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Biology > Unit 3 AOS1: DNA > Flashcards

Unit 3 AOS1: DNA Flashcards

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1
Q

DNA structure and function

A

DNA is made of chemical building blocks called nucleotides. These building blocks are made of three parts: a phosphate group, a sugar group and one of four types of nitrogen bases. To form a strand of DNA, nucleotides are linked into chains, with the phosphate and sugar groups alternating

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2
Q

DNA vs RNA

Sugar
Function
Subunits (bases)
Structure

A

Sugar
DNA: Deoxyribose
RNA: Ribose (has an extra OH group)

Function
DNA: Makes up the genetic code
RNA: Involved in every stage on gene expression

Subunits	
DNA nucleotides:
-Thymine
-Adenine
-Cytosine
-Guanine	
RNA nucleotides:
-Uracil
-Adenine
-Cytosine
-Guanine
Structure	
DNA: Double-stranded	
RNA: Single-stranded
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3
Q

DNA replication

A

DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritance

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4
Q

RNA structure and function

A

RNA is typically single-stranded and is made of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and a phosphate group.

Function: Involved in every stage on gene expression

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5
Q

pre-mRNA

A

The first (primary) transcript from a protein-coding gene is often called a pre-mRNA and contains both introns and exons. Pre-mRNA requires splicing (removal) of introns to produce the final mRNA molecule containing only exons.

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6
Q

mRNA

A

An RNA molecule transcribed from the DNA of a gene, and from which a protein is translated by the action of ribosomes. The basic function of the nucleotide sequence of mRNA is to determine the amino acid sequence in proteins.

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7
Q

tRNA

A

Transfer RNA. Small RNA molecules that carry amino acids to the ribosome for polymerization into a polypeptide. During translation the amino acid is inserted into the growing polypeptide chain when the anticodon of the tRNA pairs with a codon on the mRNA being translated.

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8
Q

rRNA

A

A class of RNA molecules, coded in the nucleolar organizer, that have an integral (but poorly understood) role in ribosome structure and function. RNA components of the subunits of the ribosomes.

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9
Q

mRNA formation

A

During transcription, the DNA of a gene serves as a template for complementary base-pairing, and an enzyme called RNA polymerase II catalyzes the formation of a pre-mRNA molecule, which is then processed to form mature mRNA

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10
Q

transcription

A
  • Purpose is to copy a template strand of DNA into mRNA to carry the instructions for a polypeptide chain to a ribosome
  • Occurs in the nucleus of eukaryotic cells and cytoplasm of prokaryotic cells
  • Amount of water in the nucleus increases.
  • Prokaryotes are faster because mRNA is produced without the need for splicing.

Step 1. the enzyme RNA polymerase attaches to the promoter region of DNA just upstream of the gene
Step 2. The double stranded DNA making up this gene is unwound by the transcription factors by breaking the weak hydrogen bonds existing between its two strands – unpaired bases on the template strand are now exposed
Step 3. RNA polymerase constructs pre-mRNA by collecting free complementary RNA nucleotides using the exposed DNA template strand. It assembles the RNA nucleotides according to complementary base pairing rules. The nucleotides in eukaryotic cells are joined to form a single stranded pre-mRNA molecule

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11
Q

splicing (exons and introns)

A

The reaction that removes introns and joins together exons in eukaryotic nuclear primary RNA transcripts.

  • “Changing pre-mRNA to prepare for translation.”
  • Introns (regions of the gene that are transcribed but not translated) are spliced out
    and exons are joined together. This is known as alternative (alternate) splicing, a form of post-transcriptional modification because both exons and introns are removed.
    1. Exons can also be spliced and rearranged in different orders to produce different proteins in addition to introns being removed.
    1. A poly-A tail is added to the 3’ end
    1. A methyl cap is added to the 5’ end
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12
Q 
protein synthesis
transcription
ini
elo
ter
A
  1. Initiation. The DNA molecule unwinds and separates to form a small open complex. RNA polymerase binds to the promoter of the template strand.
  2. Elongation. RNA polymerase moves along the template strand, synthesising an mRNA molecule.
  3. Termination. In prokaryotes there are two ways in which transcription is terminated. In Rho-dependent termination, a protein factor called “Rho” is responsible for disrupting the complex involving the template strand, RNA polymerase and RNA molecule. In Rho-independent termination, a loop forms at the end of the RNA molecule, causing it to detach itself.
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13
Q 
protein synthesis
translation
i
e
t
A
  1. Initiation. The small subunit of the ribosome binds at the 5’ end of the mRNA molecule and moves in a 3’ direction until it meets a start codon (AUG). It then forms a complex with the large unit of the ribosome complex and an initiation tRNA molecule.
  2. Elongation. Subsequent codons on the mRNA molecule determine which tRNA molecule linked to an amino acid binds to the mRNA. An enzyme peptidyl transferase links the amino acids together using peptide bonds. The process continues, producing a chain of amino acids as the ribosome moves along the mRNA molecule.
  3. Termination. Translation is terminated when the ribosomal complex reached one or more stop codons (UAA, UAG, UGA).
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14
Q

Protein structure

Primary

A

A sequence of amino acids. Covalent peptide bonds.

Monomers are joined by anabolic reactions which require energy.

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15
Q

Protein structure

Secondary

A

Gives proteins their properties; consists of alpha helixes, beta-pleated sheets and random coils. Hydrogen bonds form between carboxyl and amino groups.

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16
Q

Protein structure

Tertiary

A

The specific 3D shape of the protein that consists of a
secondary structure folded – the 3D shape of the protein determines its function. R groups interact with chemical bonds, hydrophobic interactions. Disulfide (disulphide) bonds also contribute.

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17
Q

Protein structure

Quarternary

A

Made up of 2 or more polypeptide chains joined together to form a functional protein. Note: this is different from two tertiary structures joined together.

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18
Q

Structural and Regulatory genes

A
  • Regulatory genes code for a gene product that is involved in the expression of other genes. Interacts with structural gene by switching on and off.
  • Structural genes code for a protein that is involved in everyday cellular metabolism. Produces enzymes & proteins.
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19
Q

Transcription Factors

A

A protein that binds to a cis-regulatory element (eg. an enhancer, a TATA box) and thereby, directly or indirectly, affects the initiation of transcription. Eukaryotic proteins that aid RNA polymerase to recognize promoters. Analogous to prokaryotic sigma factors.

Anything that regulates gene transcription (i.e. repressor, activator, RNA polymerase)

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20
Q

Promoter region

A

Where RNA polymerase and other transcription factors bind; where transcription of structural genes’ pre-mRNA or mRNA begin, 5’ ends – upstream of the coding region

A regulatory region a short distance upstream from the 5’ end of a transcription start site that acts as the binding site for RNA polymerase. A region of DNA to which RNA polymerase binds in order to initiate transcription.

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21
Q

Exons and Introns

A

Exon: A region of a gene that is present in the final functional transcript (mRNA) from that gene. Any non-intron section of the coding sequence of a gene; together the exons constitute the mRNA and are translated into protein

Intron: A DNA segment of largely unknown function within a gene that specifically interrupts the coding (exon) sequences of that gene. Introns are transcribed as part of the normal gene primary transcript, but intron sequences are not found in the functional mRNA. Intron sequences are removed from the primary transcript by a splicing mechanism.

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22
Q

Alternative splicing

A

Various ways of splicing out introns in eukaryotic pre-mRNAs resulting in one gene producing several different mRNAs and protein products.

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23
Q

The Lac Operon

A

Lac: digestion of lactose
Operon: “Group of linked genes that regulate protein
synthesis.”
An inducible operon including three loci involved in the uptake and breakdown of lactose in Escherichia coli.
1. Lactose binds to repressor on operator
2. Repressor is removed from operator
3. RNA polymerase activates promotor
4. Transcription of 3 pieces of protein mRNA occurs
5. Proteins are made via translation

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24
Q

Plant hormones

A

(aka. Plant growth regulators)
Source: plant cells that are undergoing growth, ripening, abscission etc.
- Act as signalling molecules that target various cells (those undergoing growth, ripening, abscission etc.) and produce specific effects
- Produced by individual cells in growing regions of the plant (e.g. roots, leaves)
- Usually transported in the phloem
Mode of transmission: ENDOCRINE (i.e. released into the bloodstream)
** The hormone ONLY acts on the target cells which possess the receptor for that specific hormone

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25
Q

Animal hormones

3 types

A

Source: endocrine glands in the body, e.g. cells, organs and glands Three types of animal hormones:

  1. Peptide and protein (hydrophilic – only have receptors on the cell membrane)
  2. Amino acid derived (hydrophilic – receptors on the cell membrane)
  3. Steroid/lipid derived – lipophilic (hydrophobic – receptors found inside the cell)
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26
Q

Cytokines

A
  • Small, protein (mostly) molecules
  • Act as messengers between cells of the immune system
  • Act on the cells in the immune system with the specific receptors
  • Secreted by cells in response to various stimuli
    Source: immune system
    Mode of transmission: AUTOCRINE, PARACRINE, ENDOCRINE
27
Q

Pheromones

A

Source: the exocrine glands of animals of the same species Mode of transmission: EXOCRINE

  • Chemical signalling molecules released by one animal that carries a signal to the cells of a second member of the same species.
  • Secreted by an animal into the external environment
  • Externally regulates others’ behaviour.
28
Q

Neurotransmitters

A

Source: nerve cells in animals (axon terminals of neurons)
Mode of transmission: PARACRINE
- Carry signals from one neuron to the next
- Also transmit nerve impulses from neurons
to muscle cells, stimulating their contraction
- Main function is to either continue or stop a
signal from happening (excitatory or inhibitory)
The neurotransmitter molecules diffuse across the synaptic cleft and bind with receptors on the surface of the post- synaptic neuron – the nerve impulses are transmitted in a one-way direction only across a synaptic cleft.
STAGES IN “CELL CHATTER” Has three stages:
- RECEPTION
- TRANSDUCTION
- RESPONSE

29
Q

3-step stimulus response model

  1. r
A

Reception: - Reception of a signalling molecule from a cell’s external environment

  • When signalling molecules reach their target cells, they bind to a specific receptor
  • Each type of receptor protein binds to one signalling molecule with a specific shape
  • Cell receptors are usually located on the plasma membrane of the specific target cell (due to polar and hydrophilic signalling molecules being unable to cross the lipid bilayer of the plasma membrane), however in some cases the receptors are in the cytosol or the nucleus of the target cell
  • Hydrophilic/hydrophobic nature of signalling molecules determines the location of the specific receptor where the signal is received
30
Q

3-step stimulus response model

trans

A
  • Converts a signal from outside a cell into a response within the cell
  • Signal is received in one form, is changed to another mode or molecule, and is relayed to the appropriate target within the cell that responds through an effector
    protein.
  • The process of signal transduction starts after a signalling molecule binds to its specific receptor, changing its 3D shape and activating it
31
Q

3-step stimulus response model

resp

A
  • The outcome of the signalling molecule

- Example: apoptosis, increased transcription/translation, cell shape change

32
Q

Hydrophilic and hydrophobic signals in terms of:

  • Position of receptors
  • Initiation of transduction
A

➢ Hydrophobic signalling molecules: the signalling molecule will pass through the plasma membrane and bind to a receptor either in the cytosol or in the nucleus
➢ Hydrophilic signalling molecules: cannot diffuse across the plasma membrane, so they bind to a membrane-bound receptor.
- This causes a shape change in the receptor, which activates a second messenger inside the cell.
- The second messenger causes a chain reaction within the cell (called a signal cascade).

33
Q

Apoptosis

A
  • Programmed cell death
  • Can be triggered via 2 mechanisms: the extrinsic pathway (death receptor pathway) or intrinsic pathway (mitochondrial pathway)
  • A balance exists when rate of cell renewal = rate of cell death
  • Used to remove cells that are: at the end of their natural life, dysfunctional, damaged or diseased or found in excessive amounts.
  • Nucleus condenses, cytoskeleton cut, blebs, DNA fragmented, cell shrinks.
  • Then apoptotic bodies form.
34
Q

Apoptosis

Extrinsic pathway/Death receptor pathway

A

EXTRINSIC PATHWAY (death receptor pathway)

  • Initiated by factors external to the cell
  • Activated when a signalling molecule from outside a cell binds to a death receptor on the plasma membrane of a cell
  • This then initiates the activation of a series of enzymes called caspases (i.e. enzymes that split protein molecules)
  • Caspases release into the cytosol.

Summary

    1. Ligand binds to receptor on target cell, changing its shape.
    1. Receptor activates a protein at the membrane
    1. Original signal is amplified during signal transduction
    1. Increased gene expression by target cell
35
Q

Apoptosis

Intrinsic pathway/Mitochondrial pathway

A

INTRINSIC PATHWAY (mitochondrial pathway)

  • Initiated within a cell
  • Depends on factors released from the mitochondria (mitochondria are important in determining how and when damaged and stressed cells recognise that it’s time to die)
  • Involves DNA damage, UV light, mitochondrial stress, heat shock and/or radiation.
  • ATP production is reduced, initiating apoptosis by damaged membranes becoming more permeable to releasing caspases.
  • Mitochondria releases caspases into the cytosol.
  • Iodine can promote apoptosis by weakening the mitochondrial membrane. This is intrinsic, because iodine activates a caspase pathway.
36
Q

Malfunctions in Apoptosis

A
  • Apoptosis is involved in foetus development. It is how the webbing between our fingers and toes, and the slit that allows our eyelids to open are removed.
  • Cancer is caused by a damaged cell not undergoing apoptosis. These cells divide rapidly, creating large lumps called tumours; many reasons why apoptosis may fail to occur
37
Q

How are the 3 types of RNA different?

mRNA (mitochondrial)
rRNA (ribosomal)
tRNA (transfer)

A
  • DNA is copied into mRNA which exits the nucleus and goes to the ribosome.
  • rRNA is structural and, along with proteins, forms the ribosome. in the ribosome, mRNA sequence is translated into a polypeptide sequence of amino acids.
  • the function of tRNA is to bring the amino acids to the ribosome
38
Q

Condensation polymerisation (reaction)

A

The formation of polymers, such as peptides and carbohydrates, by a reaction that involves the release of water molecules

39
Q

Protein functional diversity examples

A
  • providing structural support, such as in skin and hair
  • helping transport molecules across membranes
  • storing metal ions and amino acids
  • receiving and sending signals
  • defending against pathogens
  • enabling muscle contraction
  • catalysing reactions.
40
Q

Proteome

A

The proteome refers to the entire set of proteins expressed by an organism at a given time - from the keratin found in hair, to the haemoglobin in red blood cells, to the amylase in saliva.

Proteomics is the study of the proteome, including the structure, function, and interaction of proteins.

41
Q

Amino acids (proteins)

A

Amino acids are the building blocks of proteins. They are joined together via a condensation reaction. A chain of amino acids (a polypeptide) then folds to form an active protein
➔ Amino acids = monomer of proteins
➔ Proteins = polymer of amino acids

42
Q

How to form a protein

Steps
C.R

A

To form a protein, many amino acids join via condensation reaction, forming a polypeptide

➔ Condensation reaction: a reaction where two small molecules join to form one larger molecule, producing water as a by-product in the process

  1. Energy is used to remove the -OH group of one amino acid and the -H on the amino group of another amino acid. They form water, so the process is called a condensation reaction.
  2. The two amino acids bond together, forming a peptide bond. The whole molecule can now be called a dipeptide.
  3. When more amino acids bond, the molecule will become a polypeptide.
43
Q

Nucleic acids

DNA

A
  • DNA is one of the types of nucleic acids found in living things.
  • A single strand of DNA is made of covalently (sharing electrons between two non-metal atoms) linked nucleotides, and two strands of DNA bind together by complementary base pairing, forming a double helix structure
  • DNA is essential for life - differences in DNA usually mean differences in proteins
44
Q

Nucleic acids (genes)

A
  • Each gene contains the information required to make a protein.
  • A complete set of DNA in an organism is called a genome, which is inheritable and passed from parents to their child
45
Q

Structure of DNA (nucleotides)

A

They are made up of:

  • A phosphate group
  • Five-carbon deoxyribose sugar
  • Nitrogen-containing base which could be either: Adenine (A), Thymine (T), Guanine (G) or Cytosine (C).

The five carbons in the sugar are labelled 1’ to 5’. The phosphate group of each nucleotide is attached to the 5’ carbon in the sugar molecule on the same nucleotide. The nitrogen-containing base, attached to the 1’ carbon determines the overall type of nucleotide (A,T,G,C)

  • When nucleotides bond together, they form a polynucleotide chain, which bind strong covalent bonds between the sugar group of one nucleotide and the phosphate of another
46
Q

RNA

A
  • Single-strands of nucleotides
  • Assists with protein synthesis
  • RNA nucleotides contain a ribose-five-carbon sugar, which has one more oxygen than a deoxyribose molecule
  • Thymine is replaced by uracil so therefore (A-U), (G-C)
  • The variable folding of RNA allows it to perform a variety of functions throughout the cell
47
Q

mRNA
messenger

functions
structure

A

Carries genetic information from the DNA to the ribosomes for protein synthesis

mRNA is a single, linear strand of RNA

48
Q

tRNA
transfer RNA

function
structure
A

delivers individual amino acids to the ribosome after recognising specific nucleotide sequences

tRNA is formed from a single strand of RNA folded into three hairpin loops to form a ‘cloverleaf’ structure. A sequence of 3 bases called the anticodon is located on the middle hairpin.

49
Q

rRNA
ribosomal

function
structure
A

The main structural component of ribosomes in the cell

rRNA folds into a large and a small subunit to make up a ribosome

50
Q

Similarities between DNA and RNA

A
  • nucleotides follow the same basic structure (phosphate group, five-carbon sugar molecule, nitrogen-containing base)
  • contain the nucleotides adenine, guanine, and cytosine
  • nucleotides form chains along the sugar-phosphate backbone by a condensation reaction
  • follow the complementary base pairing rule: C pairs with G, A pairs with T (or U)
51
Q

Differences between DNA and RNA

A

DNA:

  • nucleotides contain a deoxyribose sugar
  • contains the base thymine (T)
  • double-stranded
  • equal numbers of the nucleotides adenine-thymine and guanine-cytosine
  • double helix
  • inherited/long-term storage

RNA:

  • nucleotides contain a ribose sugar
  • contains the base uracil (U)
  • single-stranded
  • different number of the nucleotides adenine-uracil and guanine-cytosine
  • many different structures
  • temporary molecules
52
Q

The genetic code

  • protein synthesis
A

A cell produces proteins by reading and interpreting the information within the gene of its DNA protein synthesis in 3 steps

1) Transcription
2) RNA processing
3) Translation

  • In steps 1 and 2, the nucleotide sequence in a gene is copied into an RNA form
  • In step 3, the RNA is used as a guide to order the amino acid monomers in a protein

The steps in protein synthesis are possible because genes follow the genetic code, a set of rules that define how the information in nucleotides (DNA and RNA) is translated into functional molecules (e.g. proteins)

53
Q
  • Codon
  • Triplet
  • Genetic code
A

The information in DNA and RNA is stored as 3-sequence sections of nucleotides.
In DNA, this grouping of 3 nucleotides is called a triplet.
When a DNA triplet is transcribed into an mRNA molecule, the triplet is called a codon.

Codons and triplets are important as one triplet or codon codes for one amino acid in the final polypeptide chain. There are also specific triplets and codons that instruct the cell to start and stop protein synthesis. Therefore, these rules determine which nucleotides read and translated into polypeptide sequence

The order of codons indicates the order of amino acids in a polypeptide chain. You can use a codon table to know what the sequence would be

More than one codon can code for the same amino acid. Because of this, the genetic code is said to be degenerate or redundant.

54
Q

Degenerate

Codons
Genetic code

A

A property of the genetic code which means that a single amino acid can be coded for by more than one codon.

  • UAG is the start codon. It signals the initiation of translation
  • UAA, UAG and UGA are stop codons that do not code for an amino acid, but signal the termination of translation
  • The genetic code is universal
55
Q

Transcription

A

The first step in gene expression and involves the creation of a pre-mRNA molecule from genetic information found in DNA

  • Pre-mRNA can copy and transport the information carried within the DNA. It’s produced by an enzyme called RNA polymerase.
  • Transcription is important as it creates a molecule (mRNA) that is able to transport and code for a protein around the cell
56
Q

Transcription process

  1. ini
  2. elo
  3. ter
A

Consists of 3 steps:

  1. Initiation
  2. Elongation
  3. Termination

Initiation:

  • To begin transcription, specific proteins called transcription factors bind to the promoter region to activate transcription.
  • With the help of transcription factors, RNA polymerase binds to the promoter region.

Elongation:

  • RNA polymerase moves along the template strand, reading the nucleotide sequence and bringing in free complementary RNA nucleotides.
  • This produces a new single-stranded RNA molecule, known as a precursor mRNA (pre-mRNA)
  • This is synthesised in the 5’ to 3’ direction so new RNA nucleotides are added to the exposed 3’ end.
  • Pre mRNA strand is complementary to the DNA template strand. This strand that is not read by RNA polymerase is called the coding strand

Termination:
- Transcription ends when the RNA polymerase reaches the termination sequence of a gene, signalling the end of transcription

57
Q

Summary of transcription

A
  • DNA unwinds/unzips
  • RNA polymerase catalyses transcription
  • Nucleotides are joined by RNA polymerase
  • Transcription of the DNA template strand into pre mRNA
  • pre-mRNA is complementary to the DNA template strand
  • In the pre-mRNA, A pairs with U, not with Thymine (T)
58
Q

RNA processing

5’ methyl cap
poly-A tail

A

The processing of RNA is the second step in gene expression, and involves modifying the pre-mRNA molecule into an mRNA molecule that can be used in translation

The processing modifications include:
- The addition of a 5’ methyl cap and a poly-A tail:
➔5’ methyl cap (five-prime cap) = a molecule added to the 5’ end of pre-mRNA during RNA processing
➔ poly- A tail = a stretch of adenine nucleotides added to the 3’ end of pre-mRNA during RNA processing

★ Added to stabilise the RNA, preventing it from degrading and allowing it to bind to the ribosome during translation

59
Q

Splicing

A
  • Removing introns from pre-mRNA by using a spliceosome. It joins the exon regions to form an mRNA molecule containing only protein coding regions.
  • The differences in splicing, and therefore differences in formation of mRNA, is known as alternative splicing which is when one gene has the capacity to create different mRNA strands and code for different proteins
60
Q

Translation

gene expression

A
  • Final step of gene expression
  • Involves reading and converting the information in the mRNA molecule into a polypeptide sequence.
  • In this stage, the mRNA codons are translated into a sequence of amino acids (polypeptide chain)
  • To undergo translation, mRNA exits the nucleus through a nuclear pore, and travels to a ribosome in the cytoplasm or on the rough ER
61
Q

Translation process

A

1) Initiation
2) Elongation
3) Termination

Happens in the ribosomes

Facilitated by ribosome subunits and tRNA molecules, which produces a polypeptide from mRNA

  • Ribosome reads mRNA
  • tRNA anticodons complementary to mRNA codons
  • tRNA deliver amino acids
  • Amino acids joined by condensation reaction to form a polypeptide
  • Translation ends when STOP codon reached
62
Q

RNA processing summary

A
  • Introns removed and exons joined
  • Addition of a methyl cap to the 5’ end
  • Addition of a poly-A tail to 3’ end

Located in the nucleus

Facilitated by a spliceosome

Product: mRNA from pre-mRNA

63
Q

The genetic code

A
  • Triplet nature
  • Universal
  • Degenerate
  • Non-overlapping

Biology (18 decks)

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