IB Biology HL: DNA Protein Synthesis Review
(AHL Topic 7.1-7.4)
7.1 DNA Structure
1. Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding between purines and pyrimidines
§ The carbon atoms in deoxyribose are numbered, with the nitrogenous bases attach to ____ and the phopshate group is attached to _____
§ Nucleotides are joined by a covalent ______bond between the _____phosphate group and the _____hydroxyl group
§ Hence one nucleotide strand runs ______
§ Adenine (A) and thymine (T) share _____ hydrogen bonds
§ Guanine (G) and cytosine (C) share _____ hydrogen bonds
§ In order for the bases to associate (i.e. face each other), one strand must run ______to the other (this antiparallel strand runs ______)
§ Double stranded DNA forms a double helix, with ______nucleotides per turn and the structure containing both ______
Structural Organisation of DNA
7.1.2 Outline the structure of nucleosomes
§ The DNA double helix contains major and minor grooves on its outer diameter, which expose chemical groups that can form ______
§ The DNA of eukaryotes associates with proteins called ______
§ DNA is wound around an ______of histones (146 bases and 1.65 turns of the helix per octamer)
§ The octamer and DNA combination is secured to a ______, forming a ______
7.1.3 State that nucleosomes help to supercoil DNA and help to regulate transcription
Nucleosomes serve two main functions:
§ They ______from damage
§ They allow long lengths of DNA to be packaged (______) for mobility during mitosis / meiosis
§ When supercoiled, DNA is ______
§ Cells will have some segments of DNA permanently supercoiled (______) and these segments will differ between different cell types
7.1.4 Distinguish between unique or single copy genes and highly repetitive sequences in nuclear DNA
§
7.1.5 State that eukaryotic genes contain introns and exons
· Intron:A ______sequence of DNAwithina gene (intervening sequence) that is ______by enzymes when RNA is made into mature mRNA
· Exon:The part of the gene which ______(expressing sequence)
· ______DNA contains introns but ______DNA does not
7.2 DNA Replication
7.2.1 State that DNA replication occurs in a 5' - 3' direction
§ DNA replication is ______, meaning that a new strand is synthesized from an original template strand
§ DNA replication occurs in a 5' - 3' direction, in that new nucleotides are added to the ______such that the strand grows from the _____ end
§ This means that the DNA polymerase enzyme responsible for adding new nucleotides moves along the original template strand in a ______direction
Direction of DNA Replication
7.2.2 Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates
§ DNA replication is semi-conservative and occurs during the ______of interphase
§ ______unwinds and separates the double stranded DNA by breaking the ______between base pairs
§ ______synthesizes a short RNA primer on each template strand to provide an attachment and initiation point for DNA polymerase III
§ ______addsdeoxynucleoside triphosphates(______) to the _____ end of the polynucleotide chain, synthesizing in a ______direction
§ The dNTPs pair up opposite their ______base partner (A-T, C-G)
§ As the dNTPs join with the DNA chain, two phosphates are ______, releasing the energy needed to form a ______bond
§ Synthesis is continuous on the strand moving ______the replication fork (______strand)
§ Synthesis is discontinuous on the strand moving ______the replication fork ______strand) leading to the formation of______
§ ______removes the ______and replaces them with ______
§ ______joins the Okazaki fragments together to create a continuous strand
Overview of DNA Replication
7.2.3 State that DNA replication is initiated at many points in eukaryotic chromosomes
§ Because eukaryotic genomes are (typically) ______than prokaryotic genomes, DNA replication is initiated at ______simultaneously in order to limit the time required for DNA replication to occur
§ The specific sites at which DNA unwinding and initiation of replication occurs are called ______and form replication bubbles
§ As replication bubbles expand in both directions, they eventually fuse together, and generate two separate ______.
7.3 Transcription
7.3.1 State that transcription is carried out in a 5' - 3' direction
· Transcription is carried out in a 5' - 3' direction (of the new RNA strand)
7.3.2 Distinguish between the sense and antisense strands of DNA
· DNA consists of two polynucleotide strands, ______of which is transcribed into RNA
§ The______is transcribed into RNA
§ Its sequence will be complementary to the RNA sequence and will be the "DNA version" of the ______
§ The______is not transcribed into RNA
§ Its sequence will be the "DNA version" of the ______(identical except for T instead of U)
7.3.3 Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator
A gene is a sequence of DNA which is transcribed into RNA and contains three main parts:
§ Promoter:Responsible for the ______(in prokaryotes, a number of genes may be regulated by a single promoter - this is an ______)
§ Coding Sequence:The sequence of DNA that is actually ______Terminator:Sequence that serves to ______(mechanism of termination differs between prokaryotes and eukaryotes)
Transcription is the process by which a DNA sequence (gene) is copied into a complementary RNA sequence and involves a number of steps:
§ RNA polymerase binds to the promoter and causes the unwinding and separation of the DNA strands
§ ______(NTPs) bind to their complementary bases on the antisense strand (uracil pairs with adenine, cytosine pairs with guanine)
§ RNA polymerase covalently binds the NTPs together in a reaction that involves the ______to gain the required energy
§ RNA polymerase synthesizes an RNA strand in a 5’ – 3’ direction until it reaches the terminator
§ At the terminator, RNA polymerase and the newly formed RNA strand both detach from the antisense template, and the DNA rewinds
§ ______is necessary in eukaryotes
Overview of Transcription
7.3.4 State that eukaryotic RNA needs the removal of introns to form mature mRNA
§ Eukaryotic genes may contain non-coding sequences called ______that need to be removed before mature mRNA is formed
§ The process by which introns are removed is called ______
§ The ______(alternative splicing) can generate different mRNA transcripts (and different polypeptides) from a single gene
7.4 Translation
7.4.1 Explain that each tRNA molecule is recognized by a tRNA-activating enzyme that binds a specific amino acid to the tRNA using ATP for energy
§ Each different tRNA molecule has a unique shape and chemical composition that is recognized by a specific ______
§ The enzyme (aminoacyl-tRNA synthetase) first binds the ______to a molecule of ______(to form an amino acid-AMP complex linked by a high energy bond)
§ The amino acid is then transferred to the ______of the appropriate tRNA, attaching to a terminal ______sequence on the acceptor stem and releasing the ______molecule
§ The tRNA molecule with an amino acid attached is thus said to be '______' and is now capable of participating in translation
§ The energy in the bond linking the tRNA molecule to the amino acid will be used in translation to form a ______between adjacent amino acids
7.4.2 Outline the structure of ribosomes, including protein and RNA composition, large and small subunits, three tRNA binding sites and mRNA binding sites
§ Ribosomes are made of ______(for stability) and ______(rRNA - for catalytic activity)
§ They consist of two subunits:
- The small subunit contains an ______binding site
- The large subunit contains three ______binding sites - an aminacyl (___) site, a peptidyl (___) site and an exit (___) site
§ Ribosomes can be either found freely in the ______or bound to the ______(in eukaryotes)
§ Ribosomes differ in size in eukaryotes and prokaryotes (eukaryotes = ___ ; prokaryotes = ___)
7.4.3 State that translation consists of initiation, elongation, translocation and termination
Translation occurs in four main steps:
§ Initiation:Involves the assembly of an active ______
§ Elongation:New amino acids are brought to the ribosome according to the ______sequence
§ Translocation:Amino acids are translocated to a growing ______
§ Termination:At certain "______" codons, translation is ended and the polypeptide is released
7.4.4 State that translation occurs in a 5' - 3' direction
§ The start codon (______) is located at the ____ end of the mRNA sequence and the ribosome moves along it in the ___ direction
§ Hence translation occurs in a 5' - 3' direction
7.4.5 Draw and label a diagram showing the structure of a peptide bond between two amino acids
7.4.6 Explain the process of translation, including ribosomes, polysomes, start codons and stop codons
Pre-Initiation:
§ Specific tRNA-activating enzymes catalyse the attachment of amino acids to tRNA molecules, using ATP for energy
Initiation:
§ The small ribosomal subunit binds to the 5' end of mRNA and moves along it until it reaches the start codon (AUG)
§ Next, the appropriate tRNA molecule binds to the codon via its anticodon (according to complementary base pairing)
§ Finally, the large ribosomal subunit aligns itself to the tRNA molecule at its P-site and forms a complex with the small ribosomal subunit
Elongation:
§ A second tRNA molecule pairs with the next codon in the ribosomal A-site
§ The amino acid in the P-site is covalently attached via a peptide bond to the amino acid in the A-site
Translocation:
§ The ribosome moves along one codon position, the deacylated tRNA moves into the E-site and is released, while the tRNA bearing the dipeptide moves into the P-site
§ Another tRNA molecules attaches to the next codon in the newly emptied A-site and the process is repeated
§ The ribosome moves along the mRNA sequence in a 5' - 3' direction, synthesizing a polypeptide chain
§ Multiple ribosomes can translate a single mRNA sequence simultaneously (forming ______)
Termination:
§ Elongation and translocation continue until the ribosome reaches a stop codon
§ These codons do not code for any amino acids and instead signal for translation to stop
§ The polypeptide is released and the ribosome disassembles back into subunits
§ The polypeptide may undergo post-translational modification prior to becoming a functional protein
Overview of the Process of Translation
7.4.7 State that free ribosomes synthesis proteins for use primarily within the cell, and that bound ribosomes synthesis proteins primarily for secretion or for lysosomes
§ Ribosomes floating freely in the cytosol produce proteins for use within the cell
§ Ribosomes attached to the rough ER are primarily involved in producing proteins to be exported from the cell or used in the lysosome
§ These proteins contain a ______on their nascent polypeptide chains which direct the associated ribosome to the rough ER