21 terms

DNA, RNA, Proteins, Enzymes

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Explain how polar and non-polar amino acids help channel proteins and enzymes carry out their functions.
non-polar amino acids cause channel proteins to embed in a membrane;
-polar amino acids at either end cause channel proteins to be transmembrane;
-polar amio acids lining pore allow polar particles to pass through;
-polar amino acids on the surface of the enzyme allow it to dissolve in water;
-polar and non-polar amino acids contribute to the specificity of an enzyme;
-non-polar amino acids of surface of the enzyme allow it to embed in a membrane;
-polar amino acids at active site of enzyme attract polar substrates and vice versa
Compare competitive and non-competitive inhibition of enzymes.
Competitive Inhibition:
-substrate and inhibitor are same shape
-inhibitor binds to the active site
-inhibitor does not change the shape of the active site
-increases in sub. concentration reduce the inhibition
-example: succinate
Non-Competitive Inhibition/Allosteric:
-substrate and inhibitor are not the same shape
-inhibitor binds away from active site
-inhibitor changes the shape of the active site
-increases in sub. concentration do not affect inhibition

Both:
-both reduce enzyme activity
-bind to the enzyme
-prevent the substrate from binding to active site
Structure of a ribosome. (4 marks)
small subunit and large subunit;
mRNA binding site on small subunit;
three tRNA binding sites (A,P,E);
protein and RNA composition
Fibrous vs. globular proteins (6 marks)
Fibrous Proteins:
-strands/sheets
-are usually insoluble
-have structural roles
-example: keratin, fibrin, collagen, actin, myosin

Globular Proteins:
-more sensitive to changes in pH/temperature
-rounded proteins, soluble
-used for catalysis/transport
-example: insulin, hemoglobin
Functions of proteins (4 marks)
structure-collagen;
transport-hemoglobin;
movement-actin;
hormones-insulin;
storage-albumin;
antibodies-immunoglobin
Explain the process of transcription leading to the formation of mRNA. (8 marks)
RNA polymerase binds to a promoter on the DNA;
unwinding of the DNA strands;
binding of nucleoside triphosphates to the antisense strand of DNA along a 5' to 3' direction;
using complementary base pairing;
losing two phosphates to gain the required energy, until a terminator signal is reached;
RNA detaches from the template and the DNA rewinds;
RNA polymerase detaches from DNA;
introns have to be removed in eukaryotes to form mature RNA.
DNA strand structure (4 marks)
-one nucleotide with deoxyribose linked to base and phosphate
-complementary bases labelled
-hydrogen bonds between bases
Outline the structure of a nucleosome.
eight histone proteins;
DNA wrapped around histones;
further histone holding these together
Primary and tertiary structures of a protein. (3 marks)
primary structure is a sequence of amino acids;
joined by peptide bonds;
tertiary structure is the folding of the polypeptide structure/alpha helix;
stabilized by disulfide bridges/hydrogen bonds/hydrophobic interactions;
tertiary structure gives three dimensional shape and purpose
Outline condensation and hydrolysis reactions.
condensation reactions involve joining subunits with the release of water;
hydrolysis reactions involve splitting molecules into subunits with the addition of water;
Outline the effect of temperature and substrate concentration of the activity of enzymes.
enzymes most active at optimum temperature;
any deviation lowers enzyme activity;
denaturing in active site at high temperatures;
increasing substrate concentration increases enzyme activity (more collisions between substrate and enzyme);
eventually no increase in enzyme activity with increased substrate concentration (all are saturated)
Explain the control of metabolic pathways.
metabolic pathway is a series of reactions carried out in a particular sequence;
products of one reaction become substrate for the next;
each reaction is enzyme catalyzed;
some enzymes are allosteric;
negative feedback;
end product acts as the inhibitor of beginning enzyme;
product binding changes the conformation of the active site so substrate of the pathway can no longer bind
DNA vs. RNA
-DNA is double stranded while RNA is single stranded
-DNA contains deoxyribose and RNA contains ribose
-thymine found in DNA and uracil in RNA
-one form of DNA but several forms of RNA (mRNA, tRNA, rRNA)
Explain the process of DNA replication (8 marks)
-occurs during S phase of interphase
-DNA replication is semi-conservative
-unwinding of double helix by helicase
-hydrogen bonds between two strands are broken
-each strand of parent DNA is used as a template for synthesis-synthesis is continuous on leading strand but not lagging strand
-leading to the formation of Okazaki fragments on the lagging strand where replication occurs in 5' to 3' direction
-RNA primer synthesized on parent DNA using RNA primase
-DNA polymerase III adds the nucleotides to the 3' end
-added according to complementary base pairs
-adenine with thymine, cytosine with guanine
-DNA polymerase I removes the RNA primer and replaces them with DNA
-DNA ligase joins Okazaki fragments
-two phosphates broken off releasing energy to form bond
Outline how enzymes catalyze reactions (7 marks)
-increase the rate of chemical reactions
-remains unchanged at end of reaction
-lower activation energy
-activation energy is needed to overcome energy barrier that prevents reaction
-substrate joins with enzyme at the active site to form enzyme-substrate complex
-active site specific for particular substrate
-enzyme binding with substrate brings reactants closer together to facilitate chemical reactions
-induced fit model/change in enzyme conformation
-making substrate more reactive
Explain how translation is carried out (9 marks)
-involves initiation, elongation, translocation and termination
-mRNA binds to the small subunit of ribosome
-ribosomes slide along mRNA to the start codon
-anticodon of tRNA pairs with codon on mRNA
-complementary base pairing
-anticodon of tRNA with AUG (start codon)
-second tRNA pairs with next codon
-peptide bond forms between amino acids
-ribosome moves along the mRNA by one codon
-movement in 5' to 3' direction
-tRNA that lost amino acid detaches, another tRNA moves into A site
-tRNA activating enzymes
-link amino acids to specific tRNA
-stop codon eventually released
Explain the significance of complementary base pairing for replication, transcription, and translation.
A-T and C-G in DNA;
A-U and C-G in RNA;
complementary base pairing in replication ensures identical nucleotide sequence of new complementary strands;
semi-conservative replication;
transcription produces RNA sequence complementary to the
DNA sequence (of the gene);
triplets of nucleotides on mRNA are codons;
translation converts mRNA sequence of information into a
specific amino acid chain (polypeptide);
(each class of) tRNA carries a specific triplet of (three) bases
called an anticodon;
anticodons bind to codons by complementary base pairing;
(each class of) tRNA with specific complementary anticodons
carry specific amino acids;
sequence of mRNA codons translates into specific amino acid
sequence;
enables conservation of information transfer from DNA to RNA to polypeptide;
Describe the genetic code (6 marks)
-composed of mRNA base triplets called codons
-64 different codons
-each codes for the addition of an amino acid to a growing polypeptide chain
-the genetic code is degenerate
-meaning more than one codon can code for a partiuclar amino acid
-the genetic code is universal
-meaning it is the same in almost all organisms
-(AUG is the) start codon
-some (nonsense) codons code for the end of translation
The role of mRNA, tRNA and ribosomes in translation
mRNA with genetic code/ codons
tRNA with anticodon
tRNA with amino acid attached
ribosome with two sub-units
mRNA held by ribosome
start codon
two tRNA molecules attached with mRNA on ribosome
peptide bond between amino acids on tRNA
polypeptide forms
continues until a stop codon is reached
polypeptide is released
Structure of tRNA
tRNA is composed of one chain of (RNA) nucleotides
tRNA has a position/end/site attaching an amino acid (reject tRNA contains an amino acid)
at the 3' terminal / consisting of CCA/ACC
tRNA has an anticodon
anticodon of three bases which are not base paired / single stranded / forming part of a loop
tRNA has double stranded sections formed by base pairing
double stranded sections can be helical
tRNA has (three) loops (somethimes with an extra small loop)
tRNA has a distinctive three dimensional / clover leaf shape
transcription vs translation
both in 5` to 3` direction
both require ATP
DNA is transcribed and mRNA is translated
transcription produces RNA and translation produces polypeptides/ protein
RNA polymerase for transcription and ribosomes for translation/ ribosomes in translation only
transcription in the nucleus (of eukaryotes) and translation in the cytoplasm/ at ER
tRNA needed for translation but not transcription
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