Gene Expression

Question 1

Genome

Answer 1

All the genetic material in the chromosomes of an organism, including its genes and DNA sequences.

Question 2

Coding and non-coding DNA

Answer 2

The DNA that comprises chromosomes (and on a smaller scale: genes) is often classified as either coding DNA or non-coding DNA.

Question 3

Coding DNA

Answer 3

DNA that is both transcribed and translated (eg. the exon component of genes).

Question 4

Non-coding DNA

Answer 4

DNA that is not both transcribed and translated. The function of much of the non-coding DNA is unknown. Non-coding DNA has many gene regulatory functions and species complexity probably lies in the non-coding sections of the genome rather than the coding sections. So, it plays an important role in a cell’s survival.

Question 5

Major categories of non-coding DNA

Answer 5

Structural DNA
DNA sequences coding for Functional non-coding RNA
Introns
Regulatory DNA sequences

Question 6

Structural DNA

Answer 6

eg. centromeres and telomeres which are not transcribed (are composed of repeating nucleotide sequences). This DNA helps to maintain the structure of chromosomes. (See the image below left)

Question 7

DNA sequences coding for Functional non-coding RNA

Answer 7

eg. tRNA and rRNA which are transcribed but not translated (are made from DNA and move to cytoplasm)

Question 8

Introns

Answer 8

DNA sections within genes - are transcribed but RNA copies are removed before mature mRNA leaves the nucleus ie. before translation.

Question 9

Regulatory DNA sequences

Answer 9

eg. promotors, operator and enhancer sequences which influence the process of transcription

Question 10

Protein Synthesis

Answer 10

Genes are mainly expressed via their DNA sequence being used to make a functional gene product. Functional gene products are either:

proteins (made via protein synthesis)
functional noncoding RNA (eg. tRNA or rRNA molecules which are used in protein synthesis).

Question 11

Main molecules involved in protein synthesis

Answer 11

DNA and RNA (made of nucleotides).The other important type of molecule is protein (made of amino acids).

Question 12

A triplet

Answer 12

three consecutive bases in DNA (eg. template strand)

Question 13

A codon

Answer 13

three consecutive bases in mRNA

Question 14

An anti-codon

Answer 14

three consecutive bases in a particular part of tRNA

Question 15

Protein synthesis in eukaryotic cells

Answer 15

Transcription occurs in the nucleus and Translation in the cytoplasm at the ribosomes

Transcription occurs before Translation (pre-mRNA is modified in between)

Eukaryotic DNA does have introns.

Question 16

Protein synthesis in prokaryotic cells

Answer 16

Both transcription and translation occur in the cytoplasm / cytosol (as their is no nucleus).

free floating ribosomes can attach to mRNA as it forms. Thus, translation and transcription occur at the same time.

prokaryotic DNA has no introns. Thus pre-mRNA modification does not need to occur.

Question 17

Major steps of protein synthesis

Answer 17

1. Transcription
   Occurs in the nucleus
   DNA base sequence in genes is a template that is copied into a form that can leave the nucleus (mRNA).
2. Pre- mRNA processing
   Occurs in the nucleus
   Pre mRNA is modified to become mature RNA which leaves the nucleus. (Non-coding INTRONS are removed from the mRNA and coding EXONS are spliced back together. A 5’cap and a 3’polyA tail are also added to the ends of the mRNA) The modified mRNA is now called mature mRNA)(Remember: Exons are are expressed and are expelled from the nucleus while Introns go into the trash)
3. Translation
   Occurs in the cytoplasm (at the ribosomes)
   The mature mRNA is decoded by ribosomes and used to direct the sequence of amino acids in a polypeptide chain.

Question 18

Transcription

Answer 18

1. Initiation- RNA polymerase binds to a promotor region upstream of the gene. The DNA unzips (H bonds break) as a result of enzyme action.
2. Elongation- One side (Template strand) of a genes DNA is used as a recipe for making a mRNA strand. (Note the strand complimentary to the template strand is called the Coding strand).

Free floating RNA nucleotides are attracted to their complimentary exposed DNA bases (each three bases in the DNA sequence is called a triplet) and bond together (with the help of the enzyme called RNA polymerase) to form a single sided RNA chain. (Note: mRNA is always synthesised in a 5’ to 3’ direction)

3. Termination- RNA polymerase reaches a terminator region at the end of the gene and transcription ends.The DNA double helix reforms.

This initial messenger RNA (pre-mRNA) chain then breaks away from the original DNA template and is modified in three ways before it leaves the nucleus (see mRNA modification below).

Question 19

Pre- mRNA processing

Answer 19

1.- a 5’ cap is added to one end of the mRNA (thought to allow mRNA to attach to ribosomes)

2. • a 3’ poly A tail is added to the other end of the mRNA (thought to allow the final mRNA to leave via nuclear pores)
3. • introns (non coding regions of the mRNA) are removed and exons (coding regions) are spliced back together making the final / mature mRNA that goes to the ribosomes shorter.

Question 20

Translation

Answer 20

1. Initiation- The modified final mRNA attaches to a ribosome (made of rRNA) and starts to be ‘decoded’ three bases (a codon) at a time. When the sequence AUG (the start codon) is ‘read’ by the ribosome then translation will begin.

Each codon codes for a specific amino acid (see the mRNA – amino acid table below or on pg 79 of your IB Biology Biozone workbook…showing 61 codons coding for approx. 20 amino acids)

2. Elongation- Specific amino acids are brought to the ribosomes (by transfer RNA (tRNA) molecules). tRNA molecules have anticodons at their base which temporarily bond to the mRNA codons ( as they are complimentary) at the ribosome. Adjacent amino acids then bond together (via peptide bonds) to form a polypeptide chain.

tRNA decodes mRNA sequences by matching amino acids to codons of the mRNA
The tRNA molecules move back to the cytoplasm to be ‘recharged’ (pick up new amino acids).

3. Termination- Translation ends after the ribosome reads a stop codon (either UAA, UAG or UGA). Stop codons do not code for amino acids (have no corresponding tRNA molecules). The polypeptide chain is released from the ribosome.

Question 21

Structural genes

Answer 21

Code for proteins and RNA’s that are not regulatory in nature eg. enzymes, hormones, membrane proteins, cytoskeleton proteins, rRNA or tRNA molecules.

Question 22

Regulatory genes

Answer 22

Code for transcription factor proteins that are regulatory in nature

Question 23

Transcription factor proteins (TFP)

Answer 23

DNA binding proteins.

They bind to either the promotor, operator, enhancer or silencer regions of DNA (which are often located upstream of a structural gene).

Transcription factor proteins regulate transcription by influencing whether an enzyme called RNA polymerase can attach to the promotor region of DNA and then initiate transcription.

Question 24

Two major categories of Transcription factor proteins are:

Answer 24

Activator proteins
Repressor proteins

Question 25

Activator proteins

Answer 25

Bind to enhancer DNA sequences and switch transcription 'on' (up regulate structural gene expression).

Question 26

Repressor proteins

Answer 26

Bind to silencer DNA sequences and switch transcription 'off' (down regulate structural gene expression).

Question 27

Controlling gene expression in eukaryotic organisms

Answer 27

It usually involves an enhancer region of DNA (located a fair distance upstream of a structural gene) folding back over and interacting with the promotor region near the structural gene. Transcription factors bind to promotor regions which enable RNA polymerase to bind here and initiate transcription. The enhancer region is a short regulatory sequence of DNA that works to enhance or speed up the rate of transcription. The promoter region is a length of DNA to which the RNA polymerase enzyme binds to initiate transcription (mRNA nucleotides being sequenced together using the DNA template).

Question 28

Controlling gene expression in prokaryotic organisms

Answer 28

The regulation of genes often involves operons. An operon is a length of DNA made up of structural genes and control sites (eg. operator and promotor regions, which are located 'upstream on 5' side' of the structural genes). The operator region is a regulatory DNA sequence that can act as a 'switch' and turn a gene on or off. The promoter region is a length of DNA to which the RNA polymerase enzyme binds to initiate transcription. In prokaryotic organisms regulatory genes, often found upstream of the operon, can make repressor proteins that bind to the operator region (only found in prokaryotic cells) and supress gene expression by preventing RNA polymerase binding to the adjacent promotor region.

Question 29

Regulatory mechanisms

Answer 29

Regulatory genes code for proteins called transcription factors that bind to regulatory DNA sequences (eg. ‘promotor’ regions, enhancers or silencers) upstream of structural genes. Transcription factors can either 'up regulate' (enhance) or 'down regulate' (supress) the transcription of a structural gene. Environmental factors can influence the addition of chemical tags (eg. methylation or acetylation) which influences the coiling of DNA and also transcription. (NOTE: Tightly coiled and highly methylated regions of DNA seem to be transcribed less). microRNA molecules can be produced from non-coding regions of DNA which influence translation at ribosomes. The use of chemical tags or microRNA in gene regulation is sometimes also referred to as Epigenetics.

Question 30

Cell Differentiation associated with Sex determination

Answer 30

On the Y chromosome there is a gene called the Sex Determining Region Y (SRY) gene. This gene produces a transcription factor (SRY) protein that upregulates the production of other transcription factors (eg. SOX 9) triggering the embryonic gonad tissue/ cells to differentiate and the gonad becomes a testis (seminiferous tubules develop and testosterone production begins). When no SRY protein is made, low SOX9 concentrations will not stimulate testis production so the embryonic gonad remains in the female form.

Question 31

Morphological development

Answer 31

Body plan genes (the genes that control the development of body plans) are similar in plants, animals and fungi. The HOX genes are types of Homeotic (Homeobox) genes which are a collection of similar genes that are expressed in particular patterns at particular stages of development. They produce specific protein transcription factors. In animals, HOX genes control events such as the embryonic development of a head to tail axis, segmentation and the development of appendages/ limbs. Eg. HOX genes in insects specify which appendage grows from which body segment.

Question 32

Epigenetics

Answer 32

Any mechanism that alters gene expression without altering the DNA sequence. The epigenome refers to a system of gene control outside of the DNA ('above the genome') .

Question 33

Epigenetic inheritance

Answer 33

Involves the inheritance of traits transmitted by mechanisms not directly involving the DNA nucleotide sequence.

Question 34

Chemical Tags (affecting transcription)

Answer 34

Example of an epigenetic process. Histone modification: how tightly coiled the DNA is around histones (and also how tightly packed nucleosomes are) is influenced by the presence or absence of specific chemical tags. DNA acetylation -acetyl groups are added to DNA which 'relaxes' histone structures and enhances transcription DNA methylation- the addition of methyl groups to the DNA at the start of a structural gene and will often reduce transcription. Influence gene expression via enhancing or suppressing transcription.

Question 35

microRNA production (affecting translation)

Answer 35

Example of an epigenetic process. Some small RNA sequences (approx. 22 nucleotides long) that can silence genes by either degrading mRNA or blocking translation at ribosomes. These microRNA molecules can interfere with protein synthesis by stopping translation (by attaching to mRNA and either blocking mRNA from being translated by ribosomes or by degrading mRNA).

Question 36

RNA bases

Answer 36

AUGC

Question 37

DNA bases

Answer 37

ATGC

Question 38

Messenger RNA (mRNA)

Answer 38

A copy of the genetic code made from DNA in a single sided form, whose codons (3 base sequences) can be read and are used to make proteins. It carries the genetic information from the nucleus (via nuclear pores) to the ribosomes in the cytoplasm of the cell.

Question 39

Ribosomal RNA (rRNA)

Answer 39

It is located in the cytoplasm of the cell, ribosomes are made up of ribosomal RNA. The ribosome exists as two subunits (a large and a small subunit). It directs the translation of mRNA into proteins which sits between the two subunits during translation.

Question 40

Transfer RNA (tRNA)

Answer 40

It is located in the cytoplasm of the cell. It brings (transfers) amino acids to ribosomes during translation. It contains an anticodon that is complimentary to a three nucleotide codon of mRNA that is being decoded at the ribosome. The amino acids carried by tRNA can then be joined together and processed to make a polypeptide chain and proteins.

Question 41

DNA --> Protein

Answer 41

DNA Transcription RNA Translation Protein