and have double helix character
what is the function of minor and major grooves in DNA
These grooves allow proteins to bind to and recognize DNA sequences from the outside of the helix. The grooves expose the edges of each base pair located inside the helix, which allows proteins to chemically recognize specific DNA sequences.
how do major/minor grooves form in DNA
Since the glycoside bonds between the sugars and bases of a particular base pair are not directly opposite to each other, grooves along the outside of the double helix array are unequal in with giving rise to what is known as the minor groove and major groove.
DNA replication proceeds in three enzymatically mediated steps, what are they?
- initiation
- elongation
- termination
where does the initiation process occur?
at the origins, which contain replicons that have specific DNA sequences where DNA replication starts
what is an initiator
specific DNA binding protein whose task is to recruit additional factors to open the double stranded chromosomal DNA and start synthesis
what do DNA polymerase do
responsible for copying DNA and catalyse nucleotide polymerization exclusively in a 5’ to 3’ direction
