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Advanced cell biology/Molecular biology and genomics Flashcards

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1
Q

Oocyte

Cell type

A

Consists of 22 autosomes and a X-sex chromosome

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2
Q

Spermatocyte

Cell type

A

Consists of 22 autosomes and a X or Y sex chromosome

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3
Q

Autosomes

Chromosomes

A

An autosome is one of the numbered chromosomes, as opposed to the sex chromosomes. Humans have 22 pairs of autosomes

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4
Q

Meiosis

A

Meiosis is a type of cell division in sexually reproducing organisms that reduces the number of chromosomes in gametes (the sex cells, or egg and sperm)
- Recombination happens during chromosome cross-over

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5
Q

Mitosis

A

Mitosis, a process of cell duplication, or reproduction, during which one cell gives rise to two genetically identical daughter cells.

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6
Q

Chromosome (roles)

A
  • Transmits genetic information through meiosis/mitosis
  • Control expression of genetic information
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7
Q

Chromosomal territories

A

Territories are specific and interfere with expression, where chromosomes with many active genes are located in the center.
This placement of chromosomes are fluid

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8
Q

TADS

Chromosomes

A

Topological associating domains, and are highly heterogeneous structures due to their formation of loop extrusion by a cohesion complex and CTCF.
contribute to the regulation of gene expression by restricting interactions of cis-regulatory sequences to their target genes. Compartment A/ active genes and compartment B/nonactive genes

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9
Q

Chromatin loops

Chromosomes

A

stretches of genomic sequence that lie on the same chromosome (configured in cis) are in closer physical proximity to each other than to intervening sequences.
associated with DNA replication, gene expression and higher order packaging.

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10
Q

Structural abnormalities

Chromosomes

A

Happens during recombination and can lead to:
Translocations, Inversions, Duplications, Deletions, Ring, Marker

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11
Q

Numerical abnormalities

Chromosomes

A

Happens during first and second division of meiosis and can lead to:
Polyploidies and Aneuplodies

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12
Q

pseudoautosomal region cross-over

Chromosomes

A

Recombination of pseudoautosomal region at SRY can lead to XX-Male or XY- female

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13
Q

Reciprocal translocation

Chromosomes

A

occur due to the exchange of chromosome material between two nonhomologous chromosomes. When the amount of genetic material is balanced, there is no phenotypic effect on the individual because of a balanced complement of genes.
- Breakpoint disturbs dominant gene and increases ininfertility

  • Segregation can lead to balanced and unbalanced segregation
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14
Q

Robertsonian Translocation

Chromosomes

A

type of translocation caused by breaks at or near the centromeres of two acrocentric chromosomes. The reciprocal exchange of parts gives rise to one large metacentric chromosome and one extremely small chromosome that may be lost from the organism with little effect because it contains few genes.

  • Segregation can lead to trisomy, monosomy, carrier and normal phenotype
  • Chromosomes 13, 14, 15 and 21 are robertsonian chromosomes
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15
Q

Locus

Chromosomes

A

Unique location of a gene on a chromosome

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16
Q

Allele

Chromosomes

A

Alternative version of a gene

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17
Q

Monogenic

Genes

A

Mutation in one gene

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18
Q

Multifactoral

Genes

A

Mutations in several genes plus milieu, complex pattern of inheritance
- Higher risk if more than one member is affected
- increased severity equals greater recurrance

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19
Q

Locus heterogeneity

Genes

A

Mutations in different genes leads to same disease

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20
Q

Allelic heterogeneity

Genes

A

Mutation in same gene leads to same disease

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21
Q

Compound heterozygote

Genes

A

Two different allele mutations and no healthy allele, leads to an in between phenotype

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22
Q

X-inactivation

Chromosomes

A

process by which one of the copies of the X chromosome is inactivated in therian female mammals. The inactive X chromosome is silenced by being packaged into a transcriptionally inactive structure called heterochromatin

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23
Q

Negative selection

A

Reduced fitness

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24
Q

Positive selection

A

Increased fitness

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25
Q

Loss of function

Genes

A

Function of gene product is lost or reduced

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26
Q

Gain of function

Genes

A

Gene product gains new function or increased function

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27
Q

Haploinsufficiency

Genes

A

50% of gene product is not sufficient to maintain function

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28
Q

Missense mutations

Genes

A

Nucleotide mutation leads to change of amino acid

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29
Q

Non-sense mutation

Genes

A

Nucleotide substitution leading to premature stop-codon

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30
Q

Synonymous mutation

Genes

A

Nucleotide substitution with no amino acid change

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31
Q

polymorphisms

Genes

A

Mutation with a population frequency larger than
0,01.

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32
Q

False discovery rate

A

The False Discovery Rate (FDR) is a statistical concept used in hypothesis testing and multiple comparisons, less conservative approach than traditional methods described earlier.

FDR = FP / (FP + TP)

  • Standard adjusted P-value in GWAS studies

FP = false positives, TP= True positives

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33
Q

Splice site mutations

A

Abnormal mRNA splicing caused by mutations in acceptor splice-site, donor splice-site or branch site

  • May cause introns not spliced out or exon skipping, mutations in donor sequence (upstream exon skipping) and in acceptor sequence (downstream exon skipping)
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34
Q

Regulatory region mutations

A

mutations outside coding regions, may cause changes to promotor region, enhancers/repressors, splice-enhancers, non-coding RNA.

  • may lead to changes in expression level of genes
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35
Q

trinucleotide repeats

A

Repeats of a codon

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36
Q

anticipation
(Genetics)

A

correlation between onset and length of trinucleotide repeats

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37
Q

Copy number variation

A

segment of DNA in which copy-number differences have been found by comparison of two or more genomes

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38
Q

Chiasmata

chromosomes

A

the point of contact, the physical link, between two (non-sister) chromatids belonging to homologous chromosomes

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39
Q

Non-allelic homologous recombination

Chromosomes

A

form of homologous recombination that occurs between two lengths of DNA that have high sequence similarity, but are not alleles.

  • leads to duplication or deletion
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40
Q

Sanger sequencing

Method

A

Sanger sequencing is a targeted sequencing technique that uses oligonucleotide primers to seek out specific DNA regions.

  1. DNA Replication: The DNA fragment to be sequenced is replicated in a test tube using DNA polymerase, just like in regular DNA replication.
  2. Modified Nucleotides: Special dideoxy nucleotides (ddNTPs) are added to the reaction mix. These ddNTPs lack a 3’ hydroxyl group, which prevents further DNA strand elongation when they are incorporated into the growing DNA strand.
  3. DNA Fragment Termination: The DNA polymerase randomly incorporates regular nucleotides (dNTPs) and the ddNTPs into the growing DNA strand. When a ddNTP is added, it terminates the strand’s growth at a specific position.
  4. Separation by Size: The resulting DNA fragments of varying lengths are separated by size through gel electrophoresis or capillary electrophoresis.
  5. Readout: The separated fragments are detected, and their order is determined based on their size
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41
Q

Next generation sequencing

Method

A
  1. LibraryPreparation—The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed
    by 5′ and 3′ adapter ligation. Adapter-ligated fragments are then PCR amplified and gelpurified.
  2. ClusterGeneration—Library is loaded into a flow cell where fragments are captured on a lawn of surface-bound oligoscomplementary to the library adapters. Each fragment is then amplified into distinct, clonal clusters through bridge amplification .
  3. Sequencing—detects single bases as they are incorporated into DNA template strands by DNA polymerase. As all four reversible terminator–bound dNTPs are present during each sequencing cycle, natural competition minimizes incorporation bias and greatly reduces raw error. After each nucleotide addition, there is a cleavage step facilitated by exonuclease to remove unincorporated nucleotides and terminators
  4. DataAnalysis—Duringdata analysis and alignment, the newly identified sequence reads are aligned to a reference
    genome
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42
Q

Single cell sequencing

Method

A
  • Single-Cell RNA Sequencing (scRNA-seq): This technique analyzes the transcriptome of individual cells, revealing their gene expression profiles. It’s valuable for understanding cell types, differentiation, and gene regulation.
  • Single-Cell DNA Sequencing: Focuses on the DNA content of single cells, helping to detect genetic mutations, variations, and genomic changes at the individual cell level.
  • Single-Cell Proteomics: Characterizes the protein content of individual cells, providing insights into the proteomic landscape of cells. It’s often used to study protein expression and post-translational modifications.
  • Single-Cell Epigenomics: This method examines epigenetic modifications within individual cells, revealing how gene expression is regulated through epigenetic mechanisms like DNA methylation and histone modifications.

These techniques enable researchers to explore the biology of individual cells, uncovering heterogeneity and insights that bulk analyses might miss.

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43
Q

Functional test-enzymatic activity

Method

A

Function of a gene product can be analysed in the lab.
- it is specific for a given gene – DNA technology is generic

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44
Q

RNA-analysis

Method

A

conversion of RNA, either total, enriched for mRNA, or depleted of rRNA, into cDNA. After fragmentation, adapter ligation, and index ligation, each cDNA fragment is subsequently sequenced or “read” using a high-throughput platform

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45
Q

Types of DNA-analysis

Method

A

DNA analysis methods encompass a range of techniques used to study and analyze DNA, which is the genetic material in living organisms.
- Polymerase Chain Reaction (PCR)
- Short Tandem Repeats (STR)
- Y-Chromosome.
- Mitochondrial DNA
etc.

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46
Q

Diagnosis methods of specific defined genomic variants

Method

A
  • Presence/absence of restriction site
  • Allele-specific PCR amplification (primer differentiation)
  • Allelic discrimination (PCR)
  • Sequencing
  • Single base primer extension
  • Oligonucleotide ligation assay
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47
Q

Allelic discrimination

Method

A

Allelic discrimination relies on the differences in DNA sequences between the two alleles being analyzed. These differences can involve single nucleotide polymorphisms (SNPs), insertions, deletions, or other genetic variations.
- two different SNP-specific probes, labeled with different reporters

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48
Q

Oligonucleotide ligation

Method

A

The oligonucleotide ligation assay (OLA) is a genotypic assay which has been used to identify point mutations in DNA for a variety of diseases.

  • covalent joining of two adjacent oligonucleotides by a DNA ligase when they are hybridized to a cDNA target.
  • This happens if there is a point mutation between the two oligonucleotides
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49
Q

Pharmacokinetics

A

Genetic variations affecting how a drug is absorbed, distributed, metabolized and activated and eliminated

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50
Q

Pharmacodynamics

A

genetic variations affecting how a target patient responds to a drug

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51
Q

PCR in identification

Method

A
  • restriction enzymes
  • PCR product

method is aplicable in essential genes to identify abnormalaties to identify diseases

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52
Q

PCR cloning

Method

A

PCR product is digested by restriction enzymes and transfered into a vector, with overhang or blunt ends
1. PCR
2. Digestion with restriction enzymes
3. ligase ligases product into plasmid vector

  • Make multiple copies
  • express proteins
  • Transfect mamalian cells
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53
Q

qPCR

Method

A

Quantitative PCR (qPCR), also called real-time PCR or quantitative real-time PCR, is a PCR-based technique that couples amplification of a target DNA sequence with quantification of the concentration of that DNA species in the reaction.
- Uses flourescense to measure amount of amplicon product pr. cycle (SYBR green dobbelstranded DNA or Taqman probe cleaved when transcribed)

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54
Q

Cancer cells

A

Self-sufficiency in growth signals, insensitivity in growth signals, evading apoptosis, unlimited replication potential, sustained antigonesis and metastesise
- 6-7 key mutations needed

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55
Q

Carcinoma

cancer

A

In external tissue and internal body surfaces

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56
Q

Sarcoma

cancer

A

In supporting tissue

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57
Q

Lymphoma

cancer

A

In lymphocytes

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58
Q

Leukemia

cancer

A

In bloodcells

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59
Q

Proto-oncogenes

A

Normal gene and it plays a role in regulating normal cell division

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60
Q

Oncogenes

A

mutated gene that has the potential to cause cancer

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61
Q

loss of heterozygosity

A

loss of one parental copy in a region is also called hemizygosity in that region. Originally, a heterozygous state is required and indicates the absence of a functional tumor suppressor gene copy in the region of interest.

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62
Q

Types of DNA damage

A

Chemical mutagens
thymidine dimers
Interstrand crosslinks

Base changes:
- base excision
- mismatch pair
- insertions
- deletions

Single strand breaks:
- ligase
- topoisomerase

Double strand breaks:
- Non homologous end joining (error prone)
- Microhomology-mediated break-induced replication (error prone)
- Homologous recombination (error free)

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63
Q

Heteroplasmy

A

mixture of different versions of DNA

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64
Q

Homoplasmy

A

Uniform collection of mtDNA

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65
Q

Mitochondria segregation

A

randomly dispersed, which can cause a random occurance of nonfunction of dysfunctional mitochondria

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66
Q

Transgenic mice

A

Advantages:
- quick
- dominant active mutants
- dominant negative inhibition of protein families
- over- or regulatable expression possible

Disadvantages:
- unphysiological expression
- expression level determines effect
- endogenous wild type protein still present

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67
Q

Pluripotent cells

A

stem cell that has the potential to differentiate into any of the three germ layers

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68
Q

Conditional mutagenesis

A

technique used to study the function of genes in a specific tissue or at a specific time. It involves the insertion of loxP sites into the genome of an organism, which can be used to control the expression of a gene.
It allows the DNA modification to be targeted to a specific cell type or be triggered by a specific external stimulus.

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69
Q

off target precision CRISPR

A

Off-target effects in CRISPR refer to unintended genetic modifications that can arise through the use of engineered nuclease technologies such as CRISPR-Cas91. These off-target effects consist of unintended point mutations, deletions, insertions, inversions, and translocations

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70
Q

Mitochondria in aging

A

mtDNA dontent decreases with age

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71
Q

Mitochondrial inhibition

A

reduces proliferation of activated T-cells, which can lead to:
- Increased infections
- Senescent cells (age-related diseases)
- Transforming cells (cancer)

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72
Q

Genome organisation

A
  • Chromatin loops
  • TADS
    -A/B compartments
  • Histones
  • Chromosome territories
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73
Q

Aneuploidies

A

the presence of an abnormal number of chromosomes in a cell, for example a human cell having 45 or 47 chromosomes instead of the usual 46

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74
Q

Histone methylation/acetylation

A
  • Histone acetylation tend to define openess of chromatin
  • Histone methylation correlate with activation of genomic regions, depending on methylation and happens in the CG pslindorme (only cystien can be methylated on 5th position)
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75
Q

Genomic inprinting

A

Some genes are only expressed by paternal and maternal genes
- Mutations in these genes lead to diseases

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76
Q

Epigenome

A

Complete description of all epigenetic marks/changes/features that regulate expression of genes within genome

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77
Q

Uniparantal dysomies

A

Meiosis I/II non-disjunction trisomy, can be rescued and lead to two paternal or maternal chromosomes inn child

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78
Q

DNA methyltransferase

A

Conserves methylation during cell devision by copying methylation from leading strand

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79
Q

Lipid membrane

A

Lipid membranes form spontanously as a membrane bilayer (semi-permeable)
- Hydrophobic tail (fatty acid)
- Glycerol
- Variable portion of head group (PE, PC, PS, PI)

Lipid membrane structure is fluid, except structures kept in place by the cytoskeleton

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80
Q

sphingolipids

A

Sphingolipids are a class of lipids that contain a backbone of sphingoid bases. These compounds play important roles in signal transduction and cell recognition.

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81
Q

Sterols (cholesterol)

A

Forms micro domains. It helps to maintain the fluidity and stability of the membrane by preventing the phospholipids from packing too closely together 2. The amount of cholesterol in the cell membrane varies depending on the type of cell

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82
Q

Membrane proteins

A

There is 7 different structures, most are associated by an alpha helix in both layers, some however only associates with one bilayer with an anchor and one by a beta-barrel structure.

  • Integral membrane proteins are a permanent part of a cell membrane and can either penetrate the membrane (transmembrane) or associate with one or the other side of a membrane (integral monotopic).
  • Peripheral membrane proteins are transiently associated with the cell membrane
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83
Q

Transmembrane Channels

A

Mainly transport Ions, exception being aquaporins.
- Facilitate diffusion down a concentration gradient

  • gated by being directed into various membranes(trafficking) or by regulation (gating)
  • Selectivity through transcient binding through the pore
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84
Q

Transporters

A

Facilitates transport through the membrane passive or active:
Uniporter (passive) allows flow down the concentration gradient

Symporter, antiporter, ATP-powered pumps (active) allows flow agianst the concentration gradient.
- The symporter and antiporter is secundary active and the transport is facilitated by a co-transport of a molecule down the gradient
- ATP-powered pumps (P-class, V-class, F-class, ABC-class) are primary active

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85
Q

The eukaryotic cell cycle

A

process by which eukaryotic cells divide and reproduce. It consists of four distinct phases: G1 phase, S phase (synthesis), G2 phase (collectively known as interphase) and M phase (mitosis and cytokinesis).
- During interphase, the cell grows, accumulates nutrients needed for mitosis, and replicates its DNA and some of its organelles.
- During the mitotic phase, the replicated chromosomes, organelles, and cytoplasm separate into two new daughter cells.

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86
Q

S phase

A

DNA synthesis
- Cyclin E and CDK2

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87
Q

G1 phase

A

cell decides wether it is dividing or not at start/restriction point
- Cyclin D and cdk4 (cyclin D is present in all phases, however it is decreased in the end of M-phase to inhibit direct transition to G1)

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88
Q

G2 phase

A

Preparation for M phase
- Cyclin A and CDK2

89
Q

M phase

A

Chromosomes is distributed
- Cyclin B and CDK1

90
Q

Cyclins

A
  • only present in stage they control and binds and activates CDKs
  • Cyclins also propel the cell cycle forward
  • Cyclins are subunits of CDKs
  • degraded via. ubiquitin-proteasome degradation: SCF, and APC/C complex
91
Q

Protein transport

A
  • Cytosol <–> Nucleus
  • Cytosol –> mitochondria
  • Cytosol –> ER <–> Golgi <–> late endosome –> lysosome
  • Cytosol –> ER <–> Golgi <–> late endosome <– early endosome <–> cell surface
  • Cytosol –> ER <–> Golgi –> cell surface
  • Cytosol –> ER <–> Golgi –> secretory vesicles –> cell surface
  • Cytosol –> plastids
  • Cytosol –> peroxisomes
92
Q

CDKs

A
  • CDK activities oscillate during the cell cycle. Positive and negative feedback
    loops drive these up-and-downs.
  • CDKs are activated by cyclin subunits, and controlled at multiple levels
  • CDK inactivation triggers mitosis exit
93
Q

Regulation of CDKs

A
  • Binding to cyclins
  • Activating phosphorylation: by CDK-kinase (CAK)
  • Inhibatory phosphorylation
  • CDK inhibitors (CKI)
94
Q

Cohesin complex

A

a protein complex that mediates sister chromatid cohesion, homologous recombination, and DNA looping
- keep duplicated chromatids together to ensure accurate segregation
- start to form behind replication fork
- Released in the end of G2 and early M phase

Shagoshin-PP2A retains cohesin complex at centromers until end of metaphase.
APC/C mediates its degradation and activates seperase.

95
Q

Mitosis requirements

A
  1. Change shape of chromatins
  2. Chromosomes need to be attached to mitotic spindle
  3. Nuclear envelope broken down
  4. Organelles rebuilt or modified
96
Q

Chromosomal condensation

A

Condensin which condensates the chromosomes is activated by mitotic CDKs and aurora B kinase

97
Q

Topoisomerase II

A

detanglement of “tangled DNA”

98
Q

Mitotic phases

A
  1. Prophase: The chromatin condenses into discrete chromosomes and kinetochores assembles on centromers
  2. Prometaphase: Mitotic spindle microtubules attach to kinetochores and nuclear envelope breaks down
  3. Metaphase: Chromosomes are ligned up at the metaphas plate
  4. Anaphase: Sister chromatids are pulled apart towards opposite poles
  5. Telophase: Nuclear envelope engulfing each set of chromosomes, mitotic spindle breaks down and contractile ring assembles under plasma membrane
  6. Cytokinesis: The cytoplasm of a single eukaryotic cell divides into two daughter cells
99
Q

Protein transport

A

Happens through:
- gated transport
- Transmembrane transport
- Vesicular transport

100
Q

Transmembrane transport (requirements)

A
  1. Signal sequence
  2. Receptor at cytosolic side of membrane
  3. Translocator
  4. Energy often in form of ATP
101
Q

Co-translational translocation

A
  • Cytosolic protein is transported by mRNA
  • Signal sequence binds to SRP-particle
  • SRP binds to receptor
  • Translocon carries the polypeptide through the membrane while it´s being translated
  • ADP is bound to the translocating polypeptide
  • ADP is phosphorylated to ATP and seperated from the polypeptide, after which it folds
102
Q

Topogenic sequence

A

Transmembrane aplha helix, that directs the insertion and orientation of the proteins in the
ER membrane

103
Q

Transmembrane protein classification

A
  • Type I: NH3 end in exoplasmic space
  • Type II: NH3 end in cytosolic space
  • Type III: NH3 end in exoplasmic space, but protein fold in cytosolic space.
  • Type IV: G-protein
  • GPI-anchored protein: anchored to membrane bound GPI
  • Tail-anchored protein:
104
Q

Protein modifications

A
  • N-Glycosylation
  • Formations of disulfide bonds
  • Oligomerization
  • Quality control
105
Q

Signal transduction

A
  • Hydrophilic signals: eg. Small molecules bind to cell-surface receptor, which gives rise to a signal pathway response
  • Hydrophobic signals: eg. Steriods bind to cytosolic receptors, which gives rise to a nuclear response
106
Q

secretion and transportation of signals

A
  • Endocrine signaling: Hormone secretion into blood
  • Paracrine signaling: cell to cell (local)
    -Autocrine signaling: same cell
  • Plasma-membrane attached proteins: adjacent cells
107
Q

Ion channel linked receptors

A

Have ion channels for anions and cations, and constitute a large family of multipass transmembrane proteins. They participate in rapid signaling events usually found in electrically active cells such as neurons. They are also called
ligand-gated ion channels.

108
Q

G-protein coupled receptors

A

are integral membrane proteins that possess seven
transmembrane helices. These receptors activate a G protein with ligand binding. The G protein is activated by binding of GTP and directly affect intracellular signaling

109
Q

Enzyme-linked receptors

A

are either enzymes themselves, or directly activate
associated enzymes. These are typically single-pass transmembrane receptors, with the enzymatic component of the receptor kept intracellular. The majority of enzyme-linked receptors are, or associate with, protein kinases and eventually affect gene transcription.

110
Q

Second messengers

A
  1. Quick response determined by rapid changes in concentration and quick diffusion in the cytosol.
  2. Amplification of the extracellular signal.
111
Q

GTP-binding proteins

A

act as “switches” regulating many signal transduction pathways through phosphorylation.
- GAP inactivator protein
- GEF Activator protein

112
Q

GPCRs

A

trimeric G proteins, which contains a, b and g subunits. The Ga subunit is a GTPase
switch protein that in active GTP bound form separates from b and g subunits and activates membrane bound effector protein. GPCR functions as guanine nucleotide exchange factor (GEF) for the Ga subunit to facilitate its activation. The Ga subunit determines the the specificity and function of the G protein

113
Q

Four basic types of receptor and transduction pathways

A
  1. Receptor-associated kinase (RTK)
  2. Cytosolic kinase (GPCR)
  3. Protein subunit dissociation (GPCR)
  4. Protein cleavage
114
Q

Receptor tyrosine kinase (RTK)

A

They are activated by binding to polypeptide growth factors, cytokines, and hormones.

RTKs are involved in mediating cell-to-cell communication and controlling a wide range of complex biological functions, including cell growth, motility, differentiation, and metabolism

  • Once activated cross phosphorylation by activated kinase domains, which initiate downstream pathway activation.’
  • Ras/ Map kinase
  • AKT (anti apoptic factor)
115
Q

JAK-STAT pathway

A

JAK binds to phosphorylated tyrosine domain, STAT binds to DNA and activates transcription
- High affinity interaction
- Short term regulation SHP1
- Long term regulation SOCs

116
Q

TGF-b receptors

A

TGFR I - dimeric transmembrane protein that contains serine/threonine kinase activity in the cytosolic domain

TGFR II - dimeric transmembrane protein that contains serine/threonine kinase activity in the cytosolic domain. Exhibits constitutive kinase activity

TGFR III – cell surface proteoglycan that binds and
concentrates TGF-b

  • SMAD2/3 is phosphorylated, which activates SMAD4 and importin, these are then imported into the nucleus and induce transcription of p15, p21, ECM proteins (collagen, etc. ) and negative SMAD regulator - SKi
117
Q

Wnt

A

signals through two cell surface receptors – Frizzled and LNP and an intacellular complex containing
b-catenin. Upon activation b-catenin is released from its inhibitory complex and translocated to the nucleus where it activates the TCF transcription factor.

118
Q

Hedgehog signal

A

acts trough two cell-surface proteins Patched and Smoothened. Activation signal stimulates release of an active transcription factor Gi and facilitates its translocation to the nucleus to activate gene expression.

119
Q

NF-kB pathway

A

responsible to the cells’ response to the infection and inflammation. NF-kappa B pathway is activated by releasing of NF-kB heterodimer from its inhibitory complex by proteolytic degradation of the inhibitory protein

120
Q

Key concepts of vesicular traffic, secretion and endocytosis

A
  1. Preservation of topology (cytoplasmic side)
  2. Trafficking of protein and lipid membrane is tied together
  3. Transport vesicles mediate all protein traffic in the secretory and endocytic pathways
121
Q

Budding and fusion of vesicles

A

Arf/Sar GTPases are responsible for coat
recruitment and vesicle budding
- COPI in Golgi-ER transport
- COPII in ER-Golgi transport
- Clathrin and dynamin to pinch of in Golgi-endosome transport and endocytosis

Fusion is facilitated by the binding of V- and T-snare Rab * GTP facilitates it and binds to tethering complex
- NSF disassambles snare complex

122
Q

Secretory pathway

A
  • Consititutive secretion
  • Regulated secretion: regulated often through Ca+
  1. Newly synthesized proteins are translocated to the rough endoplasmatic reticulum (ER).
  2. In the ER, the proteins are folded and receive covalent modifications (disulfide bonds and carbohydrates).
  3. The proteins are then transferred to the cis-Golgi network, which is formed by fusion of the transport vesicles (anterograde transport).
123
Q

Processing in golgi cisternae

A
  • From the cis-Golgi network, the secretory proteins
    move through the Golgi stack.
  • During the passage through the Golgi stack, the
    carbohydrates linked to the secretory proteins are
    further modified by specific glycosyl transferases.
  • In the trans-Golgi network proteins are sorted into different types of transport vesicles, where some proteins are cleaved by endopeptidases to activate them.
124
Q

Golgi maturation

A
  1. The cis-Golgi cisterna moves away from the ER, becoming first a medial–Golgi cisterna and then a trans-Golgi cisterna. This is called cisternal maturation.
  2. During cisternal maturation, enzymes and other resident Golgi proteins are retrieved from later to earlier cisternae by retrograde transport.
  3. Each of the different Golgi cisternae has a characteristic composition of enzymes, which is kept constant by the combination of cisternal maturation and retrograde transport.
125
Q

Secretory proteins sorting pathways

A
  1. Immediate exocytosis, without the need of a Ca2+ trigger (constitutive secretion).
  2. Temporary storage in secretory vesicles that later
    undergo exocytosis in response to Ca2+ influx
    (regulated secretion).
  3. Transport to endosomes and lysosomes. Lysosomal hydrolases and membrane proteins follow this pathway.
126
Q

Proteolytic processing of secretory proteins/enzymes

A
  1. Conversion of inactive prohormones to active hormones
    - typically occurs in regulated secretory vesicles that have budded from the trans-Golgi network.
  2. Conversion of inactive proenzymes to proteolytic
    enzymes that are active in digestion.
    - sometimes involves autocatalysis.
  3. Conversion of some constitutively secreted proteins to their mature functional forms.
    - typically occurs in the trans-Golgi network
127
Q

Endocytosis

A
  1. Phagocytosis
    - Ingestion of large insoluble particles, such as bacteria.
  2. Endocytosis
    a process where a small patch of membrane invaginates to form a vesicle (Clathrin/AP-2). Endocytosis may be:
    - unspecific: droplets of extracellular fluid and
    solutes are taken up indiscriminately. Sometimes
    called pinocytosis.
  • specific: a receptor on the plasma membrane binds an extracellular ligand and the ligand-receptor complex is internalized. Also called receptor-mediated endocytosis
128
Q

Lysosomes

A

Contain unspecific hydrolytic enzymes
- degrade internalized meterials and cellular components
- Membrane is protected from degredation with sugars

Multivesicular late endosome solve the topology problem, how integral membrane proteins, which
face the cytosol, be degraded in lysosomes.

129
Q

Autophagic pathway

A
  • Degradation pathway’
  • Involves the formation of double-membrane
    autophagosomes that wrap around cytosolic
    proteins and organelles.
  • Autophagosomes can fuse with lysosomes,
    leading to degradation of the contents and reuse
    of their constituents.
  • Is upregulated in starved cells
  • Also involved in protein and organelle quality
    control
130
Q

Protein folding

A
  • Electrostatic attractions (Strong)
  • Van der Whaals attractions (weak)
  • Hydrogen bonds (strong)
131
Q

Four broad protein structure categories

A

Globular proteins (eg. hemoglobin, antibodies)
- water soluble (generally)
- compact folded structures
- consist of a mixture of secondary structures

Integral membrane proteins (eg. Receptors, pumps, ion channels, aquaporins, transporters)
- embedded within the phospholipid bilayer (cell surface, organelles)

Fibrous proteins (eg. myosins, collagen, keratins)
- large, enlongated, often stiff molecules
- do not readily dissolve in water (insoluble)
- usually play a structural role or participate in cellular movement

Intrinsically disordered proteins (eg. PUMAs)
- very flexible polypeptide chain
- may fold into a well-defined conformation on interaction with specific proteins
- serve as signaling molecules, regulators of other molecules activity, and
scaffold multiple proteins.

132
Q

ways to regulate protein activity

A

1) Increase or decrease the steady-state level of the protein
- altering rate of synthesis (transcription rate, translation rate)
- altering rate of degradation (degradation in lysosomes or proteasomes)

2) Change the intrinsic activity of the protein
- through non-covalent interactions (eg. allosteric effectors)
- through covalent interactions (eg. phosphorylation, ubiquitination)
- proteolytic cleavage of inactive precursor protein to active protein

3) Change the location of the protein within the cell away from site of action

133
Q

feedback inhibition

A

The end product of a multistep pathway bind and reduce activity of an enzyme that catalyses an early, rate-controlling step for that pathway

134
Q

Purification of protein methods:

A

Purification based on physical properties of protein of interest
- size: Gel filtration (size exclusion chromatography)

  • charge: Ion-exchange chromotography (IEC)
  • affinity: Immobilized metal-ion affinity chromatography (IMAC) eg. histidine tag
  • Antibody affinity chromotography (immunochromatography) eg. against epitope 10-15 or against protein itself
  • Ligand affinity chromatography (immobilized substrate, receptor antagonist)
135
Q

Regulating the intrinsic activity of the protein

A
  • feedback inhibition
  • Ca2+/calmodulin-mediated switching
  • Switching mediated by guanine-nucleotide-binding proteins (GTPases)
  • Phosphorylation and dephosphorylation covalently regulate protein activity
  • Ubiquitination (Ub) and deubiquitination covalently regulate protein activity
  • Activation or inactivation of protein activity by proteolytic cleavage
136
Q

metaplasia

A

the cells of the tissue are reprogrammed to follow an alternative differentiation pattern, allowing for changes of the tissue that makes it better cope
with the irritation

137
Q

dysplasia

A

Proliferation results in abnormal tissue organization

138
Q

Neoplasia

A

An abnormal mass of tissue in which the cell deviates from normal with regard of:
- Growth
- Differentiation
- Organization
- Function

139
Q

Hallmarks of cancer

A
  • DNA repair defects
  • Defects in growth factor signalling pathways
  • evasion of apoptosis
  • evasion of cellular sensecence (shortening of telomers)
  • development of sustained angiogenesis
  • invasion and metastesis
  • Tumor promoting inflamation
  • avoiding immune destruction
  • Genome instability and mutation
140
Q

Telomerase

A

ribonucleoprotein complex, consising of RNA template and telomerase catalytic subunit
(reverse transcriptase)

141
Q

End-replication problem

A

The polymerases that copy the chromosomes of DNA strands are unable to copy completely to the end. Consequently, the new DNA molecule is shorter than the parent DNA molecule shortening the telomeres.

142
Q

miRNAs

A

short non-coding RNAs (~22nt)
- bind in the 3’ untranslated region of their target mRNA

  • inhibit translation and/or cause degradation of the target mRNA
143
Q

Resting membrane potential (Vm)

A

-70

  • K+ 140 mM intracellular and 5 mM extracellular
  • Na+ 10 mM intracellular and 145 mM extracellular
144
Q

Sodium-potassium ATPase pump

A

Uses ATP to transport ions back to up the gradient

145
Q

Neuron

A

Reception, formation and transfer of signals in the
form of nerve impulses and synaptic activity

146
Q

Glial cells

A

Supporting function:
- structurally
- metabolic
- functionally

147
Q

Structural classification of neurons

A

Unipolar: cell bodyhas one axon arm
Multipolar: cell body has several axon arms
Bipolar: has two axon arms, with cell body in the middle
Pseudounipolar: has two axon arms, with cell body connected axon arm

148
Q

Motor proteins

A

Dynein and kinesin are two types of motor proteins that move along microtubules in cells and play essential roles in intracellular transport

  • Kinesin moves along microtubules in an anterograde direction (center to periphery)
  • dynein moves along microtubules in a retrograde direction to transport various cellular cargos (periphery to center)
149
Q

Action potentials can be evoked by incoming synaptic activity

A
  • EPSP
  • IPSP
  • EPSP train
  • EPSP train + IPSP

These signals are added together, to find final stimulus input and if it is enough to provoke further action potentials

150
Q

Myelin

A

Myelin is formed by glial cells called oligodendrocytes in the central nervous system (CNS) and Schwann cells in the peripheral nervous system (PNS)
- increases velocity of impulses in nerves

151
Q

Microglial

A

neuronal support cell (neuroglia) in the central nervous system of invertebrates and vertebrates that mediates immune responses by acting as macrophages, clearing cellular debris and dead neurons from nervous tissue through the process of phagocytosis (cell eating).

152
Q

Synapse transmission

A

The presynaptic neuron releases neurotransmitters, which bind to receptors on the postsynaptic neuron and activate them. Synaptic transmission is dependent on the availability of neurotransmitters, the release of neurotransmitters by exocytosis, the binding of neurotransmitters to postsynaptic receptors, the functional response from postsynaptic cells, and the removal or deactivation of neurotransmitters through ezymes and reuptake.

153
Q

Electrical synapses

A

are fast (synaptic delay 0.1-0.5 ms)
are bi-directional (transmission in both directions)
Maintain the sign (depolarisation  depolarisation)
Function in synkronisation
Can vary their strength by opening/closing gap junctions make out approx. 1% of all synapses

154
Q

Chemical synapses

A
  • Pre-synapse: 1) filling of synaptic vesicle with neurotransmitter 2) synaptic vesicle cluster 3) vesicle docking 4) vesicle priming 5) Calcium influx and vesicle fusion 6) Direct use 7) Kiss and run 8) Clathrin-dependent endocytosis 9) recicling via. endosome and 10) break down of neurotransmitter diffusion and reuptake
    (point 6 and 4 are up to debate)
  • Post-synapse:
    Ionotropic receptors: group of transmembrane ion-channel proteins which open to allow ions such as Na , K , Ca , and/or Cl to pass through the membrane in response to the binding of a chemical messenger
    Metabotropic receptors (G-protein coupled): when activated, a series of intracellular events are triggered that can also result in ion channels opening or other intracellular events, but involve a range of second messenger chemicals
155
Q

Excitatory neurotransmitters acting on ionotrope receptors

A

glutamate, acetylcholine (nikotinic-Rec.), (serotonin)

156
Q

Inhibitory neurotransmitters acting on ionotrope receptorer

A

GABA, glycine

157
Q

Modulatoric neurotransmitters acting on metabotrobic receptors:

A

nor)adrenaline, dopamine, serotonine, histamine
acetylcholine (muscarinic-Rec.

158
Q

Spatial summation

A

The reception of several action potentials that increase EPSP above threshold (-50)

159
Q

Temporal summation

A

Reception of a action potential train from one neurotransmitter that increases ESPS above threshold

160
Q

Lambda

A

the length constant at which the action potential has decreased by 63% due to leaks along axon

161
Q

Shunting inhibition

A

Inhibitory short circut (garden hose)

162
Q

GABBA function inhibitory or excitatory

A

Depends on chloride concentration (high if inhibatory and low if excitatory)

163
Q

Associative learning depends on changing synaptic strength

A

When an axon of cell A is near enough to excite B and repeatedly or persistently
takes part in firing it, some growth process or metabolic change takes place in one or
both cells such that A’s efficiency, as one of the cells firing B, is increased

164
Q

SNARE cycle in neurons

A
  1. Assembly of pre-fusion SNARE/SM protein complex
    - Synaptobrevin/VAMP binds to Munc18 complex
    - SNAP 25
  2. Activation of pre-fusion SNARE/SM protein complex by complexin
  3. Ca2+ triggering of fusion-pore opening
  4. Fusion-pore expansion + NSF and SNAP binding
  5. NSF-mediated SNARE-complex dissasembly and vesicle recycling
165
Q

miRNA

cancer

A

MiRNA may function as either tumor suppressor or oncogene under certain circumstances. Although miRNAs have multiple targets, their function in tumorigenesis could be due to their regulation of a few specific targets.

regulate the expression of their target genes by degrading mRNA transcripts or by inhibiting mRNA translation

166
Q

Two hit model

Cancer

A

explains how certain hereditary cancer syndromes occur. It involves inheriting one mutated copy of a tumor suppressor gene (first hit) and then acquiring a second mutation in the other copy of the gene (second hit) within specific cells. This second mutation leads to the development of cancer. The model is associated with conditions like retinoblastoma and highlights the genetic basis of these cancers.

167
Q

Cell cycle

A

The cell cycle is the series of events through which a cell duplicates its DNA, grows, and divides into two daughter cells. It consists of phases:
- G1 (cell growth)
- S (DNA synthesis)
- G2 (further growth and preparation)
- M (mitosis or meiosis, where division occurs).
The cell cycle is crucial for cell reproduction and tissue growth, with checkpoints to ensure accurate DNA replication and division.

168
Q

Epigenetics

A

Factors that change expressionof a geneor DNA sequence without causing a change in that sequence. The changes are reversible
-DNA methylation (X-inactivation)
- Histone modification
- Non-coding RNA

169
Q

Imprinted genes

Epigenetics

A
  • A imprinted gene is expressed either from the maternal or the
    paternal allele
  • Th other allele is inactivated (hemizygoteic for imprinted genes)

Imprinted genes are inactivated through methylation

170
Q

Non-homologous end joining (NHEJ)

Genetic

A

pairs DNA ends in a multi-protein synaptic complex to promote their direct ligation. NHEJ is a highly versatile pathway that utilizes an array of processing enzymes to modify damaged DNA ends and enable their ligation. It’s rapid but error-prone, often leading to mutations at the repair site.
- Nuclease-dependent subpathways
- Blunt-end ligation by Ku–XRCC4–DNA ligase IV
- Polymerase-dependent subpathways
- Ligation by the XLF and PAXX subpathways

171
Q

microhomology-mediated break-induced replication (MMBIR)

Genetic

A

is a DNA repair pathway initiated by polymerase template switching at microhomology, which can produce templated insertions that initiate chromosomal rearrangements leading to neurological and metabolic diseases, and promote complex genomic rearrangements (CGRs) found in cancer

172
Q

Oxadative phosphorylation

cellular process

A

a cellular process that harnesses the reduction of oxygen to generate high-energy phosphate bonds in the form of adenosine triphosphate (ATP)
- It is a series of oxidation-reduction reactions that involve the transfer electrons from NADH and FADH2 to oxygen across several protein, metal, and lipid complexes in the mitochondria known as the electron transport chain (ETC)

173
Q

electron transport chain (ETC)

Cellular process

A

a collection of proteins bound to the inner mitochondrial membrane and organic molecules, which electrons pass through in a series of redox reactions, and release energy. The energy released forms a proton gradient, which is used in chemiosmosis to make a large amount of ATP by the protein ATP-synthase

174
Q

T-cell glycolysis

A

T cells upregulate glycolysis, the process in which glucose is converted into pyruvate, thereby generating ATP and reducing NAD+ to NADH.

175
Q

Homologous recombination (HR)

Genetic

A

HR is a highly accurate and conservative repair pathway that primarily deals with repairing double-strand breaks (DSBs) and single-strand gaps in DNA. Slower process.

  1. Recognition of DNA Damage: Detection of a double-strand break (DSB) or single-strand gap in DNA.
  2. Resection: Enzymes trim back broken DNA ends, creating single-stranded DNA (ssDNA) tails.
  3. Search for Homology: Resected ssDNA tails search for and base-pair with a homologous sequence in a sister chromatid or homologous chromosome.
  4. Formation of D-Loop: Resected strand invades the homologous DNA molecule, forming a displacement (D)-loop with base-pairing.
  5. DNA Synthesis: DNA polymerases extend the resected strand using the complementary sequence from the template.
  6. Branch Migration and Holliday Junction Formation: Branch migration can lead to the formation of a Holliday junction, a four-way DNA structure.
  7. Resolution and Ligation: Holliday junctions are resolved, and the repaired DNA ends are ligated, completing the HR process. The choice of resolution can lead to crossover or non-crossover events, impacting genetic diversity and chromosome structure.
  • ouble HJs are primarily dissolved by the BLM helicase-TopoisomeraseIIIα-RMI1-RMI2 (BTR) complex, whereas single HJs (and double HJs that have escaped the attention of BTR) are resolved by structure-selective endonucleases known as HJ resolvases
176
Q

Linkage analysis

Genetic

A

concerns the estimation of genetic distance between two or more genetic loci. In genetic epidemiology, used to identify, or map, a genetic locus that is associated with quantitative trait variation or, in the case of binary or discrete traits, modification of the risk of being affected with a disease or phenotype.

  • uses a panel of reference genetic markers to track the segregation of genomic segments within families or sets of relatives
177
Q

Association studies

Genetic

A

research approach used to identify genomic variants that are statistically associated with a risk for a disease or a particular trait

178
Q

Chromosome aberations

A

is a disorder characterized by a morphological or numerical alteration in single or multiple chromosomes, affecting autosomes, sex chromosomes, or both.

The four main types of structural chromosomal aberrations are deletion, duplication, inversion, and translocation.

179
Q

Microdeletions

Chromosomes

A

Involve chromosomal deletions that include several genes, but are too small to be detected by karyotype. They are usually de novo, and tend to recur in the same regions due to homologous recombination of flanking low-copy repeat gene clusters.

180
Q

Euchromatin

chromosomes

A

decondensed form and is found in the distal arms of the chromosome. It is usually dispersed all around the nucleus and is replicated throughout the S phase. Euchromatin is the transcriptionally active form of chromatin.

181
Q

Heterochromatin

chromosomes

A

is a cytologically dense material that is typically found at centromeres and telomeres. It mostly consists of repetitive DNA sequences and non-coding RNA transcripts and is relatively gene poor

182
Q

Interspersed repetitive non-coding DNA

A

Interspersed repetitive sequences that are identical or nearly identical DNA sequences that are scattered throughout the genome, as a result of transposition or retrotransposition events.
include short-interspersed nuclear elements (SINEs) and long-interspersed nuclear elements (LINEs):

  • LINEs are autonomous retroelements,which can retropositiondue to reverse transcriptase/endonuclease functions
  • SINEs are similar to LINEs, but shorter, simpler, and almost certainly dependent on LINE RT/EN functions for retroposition
183
Q

Zinc fingers

A
  • first-generation gene editing technique that utilizes a fused nuclease comprising a zinc finger protein (ZFP) and a Fok I restriction endonuclease.
  • ZFP recognizes and binds to a specific DNA sequence while the dimerized Fok I, which possesses endonuclease activity, cuts the recognized sequence, thereby resulting in a DNA double-strand break (DSB).
  • The DSB repaired through non-homologous end-joining (NHEJ) or homologous recombination (HR), during which mutations such as gene deletions or insertions are introduced, thereby achieving the goal of gene editing.
184
Q

TALENs

A
  • TALE recognizes and binds to a specific DNA sequence, whereas Fok I, which possesses endonuclease activity after dimerization, cuts the recognized DNA to make a double-strand break.
  • The double-strand break induces DNA repair through non-homologous end-joining or homologous recombination, performing gene editing
  • TALE proteins are composed of a central domain responsible for DNA binding, a nuclear localization signal, and a domain that activates the target gene transcription
185
Q

CRISPR/Cas9

A

comprises a leader sequence, several repeat sequences and several spacer sequences
- The leader sequence is located upstream of the CRISPR gene cluster, serves as a species-specific promoter.
- The repeat sequences are highly conserved palindromic sequences that can form hairpin structures. The repeat sequences are not tandem arranged but interrupted by spacer sequences.
- The spacer sequences are homologous to some sequences in the genome of phages or plasmids
- Cas9 nuclease complexes comprised of a Cas9 protein, a specific CRISPR RNA (crRNA), and a transactivation CRISPR RNA (tracrRNA).
- The complex recognizes and cuts target DNA at specific sites to generate double-strand breaks that induce DNA repair in cells. In the absence of homologous DNA, repair occurs through NHEJ, which facilitates gene deletion. When homologous DNA is present, repair occurs through HR, which facilitates gene insertion

186
Q

tandemly repeated dna

chromosome

A

a sequence of two or more DNA bases that is repeated numerous times in a head-to-tail manner on a chromosome

187
Q

Genome organisation

A

Genomes are organized at multiple levels.
- DNA is wrapped around the nucleosome, which is made up of an octamer of core-histones, forming the chromatin fiber which folds into loops, often bringing upstream gene regulatory, such as enhancers, into proximity to genes to control their transcription. -
- The fiber then folds into chromatin domains, referred to as topologically associating domains (TADs), which associate with each other to create chromatin compartments.
- The DNA of each chromosome occupies a distinct volume, or chromosome territory, within the cell nucleus, generating non-random patterns of chromosome and gene locations.
- In the DNA-free space, the nucleus also contains RNA and proteinaceous protein aggregates which form nuclear bodies.

188
Q

methyl-CpG-binding domain (MBD)

Cellular process

A

primary candidates for the readout of DNA methylation as they recruit chromatin remodelers, histone deacetylases and methylases to methylated DNA associated with gene repression

189
Q

Epigenetic reprogramming

A

process by which an organism’s genotype interacts with the environment to produce its phenotype and provides a framework for explaining individual variations and the uniqueness of cells, tissues, or organs despite identical genetic information.

190
Q

phosphorlipid synthesis

Cell membrane

A
  1. Fatty Acid Synthesis: Acetyl-CoA is converted into malonyl-CoA by the enzyme acetyl-CoA carboxylase. Malonyl-CoA is used in the synthesis of fatty acids, which are long hydrocarbon chains. This step takes place in the cytoplasm of the cell.
  2. Fatty Acid Elongation: The fatty acids are elongated through a series of enzymatic reactions in the endoplasmic reticulum. This process involves adding two-carbon units (acetyl-CoA) to the growing fatty acid chain.
  3. Formation of Phosphatidic Acid (PA): Once the fatty acids are sufficiently long, they are esterified to a molecule called glycerol-3-phosphate, derived from glycolysis. This reaction forms phosphatidic acid (PA).
  4. Phospholipid Head Group Addition: The final step involves the addition of a phosphate group and a head group, such as choline, ethanolamine, or serine, to the phosphatidic acid molecule. This step is catalyzed by various enzymes depending on the specific head group, resulting in the formation of different phospholipids like phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS)
191
Q

membrane assymetry

Cell membrane

A

Membrane asymmetry refers to the unequal distribution of lipids and proteins in a cell’s membrane. This asymmetry is vital for maintaining cell structure and function.

  • Lipid Distribution: Membrane asymmetry primarily involves the uneven distribution of lipids across the two leaflets (layers) of the lipid bilayer. The two primary classes of lipids involved are phospholipids and glycolipids.
  • Phospholipids: In most eukaryotic cell membranes, phospholipids like phosphatidylcholine (PC) and sphingomyelin are more abundant in the outer leaflet (extracellular-facing side) of the lipid bilayer. In contrast, phosphatidylethanolamine (PE) and phosphatidylserine (PS) are typically found more in the inner leaflet (cytoplasm-facing side).
  • Flippases move specific lipids from one leaflet to the other to establish and maintain the asymmetry, while floppases work in the opposite direction, equilibrating lipids between the leaflets.

Biological Significance:
- Membrane Function: Asymmetry is critical for the structural integrity and function of cellular membranes.
- Cell Signaling: Membrane asymmetry is involved in various cell signaling processes. The exposure of certain lipids on the outer leaflet can trigger responses in neighboring cells or immune system recognition.
- Dynamic Process: Membrane asymmetry is not a static condition; it can change in response to various stimuli or cellular processes.

192
Q

Replication origin

replication

A

sequences essential for initiation of DNA replication, because they contain binding sites for either their cognate helicase loader or cognate DNA helicase

193
Q

Origin-recognition complex

replication

A

a central component for eukaryotic DNA replication. The ORC binds to DNA at replication origin sites in an ATP-dependent manner and serves as a scaffold for the assembly of other key initiation factors.

194
Q

Pre-replikation complex

replication

A

composed by initiation factors, origin recognition complex, Cdc6, Cdt1 and mini chromosome maintenance (Mcm) protein complex during G1 phase of cell cycle. Cell division cycle 45 (Cdc45) protein is fundamental for starting replication

195
Q

Replicate helicase

A
  • DNA helicases are essential during DNA replication because they separate double-stranded DNA into single strands allowing each strand to be copied. During DNA replication, DNA helicases unwind DNA at positions called origins where synthesis will be initiated
  • RNA helicases are involved in shaping the form of RNA molecules, during all processes involving RNA, such as transcription, splicing, and translation.
196
Q

Replisome

A

Replisomes are machines composed of numerous proteins that function together to accomplish the replication of duplex DNA;
- Helicase, that separates the strands of duplex DNA; primase, that makes RNA primers to initiate synthesis

  • DNA polymerases that extend primers with DNA and convert the separated single-strands into duplexes
  • a sliding clamp that encircles DNA and holds polymerases to DNA for rapid and efficient synthesis
  • a clamp loader that uses ATP to open/close the ring shaped clamp and place it onto DNA
  • single-strand DNA binding protein that protects single-strand DNA from nucleases.
197
Q

SDS-PAGE (Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis)

Method

A

is a technique used to separate proteins based on their size. It involves denaturing and loading proteins onto a gel, applying an electric field, and visualizing the separated proteins. It’s a fundamental tool in biochemistry for protein analysis and purification.

198
Q

Western blot

western blot

A

is a technique used to detect and analyze specific proteins in a sample. It involves separating proteins, transferring them to a membrane, and using antibodies to identify and quantify the target protein. It’s widely used in molecular biology and biochemistry research.
- Uses SDS-page as the first steps

199
Q

Types of receptors

A
  • Receptor associated kinases (eg. RTKs)
  • Cytosolic associated kinases (eg. GPCRs)
  • Protein sub-unit dissociation (Wnt pathway)
  • Protein cleavage pathway (Notch-delta)
200
Q

Wnt pathway

A

Draw yourself

201
Q

RTK-Map

pathway

A

Draw yourself
- Growth factor

202
Q

TGF(beta)

pathway

A

Draw yourself
- inhibits growth

203
Q

G1/S checkpoints pathway

Pathway

A

draw yourself
- G1 –> S phase transition

204
Q

Notch-delta

pathway

A

Draw yourself
- activates transcription factors

205
Q

Jak-Stat (cytokine receptors)

pathways

A

draw yourself

206
Q

IP3/DAG

Pathway

A

draw yourself

207
Q

RTK-AKT

pathway

A

draw yourself
- cell survival

208
Q

G-coupled protein - PKA

pathway

A

draw yourself
- Transcription factor

209
Q

Checkpoints

cell cycle

A
  • G1/S phase, entry is blocked if there is DNA damage (before replication)
  • S, DNA damage (after replication)
    -G2/M phase, DNA damage and uncomplete replication (inhibtion of cdc25, which activates mitotic CDKs)
  • Anaphase, spindle point (kinetochores gives signal if MT isn’t attached and APCcdc20 is inhibited)
210
Q

Regulators of transcription

Mitochonria

A
  • Glycolytic enzymes
  • Angiogenic factors
  • Apoptotic pathways
211
Q

Promotor region

Gene structure

A
  • TATA box (start position determination)
  • CAT box (gene expression)
  • CpG islands (binding site for specific transcription factors)

Enhancer, insulater, repressor and shine delgarno sequence

212
Q

Allelic disequilibrium

Patterns of inheritance

A

Non-random association of alleles at differen loci in a given population

213
Q

Hemizygote

Genetic

A

A diploid cell or organism in which there is only one allele present for a particular gene

214
Q

the Law of Segregation

Genetics

A

There are dominant and recessive traits passed
on randomly from parents to offspring

215
Q

Law of Independent Assortment

Genetics

A

Traits are passed on independently
of other traits from parents to offspring

216
Q

Replication fork

A

The helicase activities unwind DNA to create regions of singled-stranded DNA (ssDNA).
The ssDNA is coated in RPA to keep strands from reannealing. Fork protection complex (FPC) components are Timeless (TIM), Tipin (TIPIN), Claspin (CLASPIN), and And1 (AND1).
- Claspin helps connect the leading-strand polymerase epsilon to the helicase.
- And1 connects the lagging-strand polymerase alpha (tan circle) to the helicase.
Pol-alpha is part of the primase complex, which synthesizes primers on the lagging strand, allow the polymerase of the main lagging-strand (polymerase delta) to start synthesis.

216
Q

Metatropic receptor

Neurons

A

G-protein-coupled receptors on the postsynaptic neuron, which acts on an effector protein that stimulates an ion channel.
- Facilitates transmission of signal from synaptic cleft to neuron
- “Slow”

216
Q

Ionotropic receptors

Neurons

A

Ligand-gated ion channels
- Facilitates transmission of signal from synaptic cleft to neuron

217
Q
A

Human biology (3 decks)

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