Ib Biology (Chapter 7.1-7.3)

Front 1

What did the scientist Chargaff discover? (Chargaff's rule)

Back 1

the four bases were never found in equal amounts, and each species had a different ratio. However, the amount of A's were always equal to the amount of T's, and G's always equal to C's.

Front 2

How did Chargaff's findings help in the development of Crick's and Watson's DNA model? (pg. 110)

Back 2

Crick's and Watson first few suggested models did not take into account that Chargaff's rule states that the amount of adenine will always equal the amount of thymine and the amount of guanine will equal cytosine.

Front 3

Label the diagram

Back 3

1. Covalient bond

2. Phosphate

3. Sugar/Deoxoribose/Ribose/Pentose

4. Hydrogen bond

5. Purine

6. Pyrimidine

Front 4

What parts consists of a nocleusome?

Back 4

Eight histones (octameres) with DNA coiled around them.

A short section of "linker" DNA connects between one nucleosome to another.

Front 5

What is the role of the nocleusome?

Back 5

Supercoil and package the DNA

Front 6

- Replication -

What is the role of helicase and how does it work?

Back 6

unwinds DNA into 2 strands by breaking the hydrogen bonds between the nucleotides.

Occurs on special sites called origin of replication.

Front 7

- Replication -

What is the role of Topomarase and how does it work?

Back 7

unwinds DNA from its helix shape to allow DNA helicase to work

Front 8

- Replication -

What is the role of DNA Primase and how does it work?

Back 8

Creates multiple RNA primers on the lagging strand and a single primer on the leading strand

Front 9

- Replication -

What is the role of RNA primers and how do they work?

Back 9

Short sequences of about 10 RNA nucleotides created by DNA primase.

required for DNA binding.

DNA Polymerase can only start replication by binding to a RNA primer.

Front 10

- Replication -

What is the role of DNA polymerase III and how does it work?

Back 10

After binding to a primer, collects freely floating DNA nucleotides and attaches them to their complementary pair.

Can only add a nucleotide to the 3' end of the primer, so replication occurs in a 5' - 3' direction

Front 11

- Replication -

What is the rule of DNA polymerase I and how does it work?

Back 11

Since the lagging strand is replicated in short fragments with multiple primers, DNA polymerase I removes these primers and replaces them with the corresponding nucleotides.

Front 12

- Replication -

What is the rule of DNA ligase and how does it work?

Back 12

Joins the okazaki fregments formed on the lagging strand into one continuous strand by joining the sugar-phosphate backbone with a phosphodiester bond (Covalient bond)

Front 13

Where does DNA replication occur?

Back 13

Origin of replication sites

Front 14

In what direction does DNA replication occur?

Back 14

5' -> 3'

Front 15

What are Telomeres?

Back 15

Regions of repetitive DNA sequences that are non-coding found on each end of a chromatid.

Front 16

What are the effects of telomere shortening and why does it occur?

Back 16

Telomere shortening occurs during each DNA replication, as the telomeres cannot be copied. progressive shortening of telomeres is linked to senescene, aka, aging.

Front 17

What is the role of the enzyme telomerase and its possible dangers?

Back 17

Telomerase lengthens telomeres to allow for a cell to replicate past its hayflick limit.

permenant activation of telomerase causes a cell to become immortal and leads to cancer.

Front 18

What is the hayflick limit?

Back 18

The limited amount of times a cell can divide in its lifetime.

Front 19

What is the 3' end and 5' end?

Back 19

Deoxoribose connects its 5th, or 5' end carbon, to the 3' end carbon of another deoxoribose via a phosphate. Since DNA is antiparallel, one deoxoribose will be left with an unbound 5' carbon, and the other will have an unbound 3' carbon.

Front 20

Explain how tandem repeats are used in DNA profiling

Back 20

Each individual has a variable number of Tandem repeats. This can be used in identifying and profiling of individuals.

Front 21

Explain how each cell in a single organism has identical DNA, yet many have different functions/appearance

Back 21

Each cell can differentiate itself by the expression of some genes but not others

Front 22

What is transcription?

Back 22

the creation of mRNA based off a template DNA sequence created by RNA polymerase.

Front 23

- Transcription -

What is the role of RNA polymerase and how does it function?

Back 23

- RNA polymerase binds to a promoter sequence.

- It then begins to move along the gene and unwinds the DNA into single strands.

- It pairs up freely floating nucleaside triophosphates (RNA nucleotides) with their complementary base pair with covalent bonds in a 5' to 3' direction.

- RNA polymerase will continue to transcribe until reaching a terminator sequence.

Front 24

- Gene expression -

What is a promoter and its function?

Back 24

A promoter is a non-coding sequence that initiates transcription and functions as a binding site for RNA polymerase. This binding is facilitated by multiple transcription factors.

Front 25

- Gene expression -

What is needed for the binding of RNA polymerase and to initiate transcription?

Back 25

- A promoter sequence for the RNA polymerase to bind to.

- Transcriptional factors to initiate the binding of RNA polymerase.

- Regulatory proteins to interact with the transcriptional factors, regulating the levels of transcriptional factors hence regulate gene expression.

- Proximal or Distal control elements for the transcriptional factors to bind to.

Front 26

State the types of regulatory proteins and the sites they bind to.

Back 26

Activator regulatory proteins bind to enhancer sites to increase transcriptional rate and mediate a complex formation.

Repressor regulatory proteins bind to silencer sites to decrease transcriptional rate by preventing complex formation.

Front 27

compare and contrast the sense strand to the antisense strand

Back 27

antisense strand:

- transcribed into RNA

- the "DNA version" of the tRNA anticodon sequence

- aka the template strand

Sense strand:

- no transcribed into RNA

- the "DNA version" of the RNA sequence, and is identical except it has thymine and not uracil.

- aka the coding strand

Front 28

What is mature RNA?

Back 28

An RNA transcript that has been spliced and processed and is ready for translation.

Front 29

What is needed for an transcribed RNA strand to become mature RNA?

Back 29

Capping: the addition of a methyl group to the 5' end of the RNA transcript to provide a protection against degration.

Polyadenylation: the addition of a long chain of adenine (poly-a-tail) to improve stability and help export the transcript from the nucleus.

Splicing: the removal of eukaryotic non-coding DNA, or, introns and the fusing of the remaining, coding exons.

Front 30

What is RNA Capping?

Back 30

The addition of a methyl group to the 5' end of the RNA transcript to provide a protection against degration.

Front 31

What is RNA Polyadenylation?

Back 31

The addition of a long chain of adenine (poly-a-tail) to the 3' end of the transcript to improve stability and help export the transcript from the nucleus.

Front 32

What is RNA splicing?

Back 32

The removal of eukaryotic non-coding DNA, or, introns by a spliceosome and the fusing of the remaining, coding exons.

Front 33

What is alternative RNA splicing and its benefits?

Back 33

The selective removal of exons from a RNA transcript during RNA splicing. This results in different polypeptides from a single gene sequence and allows organisms to have a wider variety of synthesized proteins.

Front 34

What are transcriptional factors?

Back 34

Transcriptional factorsa are proteins that initiate the binding of RNA polymerase. These usually bind to proximal control elements. body levels of these proteins regulate gene expression.

Front 35

What are regulatory proteins?

Back 35

Regulatory proteins interact with the transcriptional factors, regulating the levels of transcriptional factors hence regulate gene expression. Usually bind to distal control elements.

Front 36

What are proximal and distal control elements and the difference between them?

Back 36

- Proximal or Distal control elements are what the transcriptional factors and regulatory proteins bind to.

- Proximal control elements are close to the promoter, while distal control elements are away from the promoter.

- Transcriptional factors usually bind to proximal CE.

- Regulatory protiens usually bind to distal CE.

Front 37

How is gene expression affected by the environment?

Back 37

external or internal changes can results in changes to gene expression patterns.

chemical signals within a cell can trigger changes to levels of regulatory proteins or transcriptional factors in response to a stimuli, changing gene expression.

Front 38

how does modification of histone tales regulate gene expression?

Back 38

for DNA to be transcribed it must be physically accessible to transcriptional machinery.

Higher accessibility will increase transcription rate.

Acetylation and methylation control the this accessibility by loosening or tightening the coiling of the DNA around the histones.

Front 39

What happens in histone acetylation?

Back 39

Acetylation is when an acetyl group binds to the histone tales, neutralizing the chemical charge and loosening the the DNA coiling, increasing replication rate.

Front 40

What happens in histone methylation?

Back 40

Methylation is when an methyl group binds to the histone tales, increasing the positive charge and tightens the the DNA coiling, decreasing replication rate.

Front 41

How are histone tales regulated?

Back 41

DNA is negatively charged, while histones are positively charged, causing them to associate tightly with each other. acetylation neutralizes the charge and loosens the DNA, while methylation increases the positive charge tightening the coiling DNA.

Front 42

What is an epigenome?

Back 42

The sum of all the epigenetic tags. these tags are the chemical modifications affecting gene expression.

Front 43

How can an epigenome be passed on the next generation?

Back 43

Chemical modification affecting gene expression impact visible characteristics of an individual.

these epigenetic tags , especially gene methylation patterns, are passed during cell replication to the daughter cell.

sperm and egg cells can develop from cells with epigenetic tags.

When two reproductive cells meet, the epigenome is erased via a process called "reprogramming", but about 1% survives and is passed on. This is called "imprinting".

Front 44

What is replication?

Back 44

The replication of a DNA sequence

Front 45

What is translation?

Back 45

The translation of the mRNA strand into an amino acid sequence to create polypeptide chains.

Front 46

Label the diagram of the tRNA

Back 46

1. D-arm: associates with the tRNA activating enzyme

2. T-arm: binds to the ribosome active site

3. Acceptor stem: carries the amino acid

4. Anticodon: associates with the complimentary mRNA bases

Front 47

Describe the structure of a ribosome

Back 47

Small sub-unit containing mRNA binding site.

Large sub-unit containing 3 tRNA binding sites. the A site, the P site and the E site.

Front 48

What are tRNA activating enzymes?

Back 48

Each tRNA molecule is recognized by a specific tRNA activating enzyme. The enzyme binds to the tRNA's D-arm and attaches the amino acid corresponding to the tRNA's anticodon by using ATP.

Front 49

How does tRNA activating enzymes activate tRNA?

Back 49

ATP and an amino acid are attached to the enzymes active site.

One AMP from the ATP binds to the amino acid in a covalent bond. (phosphorylation)

The activated amino acid is then covalently attached to a corresponding tRNA.

energy from this bond will be used later to link the amino acid to the polypeptide chain.

Front 50

State the 3 steps of translation

Back 50

Initiation

Elongation

Termination

Front 51

- Translation -

Describe what happens during Initiation

Back 51

- An mRNA molecule binds to the small ribosme sub-unit at the mRNA binding site

- An initiator tRNA molecule carrying methionine binds at the start codon AUG in the P site.

- The large ribosome sub-unit binds to the small sub-unit

- the tRNA signals another tRNA to bind to the A site.

- A peptide bond is made between the two amino acids in the P and A site.

Front 52

- Translation -

Describe what happens during Elongation

Back 52

- The ribosome moves along the mRNA strand by one codon position in a 5' -> 3' direction.

- The decylated (no amino acid) tRNA moves the the E site and is released. The tRNA in the A site moves to the P site and is now carrying the polypeptide chain.

- A new tRNA moves into the A site, and the process is repeated until a STOP codon is reached.

Front 53

- Translation -

Describe what happens during Termination

Back 53

- When a stop codon is reached to the A site, it recruits a releasing factor signaling to stop translation

- the tRNA in the P site is released, and the polypeptide chain is detached.

Front 54

- Translation -

What is a releasing factor?

Back 54

a factor recuited by a STOP codon to bind to the A site in a ribosome and terminates translation by releasing the tRNA in the P site.

Front 55

What is the difference between a free ribosome and a bound ribosome?

Back 55

A free ribosome floats freely in the cytosol

A bound ribosome is bound to the surface of the rough ER

Front 56

What determines whether a ribosome will become free or bound?

Back 56

If the synthesized protein is to be used for intercellular use, the ribosome remains free and unattached.

If the synthesized protein is to be used for secretion, membrane fixation or for the lysosome, the ribosome will become bound to the ER.

Front 57

What determines and regulates protein destination?

Back 57

protein destination is determined by the presence or absence of a signal sequence. When it is present, a signal recognition particle will bind to it and bind the ribosome to the ER surface.

Front 58

Describe the process of ribosome binding using SRP

Back 58

- when and if a signal sequence is synthesized by the ribosome, a signal recognition particle (SRP) binds to it and halts translation.

- The SRP-ribosome complex binds at a receptor located on the ER membrane.

- Translation is re-initiated and the polypeptide chain continues to grow via a transport channel into the lumen of the ER.

Front 59

What are polysomes?

Back 59

Polysomes are multiple ribosomes attached to a single mRNA strand.

Front 60

Why can transcription and translation happen at the same time in prokaryotes but not in eukaryotes?

Back 60

Prokaryotic transcription and translation can occur simultaneously as they both occur in the cytoplasm.

In eukaryotes, transcription occurs in the nucleos and translation occurs in the cytoplasm. the transcribed strand needs to first be transported outside the nucleus before it can be translated.

Front 61

What are the levels of complexity in protein structure?

Back 61

primary structure (1 degree)

Secondary structure (2 degrees)

Tertiary structure (3 degrees)

Quaternary structure (4 degrees)

Front 62

What consists of the primary structure (1 degree) in proteins and what does it determine?

Back 62

- The order and sequence of amino acids

- Formed by covalent bonds between the amine and carboxyl groups of adjacent amino acids.

- Determines the protein structure as it determines the nature of interaction between amino acid R groups.

Front 63

What consists of the Secondary structure (2 degrees) in proteins what does it determine?

Back 63

- The formation of alpha-helicase and beta-plated sheets.

- the folding is from hydogern bonds between the amne and carboxyl groups of non-adjacent acids.

- Provides polypeptide stability

Front 64

What consists of the primary structureTertiary structure (3 degrees) in proteins and what does it determine?

Back 64

- The further folding of the polypeptide stabilized by the R group interactions.

- the polypeptide coils and forms a 3D shape

- caused by R group bonds; hydrogen bonds, disulfide bridges, ionic bonds and hydrophobic interactions.

Front 65

Lable the diagram of a tertiary protein structure

Back 65

1. Hydrogen bond

2. Hydrophobic interaction

3. Disulfide bridge

4. Ionic bond

Front 66

What consists of the primary structureQuaternary structure (4 degrees) in proteins and what does it determine?

Back 66

This structure exists in protiens with more than one polypeptide chain

- multiple polypeptides and inorganic prosthetic groups may interact together to form a huge protein, held by many bonds.

Front 67

What is a conjugated protein?

Back 67

A protein with a Quaternary structure containing a prosthetic group is a conjugated protein.