Biology 2.6, 2.7 and 7.1 and 7.2

What is a nucleotide?

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base

What is DNA?

deoxyribonucleic acid

What is RNA?

Ribonucleic acid = single-stranded nucleic acid that contains the sugar ribose

What is the difference between DNA and RNA?

DNA is double stranded and RNA is single stranded
RNA has a ribose pentose sugar
DNA has a deoxyribose pentose sugar
DNA = adenine, thymine, cytosine and guanine
RNA = adenine, uracil, cytosine, guanine

What are nucleic acid? And how are they linked together?

nucleic acids are genetic material of the cell composed of recurring monomers called nucleotides that link together via condensation reactions to form phosphodiester bonds (covalent) (water is a by-product) - result in polynucleotide strands

How are the two DNA strands held together?

hydrogen bonds between the complimentary nitrogenous bases

What are the complimentary base pairs?

Adenine, Thymine,
Cytosine, Guanine

How many H bonds between A and T?

2 hydrogen bonds (A, T, 2)

How many H bonds are between C and G?

3 Hydrogen bonds ( C, G, 3)

What do sugar and phosphate form?

sugar-phosphate backbone, with the nitrogenous bases in the centre. (backbone is hydrophilic so water loving) phosphate groups are very reactive so are protected by the sugar phosphate backbone.

what is a purine?

adenine and guanine
it has 2 rings
Larger nucleotide with a double ring (halo (double ringed)

What is a pyrimidine?

single-ringed nitrogenous base
Cytosine, thymine, Uracil (y in pyrimidine and also thymine and cytosine and uracil is replacement for thymine)

what do purines pair with?

pyrimidines
double ring always pair with single ring

Who discovered the structure of DNA?

Crick and Watson, found double helix structure,
helped by other scientists eg: Rosalind Franklin X-ray crystallography discovered helical shape.

What is antiparallel?

two strands held together by hydrogen bonds and double helix with sugar phosphate and nitrogen run along side each other in different directions

When does DNA replication occur?

S phase of interphase
each cell has a genetic identical copy of the DNA

What does semi-conservative mean?

Semi-conservative means that each new copy of DNA consists half of parental DNA and half of a newly synthesized strand of DNA.
(each of the DNA molecules produced contains one old strand and one new strand)

What direction does DNA replication occur?

5' to 3' direction
DNA replication is initiated t many points in the eukaryotic chromosome, and begins at origin of replication.

Why does semi-conservative DNA replication occur?

template strand= a strand of DNA on which a new strand of DNA is assembled because of complimentary base pairing each of the new strands has the same base sequence as the old strans that was separated from the template strand. The two new DNA molecules produced are identical to each other and the original parent molecule.

What were the alternative models for DNA replication?

Conservative Model - An entirely new molecule is synthesised from a DNA template (which remains unaltered)
Semi-Conservative Model - Each new molecule consists of one newly synthesised strand and one template strand
Dispersive Model - New molecules are made of segments of new and old DNA

What was the Meselson-Stahl experiment?

Experiment to test the possible models of DNA replication. Grew bacteria in heavy Nitrogen, then transferred to light nitrogen. Put in medium and spun. Found that DNA was in the middle. Determined that DNA replicates in a semi-conservative model.

What is Helicase?

enzyme that unwinds and unzips the DNA helix breaking the hydrogen bonds between complementary base pairs

What is DNA polymerase III?

DNA polymerase links nucleotides together to form a new strand using the existing strand ad a template (creates the complimentary strand)

Which way does DNA polymerase move

from 5' to 3' direction

What is the leading strand?

The strand where DNA polymerase moves towards the replication fork (follows helicase) so replication is continuous

What is the lagging strand?

On the other strand DNA polymerases have to be moving in the opposite direction to the replication fork
It adds section of nucleotides then double backs, therefore it undergoes replication discontinuously in small fragments.

What are the stages of DNA replication?

1. DNA gyrase (enzyme) moves in advance to DNA helicase and relieves strains in the DNA molecule that are created when the double helix is uncoiled to prevent the strands forming tight supercoils.

what is the second stage to DNA replication?

DNA helicase unwinds and uncoils the double helix / splits it into two template strands (single stranded binding proteins keep the strands apart for long enough so the template strand can be copied)

what is the third stage to DNA replication?

RNA primase adds short sequence of RNA primer to both strands, the primer allows DNA polymerase 3 to bind and start replication.

what is the fourth stage to DNA replication?

DNA polymerase 3 adds nucleotides to each template strand in the 5' to 3' direction. new nucleotides being added at the 3 prime end.
- Leading strand moves in the same direction as the replication fork, close to helicase
- Lagging strand moves away from the replication form

what is the fifth stage to DNA replication?

Nucleotide triphosphates loose two phosphates to provide energy to build growing chain of nucleotides

what is the sixth stage to DNA replication?

on the lagging strand short lengths of DNA are formed between RNA primers called okazaki fragments

What are Okazaki fragments?

Short lengths of single-stranded DNA made on the lagging strand.

what is the seventh stage to DNA replication?

DNA polymerase 1 removes the RNA primers and replaces them with DNA.

what is the eighth stage to DNA replication?

DNA ligase joins the Okazaki fragments together to form a continuous strand

Labelled diagram of DNA replication

Each new strand is complementary to the template which it was made and identical to the other template. DNA sequence has been conserved

What are the processes of transcription and translation (what formation does it lead to?)

transcription and translation are the two parts that make up protein syntheisis.

Where does transcription occur?

inside the nucleus - DNA never leaves the nucleus (vital that it is kept protected)

What does transcription produce?

makes a copy of DNA in RNA form eg makes mRNA (messenger RNA)
transcription is the copying of the base sequence of a gene by making an RNA molecule

What is RNA?

Provides a means of copying genetic information in the nucleus. Its sugar is ribose, has nitrogen bases A,U,C and G.

what are the three main types of RNA?

mRNA, tRNA, rRNA

What is a polypeptide sequence?

sequence of amino acids in a protein

what is mRNA?

is called messenger RNA
Messenger RNA (mRNA) is a single-stranded RNA molecule that is complementary to one of the DNA strands of a gene. the copy is made of RNA and is carried to the ribosomes in the cytoplasm to give them the information needed to synthesise a polypeptide.
the sequence of DNA determines mRNA which then determines the sequence of connected amino acids

what are the four main stages into synthesising a protein?

DNA - mRNA - Amino Acid - Protein

What direction does transcription occur?

5' to 3' direction

What is a codon?

Three bases that code for one amino acid. ( three nucleotides/nitrogen bases in a row) there are 20 essential amino acids so 4 cubed allows enough amino acids to be synthesized.)

What is RNA polymerase?

- RNA polymerase is an enzyme that binds to DNA during transcription and separates or unwinds the DNA strands.
- RNA polymerase directly controls the process of transcription. and can only transcribe a gene length of DNA at a time.

What is a nucleoside?
What is a nucleotide?

A nucleoside consists of a nitrogenous base covalently attached to a sugar (ribose/deoxyribose) but without a phosphate group
A nucleotide contains a nitrogenous base, a sugar and one to three phosphate groups.

What are the first two step in transcription?

1. RNA polymerase binds to promoter on antisense DNA (template strand) transcription is initiated.
2. RNA polymerase moves along the gene uncoiling and separating the DNA into two single strands

What is the third step in transcription?

Free nucleotides exist in the cell as nucleoside triphosphates (NTPs), which line up opposite their complementary base partner on the template strand

What is the fourth step in transcription?

Nucleosides release energy by losing two phosphate groups and become nucleotides. the nucleotides are added in a 5' to 3' direction.

What is the fifth step in transcription?

RNA polymerase form covalent bonds between nucleotides, continually moving until reaching the terminator. ( they are linked by covalent bonds between the pentose sugar of one nucleotide and the phosphate of the next)

What is the eighth step in transcription?

The DNA strands pair up again and twist back into a double helix.

What is the sixth and seventh step in transcription?

The terminator signals RNA polymerase to stop transcription.
RNA polymerase is released when the end of the gene is reached.

what is a sense strand?

the strand not transcribed into RNA
has the same base sequence as the mRNA except thymine is replaced by uracil)

What is the antisense strand?

the template DNA strand which is transcribed 3'→5' to create mRNA
has the complementary bases to mRNA (template strand)

How can the base sequence of DNA be deduced by the mRNA strand that was tanscribed?

by deciding the complementary base pairs (+ replacing the uracil with thymine)

What are the coding sequences?

the coding sequences are transcribed and translated when a cell requires the protein they code for. Exons
The region of DNA that is transcribed by RNA polymerase is called the coding sequence

What are non-coding sequences?

introns

What are some of the functions of non-coding sequences?

1. Regulating gene expression:
non coding sequences can act as sites where proteins can bind that either promote or repress the transcription on an adjacent gene for example the
Promotor
Terminator

What is the promoter?

- The non-coding sequence responsible for the initiation of transcription
-The core promoter is typically located immediately upstream of the gene's coding sequence
- The promoter functions as a binding site for RNA polymerase (the enzyme responsible for transcription)
-The binding of RNA polymerase to the promoter is mediated and controlled by an array of transcription factors in eukaryotes

What is the terminator?

RNA polymerase will continue to transcribe the DNA until it reaches a terminator sequence

What is another function of non-coding genes (intron)

in many eukaryotes genes the coding-sequence is interrupted by one or more non-coding sequences. These introns are removed from mRNA before it is translated by RNA splicing. called JUNK DNA.

What are telomeres?

Telomeres are stretches of DNA (repetitive base sequences) at the ends of chromosomes. When the DNA of a eukaryote chromosome is replicated, the end of the molecule can't be replicated so a small section of the base sequence is lost. The telomere prevents part of important genes at the end of chromosome from being lost every time the DNA is replicated.

What is another function of non-coding DNA? (genes for tRNA and rRNA)

transcription of these genes produces the transfer RNA used during translation and also the ribosomal RNA that forms much of the structure of the ribosome.

What are tandem repeats?

Regions of a chromosome that contain multiple copies of a core DNA sequence arranged in a repeating fashion. eg: ACACACACAC (two nucleotide repeat = dimeric)
or GATAGATAGATA (four base repeat = tetrameric)

What are nucleosomes?

Globular structures that have a core of eight histone proteins with DNA wrapped around. Nucleosomes help to regulate transcription

What are the functions of nucleosomes?

protect the DNA and allow it to be packaged, this in turn allows the DNA to be supercoiled.
supercoiling = wound up compacted DNA strand

What is an octamer?

contains two copies of four different types of histone proteins

Nucleosomes continued

Nucleosomes are linked by an additional histone proteins to form a string of chromatosomes, these then coil to form solenoid structures (30nm fibres) these fibres then form loops, compressed and folded to scaffold chromatin
the chromatin will then supercoil during cell division to form chromosomes visible under light microscope
Nucleosomes look like beads on a string with DNA wrapped around them.

nucleosomes further

In order to fit DNA into the nucleus, it must be packaged into a highly compacted structure known as chromatin. This is achieved though nucleosome assembly.
The nucleosome is the smallest structural component of chromatin, and is produced through interactions between DNA and histone proteins.

What are epigenetics?

the study of environmental influences on gene expression that occur without a DNA change

Who was Lamarck and what is Lamarckism?

the fundamental theory of modern biology is that characteristics acquired during an individual's life time cannot be inherited by their offspring. However French scientist Lamarck proposed that some of these characteristics can be inherited. This theory is referred to as Lamarckism. This theory has been dismissed and falsified over the years but now there is increasing evidence that the environment can cause heritable changes.

What are chemical markers?

small chemical markers that attach to DNA in the nucleus to fix the pattern of gene expression. these markers are usually passed onto daughter cells formed by mitosis. However most of these are erased during gamete formation, but a small percentage of markers persists and is inherited by offspring.

What is an epigenome?
What are epigenetics?

Epigenome: The pattern of chemical markers established in the DNA
Epigenetics : the research into it

methylation and acetylation

process of adding the groups to DNA or any other molecule

What are methylation and acetylation?

Typically the histone tails have a positive charge and hence associate tightly with the negatively charged DNA
Adding an acetyl group to the tail (acetylation) neutralises the charge, making DNA less tightly coiled and increasing transcription
Adding a methyl group to the tail (methylation) maintains the positive charge, making DNA more coiled and reducing transcription

How does methylation occur?

Cytosine in DNA can be converted to methyl cytosine by the addition of a methyl group.

What does an acetyl group do?

increases transcription

What does adding a methyl group do?

reduces transcription ( inhibits transcription so is a means of switching off expression of certain genes)

What can cause methylation?

Environmental factors can influence the pattern of methylation and gene expression, this can be inherited by daughter cells from mitosis .

What is heterochromatin?

When DNA is supercoiled and not accessible for transcription, it exists as condensed (inactive)

How can patterns of methylation be detected?

Fluorescent markers, have shown patterns that methylation are established during embryo development and reaches a maximum at birth in humans and then decreases during the rest of an individual's life.
at birth identical twins have a very similar pattern of methylation but differences accumulate during their lifetimes (environmental differences) decreasing similarity in twins as the grow older.

what is euchromatin?

When the DNA is loosely packed and therefore accessible to the transcription machinery. less condensed. Different cell types will have varying segments of DNA packaged as heterochromatin and euchromatin Some segments of DNA may be permanently supercoiled, while other segments may change over the life cycle of the cell

what influences epigenetics?

diet, pathogen exposure,
It is influenced by heritability but is not genetically pre-determined

What is the structure of ribosomes?

- ribosomes are made of protein (for stability) and ribosomal RNA (for catalytic activity) rRNA
- They consist of a large and small subunit:
The small subunit contains an mRNA binding site
- The large subunit contains three tRNA binding sites - an aminoacyl (A) site, a peptidyl (P) site and an exit (E) site.
Only 2 tRNA molecules can binf to the ribosome at one time.

where can ribosomes be found?

Ribosomes can be found either freely floating in the cytosol (synthesize proteins primarily for use within the cell)
or bound to the rough ER (in eukaryotes) (synthesize proteins for secretion from the cell of for use in lysosomes)
Ribosomes differ in size in prokaryotes and eukaryotes (prokaryotes = 70S ; eukaryotes = 80S)

what does the A site do?

first site the tRNA binds to
holds the tRNA that carries the next amino acid to be added to the chain

What does the P site do?

holds the tRNA that carries the growing polypeptide chain

What does the E site do?

the exit site, where discharged tRNAs leave the ribosome

What is the structure of tRNA?

-double- stranded sections with base pairing
- a triplet of bases called the ANTICODON in a loop of seven bases plus two other loops.
The anticodon associates with the mRNA codon (via complementary base pairing)
- The base sequence at the 3 prime terminal, which forms a site for attaching an amino acid

how are tRNA substrate specific?

the base sequence of tRNA molecules varies causing variable features in its structure. Each has a distinctive 3D shape + chemical properties.
This allows the correct amino acid to be attatched at the 3 prime terminal by an enzyme called tRNA activating enzyme. there are 20, one for each amino acid. Each of these enzymes attaches one particular amino acid to each of the tRNA molecules that have an anticodon corresponding to that amino acid. tRNA enzyme recognises the tRNA by it's specific shape an chemical properties. example of Enzyme-Substrate specificity.

How many tRNA activating enzymes are there?

20 different enzymes one for each of the amino acids

How does energy of the ATP allow attachment of amino acid to tRNA?

Energy from ATP is needed for the attachment of amino acids to tRNA. ATP and the appropriate amino acid and tRNA bind to the active site on the activating enzyme. A pair of phosphates is released from ATP and the remaining AMP bonds to the amino acid, raising its energy level.

What does this energy allow it to do?

This energy allows the amino acid to bond to the tRNA. The energy from ATP later allows the amino acid to be linked to the growing polypeptide chain during translation.

What is the process of translation?

Translation is the process of translating the sequence of a messenger RNA (mRNA) molecule to a sequence of amino acids during protein synthesis

What direction does translation occur?

5' to 3' direction

What is the process of translation?

synthesis of polypeptides on ribosomes, using mRNA and tRNA. Used mRNA to connect amino acids together to form a polypeptide chain - protein
- mRNA determines the sequence according to the genetic code.

codons and anticodons

the mRNA has the codon, which is a triplet code, three bases code for one amino acid .
translation depends on complementary base pairing between the codon on the mRNA and the anticodon on the tRNA.
mRNA = codons
tRNA = anticodons

What bond connects the amino acids together?

peptide bonds (condensation reaction)
between carboxyl (COOH) and amine (NH3)