IB Bio 7.1

What type of bonds are between two base pairs?

Hydrogen Bonds

DNA Polymerase I

replaces RNA primers with DNA nucleotides

Single Copy Genes

sequences that code for proteins, exons are an example, 1-5% of genome, low rate of mutation, similar among individuals, may be translated

Enhancer Sequences

sequences that increase the rate of transcription (when a protein is bound to it)

Guanine (G) and cytosine (C) have how many hydrogen bonds?

share 3 hydrogen bonds

3) What are Okazaki fragments?

short sections of DNA formed during DNA replication

Tandem Repeat Sequences

short sequences of non-coding DNA, normally a length of 2-5 base pairs, that are repeated multiple times in a head-tail manner, helps with DNA profiling

Gel Electrophoresis

shows separation of bases by the length of the DNA fragment (largest to smallest). The fluorescent dye marks the last base in each fragment -- The template strand is complementary to what is on the gel

Leading strand

strand produced

Polymerase Chain Reaction (PCR)

technology in molecular biology used to amplify a single copy or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence

DNA Replication moves in what direction? why?

the 5' to 3' direction (this means the 5' end of the new strand) because the phosphate group of new DNA nucleotides is added to the 3' carbon of the deoxyribose of nucleotide at end of chain.

PCR: Denaturation

the DNA stars is heated to break the hydrogen bonds and pull the strands apart

Adenine (A) and thymine (T) have how many hydrogen bonds?

they share 2 hydrogen bonds

How are Tandem repeats used in DNA profiling?

they vary greatly in terms of the different number of copies of the repeat element that can occur in a population, allowing for identification

What does it mean to supercoil DNA?

this means the DNA has been back on itself multiple times so the DNA is condensed

DNA Helicase

unwinds and separates the double strand of DNA by breaking the hydrogen bonds between base pairs

Exon

The part of the gene which codes for a protein (expressing sequence)

What are nucleosomes composed of?

- a double strand of DNA -histone proteins combined together in groups of 8 to form a bead like structure -the strand of DNA takes two turns around this bead before continuing onto the next one -it is held in place on the bead by a ninth histone

Explain 3'-5' linkage

-carbon 3 is where next nucleotide attaches in one direction -carbon 5 has a phosphate group attached to it, which is where next nucleotide attaches in other direction This means that each nucleotide is linked to those on either side of it through carbons 3 and 5.

Describe the carbon composition in the sugar

-numbered from 1 to 5 in a clockwise direction starting after the oxygen at the apex -base is attached to carbon 1

1) Explain the process of DNA replication

-occurs during (S phase of) interphase -DNA replication is semi conservative -unwinding of double helix /separation of strands by helices -hydrogen bonds between two strands are broken -each strand of parent DNA used as template for synthesis -synthesis is continuous on leading strand but not on lagging strand -leading to formation of Okazaki fragments (on lagging strand) synthesis occurs in 5'-3' direction -DNA polymerase III adds the nucleotides (to the 3' end) according to complementary base pairing -adenine pairs with thymine and cytosine pairs with guanine -once Okazaki fragments are assembled, enzyme called DNA ligase attaches the sugar-phosphate backbones of the lagging strand fragments to form a single DNA strand

What are antiparallel strands?

-strands where the deoxyribose molecules are oriented in opposite directions -strand that runs 5'-3'

What does a DNA nucleotide consist of?

-the sugar deoxyribose -to which are attached a phosphate group and a nitrogenous base

For Prokaryotes, DNA Replication is initiated at

a single point

How are nucleosomes formed?

by wrapping DNA around histone proteins

Single Stranded Binding Proteins

hold unzipped, single stranded sections of DNA apart during replication (so that the nucleotides can bind)

Silencers

inhibit transcription

DNA Primase initiates beginning of replication

initiates beginning of replication

Highly Repetitive Sequences

introns are a kind of HRS, makes up 5-45% of genome, high rate of mutation, varies widely among individuals, never translated

DNA Ligase

joins Okasaki fragments on lagging strand

DNA Polymerase III

links nucleotides together to form a new (complementary) strand, using the pre-existing strand as a template

Telomeres

located at the end of chromosomes and contain highly repetitive DNA, they protect the DNA molecule from degradation during replication since DNA cannot be replicated all the way to the ends (thus preventing loss of important genes)

For Eukaryotes, DNA Replication is initiated at

many points

DNA Sequencing: How do you determine the sequence of bases in a genome?

many unknown copies of DNA (to be sequenced) are added to a test tube with deoxyribonucleic acids (fluorescent dye markers attached) and other enzymes to carry out replication

DNA Gyrase (topoisomerase)

moves in advance of helicase and relieves strand's strain and prevents supercoiling on the separated strands

Lagging strand

other new strand that forms more slowly

heterochromatin*

permanently supercoiled DNA, allows for cell specialization

Nucleosomes...

protect DNA and allow it to be packaged, making DNA supercoiled

RNA Primers

provide an attachment and initiation point for DNA Polymerase III (one in leading strand, multiple in lagging strand)

Purines

Adenine and Guanine, two rings

Promoter Sequences

Attachment points for RNA Polymerase adjacent to the gene, Responsible for the initiation of transcription

2) Which enzyme removes the RNA primer during replication?

DNA polymerase I

5) What happens during the formation of Okazaki fragments?

DNA polymerase III adds nucleotides in the 5'-3' direction

PCR: Annealing

DNA sample is cooled allowing primers to attach to opposite ends of the target sequence

RNA vs. DNA (four differences)

Different sugars, number of strands, type of pentose sugar, uracil/thymine

What did Watson and Crick discover from Franklin's information?

Phosphate groups are on the outside of the DNA, and the nitrogen bases were hydrophobic and on the inside

PCR: Elongation

a heat tolerant DNA-Polymerase (taq) copies the strands

DNA strands can ONLY be assembled in the

5' to 3' direction because of action of polymerase -DNA polymerase can only add nucleotide to the 3' end of a primer

Intron

A non-coding sequence of DNA within a gene (intervening sequence) that is cut out by enzymes when RNA is made into mature mRNA

What type of bond is between the phosphate and the sugar?

Covalent Bonds (stronger than hydrogen bonds)

What type of bonds are between nitrogen bases and sugars?

Covalent Bonds (stronger than hydrogen bonds)

What did the Hershey-Chase experiment prove?

DNA is genetic material

What happens during a Condensation Reaction?

Nucleotides are linked into a single strand, leaves water

Who discovered that the DNA was shaped like a double helix?

Rosalind Franklin

What did Meselson and Stahl discover?

They used DNA as a template to replicate itself and discovered that DNA is semi-conservative

How many hydrogen bonds are between Guanine and Cytosine?

Three

Pyrimidines

Thymine and Cytosine, one ring

4) What is the reason for Okazaki fragments being formed during DNA replication?

To enable replication of the 3' - 5' (lagging) strand

How many hydrogen bonds are between Adenine and Thymine?

Two