Genetics, Cell Division, and Gene Expression Flashcards

Question

Semi-Conservative Replication

Answer 1

When DNA duplicates, it keeps one strand and makes a new one

Answer 2

**Separation** ● Straightening → Topoisomerase ● "Unzipping" → Helicase ● Maintaining strands separated → Single-strand-binding proteins **Elongation** ● RNA Priming (sometimes DNA) → Primase (a kind of polymerase) ● Synthesis → DNA Polymerase III ● Proofreading → DNA Polymerase III ● Replacing RNA with DNA → DNA Polymerase I ● "Stitching" DNA → DNA Ligase

Answer 3

Topoisomerase relaxes the double helix so it can be "unzipped" without the tensions created by the twist

Answer 4

Cuts the sugar-phosphate backbone to allow for over-/under- winding, then repairs the bond once it’s done

Answer 5

Pulls apart the double strand so each strand can be accessed individually

Answer 6

3' to 5' (reading) Note, the nucleotides you're adding are from the 5' to 3' direction

Answer 7

Primase needs to create a primer of ~10 RNA NTs on the DNA template strand **DNA pol III can add dNTPs once a primer is in place**

Answer 8

Primase is a kind of RNA polymerase It adds RNA nucleotides: ● ATP ● UTP ● CTP ● GTP onto a template strand This must be done before DNA polymerase can add nucleotides to the template strand

Answer 9

Many different types exist they all: ● Add nucleotides 1 at a time Most of them also: ● Perform proofreading Some of them also: ● Remove primers

Answer 10

DNA pol has a proofreading function, if the wrong base is added, it removes it before continuing, then adds the correct base and continues with the extension

Answer 11

Leading strand follows the direction of DNA helicase. The lagging strand elongates in the opposite direction of the DNA helicase.

Answer 12

The little bits of code on the lagging strand Note: not the primer

Answer 13

Ligase joins broken DNA Useful for **joining** Okazaki **fragments** during replication but also for **repairing** DNA that has been **damaged** by environmental factors such as radiation

Answer 14

The circular bacterial chromosome has a **single origin of replication** From the OOR, two helicases begin to separate the strands in opposite directions, forming a **replication bubble** Eventually the replication forks meet and the replication is complete * Termination sequences and a special protein help to seperate the forks where they meet

Answer 15

The linear eukaryotic chromosome has a **multiple origins of replication** From each OOR, two helicases begin to separate the strands in opposite directions, forming a **replication bubble** for **every origin** In humans there are about 100000 OOR in total

Answer 16

Telomeres are repetitive sequences (TTAGGG mammals) The ends of eukaryotic chromosomes are capped by telomeres DNA pol cannot copy to the very end of a strand so capping sequences **provide a buffer to avoid information loss**

Answer 17

Telomerase maintains the telomeres The activity of the enzyme is reduced in adult cells and one of the theories of aging involves the shortening of the telomeres leading to health problems as cells divide Note: too much tlomerase activity is linked to cancer

Answer 18

Circular chromosome but multiple origins of replication

Answer 19

Origin of replication sequences tend to be AT-rich

Answer 20

A laboratory technique for rapidly producing (amplifying) millions to billions of copies of a specific segment of DNA

Answer 21

Thermophilous bacteria revolutionized molecular biology As a thermophile, its enzymes are stable at high temperatures The DNA pol used in PCR comes from *T. aquaticus* and is known as *Taq* pol

Answer 22

The synthesis of RNA from DNA RNA becomes a messenger carrying DNA instructions

Answer 23

Does everything: ● Separates DNA (no helicase needed) ● Reads DNA and synthesises RNA ● Proofreads the growing RNA strand

Answer 24

**Upstream** - Toward the 5' direction **Downstream** - Toward the 3' direction

Answer 25

Another word for template strand RNA pol only reads this

Answer 26

● A region used to recognise the "beginning" of a gene during transcription ● **Transcription factors and RNA pol bind to different sections of the promoter to begin transcription** ● TATA box is a conserved sequence of most promoters and marks the specific section for RNA pol to bind to

Answer 27

● The general TATA sequence is TATAWAW (W can be A or T) ● TATA-box binding protein binds to the TATA box sequence and crimps the DNA ● RNA pol binds downstream of this protein to begin transcription

Answer 28

The process assembling all the machinery needed for transcription to occur

Answer 29

A gene alone is not enough to make a protein, the promoter has the function of telling RNA pol to make RNA from the gene Regularly used to drive the expression of recombinant proteins in plants

Answer 30

The same transcript that is being produced signals the termination of the transcription

Answer 31

● The operon is a gene structure that allows more than one gene to be controlled by the same operator ● Example: lac operon, the genes that control proteins related to lactose acquisition and metabolism

Answer 32

Transcription coupled to translation ● No further processing of RNA is required

Answer 33

The transcribed RNA needs further processing in Eukaryotes ● In eukaryotes, transcription produces immature messenger RNA or 'pre-mRNA' ● pre-mRNA processing is known as post-transcriptional modification

Answer 34

A modified guanosine is added at the 5' end: **7-methylguanosine**

Answer 35

● 10 – 30 nt downstream of the sequence AAUAAA (or AUUAAA) the end of the capped pre-mRNA is cleaved (cut off) ● Many factors are involved

Answer 36

● A long tail of adenosines is added at the 3' end (about 250-nt long) ● This is known as polyadenylation ● Poly-(A)-polymerase adds the ATP's

Answer 37

● Introns are removed ● Messenger RNA (mRNA) is now mature

Answer 38

● mRNA — Messenger ● rRNA — Ribosomal ● tRNA — Transference

Answer 39

This is highly efficient: transcribe a single gene, obtain three separate components rRNA makes up the ribosomes together with proteins

Answer 40

tRNA is the RNA that transfers single amino acids to the ribosome during protein synthesis Processing is necessary to force the tRNA into the proper shape to fit in the ribosome

Answer 41

Modified bases let tRNA assume complex shapes not achievable with regular bases Common modifications: * Adenosine (A) → Inosine (I) * Uridine (U) →Pseudorine (♆)

Answer 42

Complex 3D twists and turns give the tRNA a functional shape

Answer 43

False * Only Eukaryotes do this

Answer 44

This is a multi-step process done to ensure the integrity of the mRNA * This is also known as * post-transcriptional * modifications * Fully-processed mRNA is also called mature mRNA Steps: * Capping * Cleaving * Polyadenylation * Splicing

Answer 45

"Cutting out" different bits of the same genetic code to make different protiens

Answer 46

The synthesis of protein from RNA (mRNA) DNA: encrypted instructions mRNA: unencrypted message Protein: translated (effected) message * **Puts the intructions in the message into action**

Answer 47

Amino acids need to be "loaded" onto tRNA **Aminoacyl-tRNA synthetase** binds the tRNA (catalytic site) and attaches the amino acid at the 3' end (editing site)

Answer 48

"Aminoacyl-tRNA synthetase" is any enzyme from a family of synthetases * There is one for each tRNA-aa pair Aminoacyl-tRNA synthetase binds the tRNA (catalytic site) and attaches the amino acid at the 3' end (editing site)

Answer 49

Before loading, aa's need to be "activated" aa + ATP → aa-AMP + PPi aa-AMP + tRNA → aa-tRNA + AMP

Answer 50

Some aa’s are encoded by multiple codons, but there is only one tRNA anticodon to match with each codon. How? → The “wobble” position. The “wobble” is made possible by modified bases Inosine (I) can pair with C, U, and also A (recall than I is A modified) Guanine (G) naturally pairs with U besides the normal C pairing

Answer 51

Prokaryotes contain a highly-conserved recognition sequence where the small ribosomal subunit binds: AGGAGG[U] There can be multiple of these sequences * Transcripts with multiple Shine-Dalgarno sequences also have multiple START and STOP codons

Answer 52

Ricin removes a **single adenine** from the sarcin/ricin loop in the ribosomal RNA, this **inactivates the ribosome**

Answer 53

It inibits RNA pol II

Answer 54

NOPE The polypeptide must be folded and have a purpose to be a protein "Protein folding is the first, most obvious change that happens to a polypeptide chain after it has emerged from the ribosome"

Answer 55

The only thing that makes a protein work is its shape!!! Wrong shape = useless or harmful * Prions * Alzheimers

Answer 56

Prions: infectious disease-causing proteins Prions force normal proteins into bad shapes

Answer 57

Chaperones help proteins fold They are proteins that protect other proteins from their surroundings so they can fold without interacting with other elements that could cause them to misfold

Answer 58

Hsp90 maintains protein “health” for a number of specific proteins Exactly what these protein does is not entirely clear but is helps to maintain proper folding during stress * It works with ATP and Sba1, a co-chaperone protein

Answer 59

Most proteins require changes before being functional Cleaving - Protein function Phosphorylation - General Activation Acetylation - Gene Expression Methylation - Protein Function

Answer 60

Bits and pieces of the polypeptide may have to be cleaved for proper function Example: pepsin and pepsinogen * Pepsin is an enzyme that digests proteins * Pepsinogen is the proenzyme and it is not active * In low pH, pepsinogen cleaves itself and becomes pepsin

Answer 61

Proteins need to be localized to their target site within the cell * Proteins have recogniseable sequences or "signals" used in trafficking Target: **cytoplasm** → Free ribosomes simply **release it in the cytoplasm** Target: **cell compartment or export** → Ribosomes **localise** to the **ER** where polypeptides can be processed in the (ER’s) lumen

Answer 62

The signal recognition particle is a ribonucleoprotein * Note: this is on the protein sequence

Answer 63

Yes Mitochondria and chloroplasts have their own ribosomes to make some proteins from their own mRNA transcribed from their own circular DNA Example: RuBisCO’s large subunit is synthesized by chloroplasts’ ribosomes.

Answer 64

**Cytosol** No signal → free ribo. → no signal **Nucleus Mitochondria*, Plastids*, Peroxisomes** No signal → free ribo. → organelle signal **Export** ER signal → ribo. @ ER → no signal **Plasma membrane, Nuclear envelope, ER, Golgi, Lysosomes** ER signal → ribo. @ ER → organelle signal

Answer 65

Localization happens by recognition of protein signal sequences

Answer 66

For protein-coding genes, the product of gene expression is the protein it encodes Note: Expression needs to be highly regulated or else chaos ensues

Answer 67

Prokaryotes mostly regulate at the transcription level How much mRNA is made dictates how much product is available

Answer 68

Eukaryotes regulate at **every possible level** and then some Every step that can be used for regulation is used for regulation Why? * Many Eukaryotes are multicellular, so unregulated protein-synthesis creates problems

Answer 69

Eukaryotes use an enhancer region Together with specific transcription factors (activators) they are part of the transcription initiation complex

Answer 70

All cells share the same genes, but different genes are expressed in different cells Multicellular Eukaryotes need to coordinate which cells express what Together with specific transcription factors (activators) they are part of the transcription initiation complex

Answer 71

miRNAs interrupt the translation process by binding to the mRNA and impeding the ribosome

Answer 72

5' UTR's imprint the half-life of the transcript Poly-A tail length affects the half-life R

Answer 73

● Regulatory protein used by most Eukaryotes ● It’s called ubiquitin because it’s ubiquitous! ● It’s a small protein, just 76 aa-long in humans **Ubiquitin proteins tag other proteins. At least 4 needed for degradation** Affects protein: ● Degradation ● Location ● Activity ● Interaction

Answer 74

**Protein shredder** ● Destroys proteins ● Active sites are on the inside to protect the cell ● The ends are capped ● Shreds proteins into 3 – 23 aa-long pieces

Answer 75

Epigenetics are changes to the DNA molecule, but not to the code! * Histone tails can be acetylated, DNA can be methylated * DNA methylation is said to "tag" the DNA in specific ways

Answer 76

**Semipermanent** and **heritable**. Large implications such as in addiction models and other social issues such as trans-generational trauma.

Answer 77

Some female mammals (including humans) randomly inactivate one copy of their X chromosome Example: the coat pattern of a calico cat

Answer 78

NOPE Mutations need not occur in the protein-coding region to have an effect Example: Haemophilia Several possible mutations. Most common forms involve a mutation to the promoter of a gene coding for a clotting factor.

Answer 79

A variant in the code of at least 1% of the population Example: sickle-cell anemia * Single-base substitution missense mutation in the 6th codon of the gene coding for haemoglobin * **Non-conservative** * mutation (aa's with different properties)

Answer 80

Yes Sickle-cell: a recessive evolutionary advantage ~4 million are homozygous ~43 million are "sickle trait" **Heterozygous "sickle-trait" individuals have resistance to malaria** * 80% of cases occur in Sub-Saharan Africa

Answer 81

False Examples: * Turner syndrome (missing X chromosome) * Cri du chat (missing part of chromosome 5) * Down syndrome (extra chromosome 21)

Answer 82

* Sickle-Cell Anemia * Cystic Fibrosis

Answer 83

● B period: cell growth ● C period: DNA replication ● D period: fission **THIS IS NOT MITOSIS!!!!** This is also exponential growth (in theory)

Answer 84

Binary Fission

Answer 85

The ParABS system ensures that the chromosome is segregated, the full mechanism is under investigation Proteins parA and parB move the chromosome, **without polymerising** into long chains * Not cytoskelital involvement **Prokaryote Exclusive!**

Answer 86

ParS is a well conserved region of DNA * It does not make a product, but s very useful in Prokaryotic DNA replication It is located next to the origin of replication, making it the first to be replicated in DNA replication

Answer 87

It binds to ParS parB proteins are guided to move toward the opposite pole guided by a concentration gradient of parA proteins

Answer 88

**ori #1 is anchored at the membrane at one of the cell's poles** * This makes it so only ori # 2 can follow the gradient ori #2 is anchored at the other pole once it gets there

Answer 89

This is a process that only occurs for some bacteria * Only occurs when environmental conditions get hard ● Fission starts but stops at cell expansion ● A double-membrane capsule is formed around one chromosome ● The rest of the cell dissolves This forms an endospore that can wait it out until conditions improve

Answer 90

Includes: ● Double membrane ● One chromosome ● A few copies of DNA pol ● A few ribosomes Excludes: ● Water (mostly)

Answer 91

G1: growth and RNA synthesis, no DNA synthesis S: Synthesis of DNA proteins and DNA replication G2: further growth and synthesis of mitosis-related RNA and proteins M: Mitosis

Answer 92

Yes * They can enter the G0 state, which stops them from starting DNA replication **Permanently**: neurons **Temporarily**: liver cells In many tissues contact inhibition is a major trigger to enter the G0 state (cells can sense their neighbours)

Answer 93

Some cells reproduce **continuously**, e.g.: ● Epithelial cells replace themselves ● Bone marrow is highly active Some cells reproduce **if required**, e.g.: ● White blood cells ● Hepatocytes (liver cells) Some cells **cannot / will not**, reproduce, e.g.: ● Neurons ● Red blood cells

Answer 94

Prophase: condensation Prometaphase: spindle formation Metaphase: chromosome alignment Anaphase: separation of chromatids Telophase: unpacking

Answer 95

Cell synthesises **proteins** and **ribosomes**, and reproduces **organelles** in preparation for cell division Assembly and loading of **cohesin** proteins

Answer 96

DNA replication Replication creates two **chromatids** from each chromosome **Cohesins** are trimeric proteins that hold **sister chromatids** together All of this happens in the nucleus

Answer 97

The centrosome (a pair of centrioles) is replicated during the S phase, along with DNA (but in the cytoplasm) Animal Only!!

Answer 98

DNA is already duplicated, awaiting further cell preparations before division **Mitotic chromosomes** are **inaccessible**, so all the components needed to carry out mitosis need to be synthesised **before** the DNA is fully **condensed**

Answer 99

Condensin proteins contribute to chromatid condensation * Cable Managment * Keeps the chromasomes condensed

Answer 100

Diploid organisms have pair of homologous chromosomes ● Humans: 23 pairs ● Jack jumper ants: ○ Females: 1 pair ○ Males: 1 single (haploid) ● Ophioglossum pycnostichum: 630 pairs!!! ← a fern

Answer 101

**Condensed sister chromatids remain attached at one point by the centromere** A complex of proteins bind to specific regions in each chromosome, holding both chromatids Centromere placement varies in each chromosome

Answer 102

**Spindle formation and nuclear dissolution** The spindle forms the tracks on which the chromosomes ride Between prophase and metaphase, the spindle forms from the centrioles It’s called a spindle for its shape, reminiscent of a drop spindle used for spinning yarn What's the spindle made of?

Answer 103

Kinetochore proteins are attached to the centromere * Attaches chormasomes to the microtubule of the spindle They link the mitotic chromosomes to the spindle

Answer 104

Chormosome alignment

Answer 105

Seperation on chromatids and elongation of the cell

Answer 106

In animal cells, microfilaments divide the cell They create a furrow by forming a ring around the equator and contracting it, like a drawstring

Answer 107

Difference #1: Cells expand during interphase, never during anaphase * Plant cell walls need to loosen up to allow expansion * Plants need to deal with the very specific process of cell expansion before or after attempting mitosis (but not during) Difference #2: **No centrosomes** * But they do still have a mitotic spindle! Difference #3: No furrow in cytokinesis * A phragmoplast forms a scaffold and vesicles deposit new cell wall

Answer 108

G1 — End of G1 Regulatory Protein: G1-CDK G2 — Start of mitosis (G2/M) Regulatory Protein: M-CDK M — Start of anaphase Regulatory Protein: APC **Regulatory proteins** give the "go ahead" at each checkpoint The cell cycle can be halted at any of these points

Answer 109

Controls the entry into the S phase **This is the “commit to division” checkpoint** Unicellular: is the cell **large enough** to reproduce? Multicellular: is the cell **supposed** to reproduce? * Neuron? * Too close to other cells? If all checks out: ● Activate G1-CDK Otherwise: ● Remain in G0

Answer 110

**Controls the entry into mitosis** Is DNA replication and repair complete? → If no, wait → If yes, form the M-CDK complex (different cyclin and different CDK from G1) M-CDK phosphorylates proteins involved with chromosome condensation

Answer 111

**Controls entry into anaphase ** Is every chromosome attached to kinetochore MTs? → If no, wait → If yes, activate APC proteins APC: anaphase-promoting complex; signals other proteins to break down cohesins

Answer 112

Growth factors regulate cyclin-CDK complexes Can be: ● Positive (Platelet-Derived Growth Factor) * Promotes cell division ● Negative (Myostatin) * Inhibits cell division

Answer 113

A single nucleotide base in a DNA sequence is swapped for another one, resulting in a different codon and, therefore, a different amino acid

Answer 114

A mutation that changes an amino acid in a protein to a stop codon which ends synthesis of the protein at that location.

Answer 115

UAA UAG UGA

Answer 116

Kinetochores (motor protiens) rachet along the the microtubules, dissassembleing them in the process

Answer 117

No furrow in cytokinesis A **phragmoplast** forms a scaffold and vesicles deposit new cell wall

Answer 118

**Loading** - A site **Creating amino acid** - P site **Exiting** - E site

Answer 119

It attaches the right amino acid onto the right RNA sequence

Answer 120

5' to 3' Note: this is the DNA be added or the "writting" direction

Answer 121

1. Capping 2. Cleaving 3. Polyadenylation 4. Splicing This is done to ensure the **integrity of the mRNA** * make sure the enzymes don't eat it

Answer 122

False This only happens in Eukaryotes * They are things like splicing factors and cleavage factors

Answer 123

The promoter * The TATA box provides the specific section for RNA pol to bind to

Answer 124

The terminator * May be intrinsic (ex. terminating hairpin) or factor dependant (ex. Rho factor)

Answer 125

When a change does not affect function but rather strength of a phenotype is often called a variant