FINAL Biol 1040 Exam 1 Flash Cards

Final set of flash cards.

Amniocentesis

Was first described in the 1950s as a medical procedure to access fetal DNA for genetic testing. Had many issues and was performed around 200,000 times prior to 2015. Had lots of risk (miscarriage every 1-200/500).

Chorionic Villus Sampling

Another form of obtaining fetal DNA by accessing placenta tissue. Is considered to be invasive.

Risk/Benefit Analysis

Is the procedure or process performed going to benefit a person more than the risk is to them?

Cell-Free DNA

Small fragments of DNA that exist in the bloodstream. In a pregnant person, you can find both fetal and maternal DNA in the bloodstream.

Noninvasive Prenatal Testing (NIPT)

Uses Cell-Free DNA in a pregnant person's blood to collect DNA.

Moore’s Law

An observation that the number of transistors on a chip doubles every two years but the cost to produce halves in that same amount of time. DNA Sequencing shares this same growth with the cost even decreasing faster.

The four bases for DNA

ATGC

The four bases for RNA

AUGC

How many chromosome pairs are there? How many chromosomes?

23 chromosome pairs; 46 chromosomes.

Genetics vs. Genomics?

Genetics = heredity; Genomics = study of genomes

What is the human genome made of?

46 chromosomes, ~3 billion base pairs

Goal of the Human Genome Project (HGP)?

Map and sequence the human genome

Sequencing method mainly used by HGP?

Sanger sequencing

Craig Venter’s sequencing approach?

Whole-genome shotgun sequencing

Francis Collins’ sequencing approach?

Clone-by-clone shotgun sequencing (map first, then sequence)

What is shotgun sequencing?

DNA is broken into fragments, sequenced, then reassembled

Challenges of sequencing the human genome?

Very large size, slow sequencing reads, many repetitive regions

What percentage of the genome did the HGP initially complete?

~92% (telomeres and centromeres missing)

What are the Bermuda Principles?

Agreements to release genome sequence data quickly and publicly

What makes DNA more than just a molecule or blueprint?

DNA is a crystal with complex structure and information storage.

What are the key sugars in DNA and RNA?

Deoxyribose in DNA and Ribose in RNA.

Why is DNA called deoxyribonucleic acid?

Its backbone is made of deoxyribose sugar.

Why is RNA called ribonucleic acid?

Its backbone is made of ribose sugar.

How are DNA sugars linked?

They are linked to phosphates

What bonds connect the bases to the DNA backbone?

Hydrogen bonds

What does one strand of DNA provide for the other?

The information to create the complementary strand

Why is DNA easy to replicate?

The two strands can separate and each serves as a template

What proteins package DNA into chromosomes?

Histones

What dual role do histones play?

They pack DNA into chromosomes and unpack DNA for gene expression

What is the Central Dogma of molecular biology?

DNA -> RNA -> Protein

Why isn't the Central Dogma enough to explain gene function?

Genes are regulated in many ways and RNA has functions beyond serving as a template for proteins

What is transcription?

The process of making RNA from a DNA template

What is the role of RNA polymerase?

It reads DNA and synthesizes an RNA strand

What is translation?

The process of making proteins from RNA

What is the role of ribosomes in translation?

They recruit mRNA and facilitate peptide bond formation to build proteins

How are amino acids delivered to the ribosome?

By transfer RNA (tRNA)

What are exons?

Parts of mRNA that are expressed as amino acid sequences and turned into proteins

What are introns?

Non-coding sequences of RNA that are spliced out during processing

What are proximal control elements?

DNA elements near a gene that help regulate transcription

What is epigenetics?

Alterations to the chromatin that influence gene expression without changing the DNA sequence

How can epigenetics be influenced?

By environmental factors such as stress or starvation

What is DNA methylation?

The addition of a methyl group (CH3) to DNA

Why is timing and location important for gene expression in development?

Genes need to be expressed in specific cells at specific times to form correct body parts

What are Hox genes?

Genes that help cells determine their position in the embryo and guide body plan development

What is the Zone of Polarizing Activity (ZPA)?

A region in embryos where cells produce the Sonic Hedgehog (Shh) protein to help form limbs and digits

Do more complex organisms always have larger genomes?

No, genome size does not directly correlate with organism complexity

What did the telomere-to-telomere project reveal?

It shed light on the 'dark matter' of the human genome

What proportion of the human genome is repetitive?

The majority of the genome is repetitive

What are transposable elements?

Genes that can copy themselves and move to different locations in the genome

Are transposable elements always harmful?

No, most are parasitic but some can have functional roles

Where are transposable elements usually found?

In "gene deserts" or regions of the genome with low gene density

What are fossilized RNA viruses in the genome?

Viral sequences integrated into the genome generations ago

How can fossilized retroviruses affect the genome?

By causing mutations, producing ncRNAs, or creating proteins with new functions

What human disorders have HERVs been linked to?

Depression, schizophrenia, and other disorders

What are non-coding RNAs (ncRNAs)?

Regions of the genome that do not code for proteins but can have regulatory or functional roles

Does "non-coding" mean "useless"?

No, non-coding regions can be functional and important

Why is most genome size considered "junk"?

Most of it comes from repetitive elements and transposable elements that do not have essential functions

Frederick Sanger (1918–2013): key achievements

Excelled in biochemistry; Nobel Prize for sequencing proteins (first: insulin) and DNA; proved proteins have defined chemical composition

Frederick Sanger: personal hardships

Both parents died from cancer while he was an undergraduate

Marie Curie: Nobel achievements

First woman to receive a Nobel Prize; first person to win two; work on radioactivity and cancer treatment

Linus Pauling: contributions

Discovered the nature of the chemical bond; peace activist

Nucleotide

A sugar + phosphate + base; building block of DNA

Sugars in DNA and RNA

DNA: deoxyribose; RNA: ribose; both linked with phosphate groups forming the backbone

Normal DNA replication

DNA unzips into two strands; DNA polymerase replicates new strands complementary to originals

Sanger sequencing: principle

Uses dideoxyribose (ddNTPs) to terminate DNA chain at specific nucleotides

Sanger sequencing: reading sequence

Fragments of different lengths separated on gel or via fluorescent labels; sequence determined by fragment length and terminating nucleotide

Sanger sequencing: tech advances

Fluorescent labeling, color-coded nucleotides, and computer automation allowed multiple sequences to be read faster

Second-generation sequencing (2006): limitations

Could not make long sequences; required many tiny fragments but was cheaper

What is Oxford Nanopore Technology?

A sequencing technology that reads single DNA molecules with relatively long reads using nanopores

How does Oxford Nanopore read DNA?

DNA strands pass through nanopores one at a time

What is a nanopore?

A tiny genetically engineered protein pore in a membrane that allows single DNA strands to pass through for sequencing

What role does the protein that delivers DNA to the nanopore play?

It unwinds the DNA and pushes it through the nanopore

Why are long read lengths important in sequencing?

They provide more complete and accurate genome assemblies

What are some applications of high-throughput sequencing?

Metagenomics

How does genetic variation manifest in humans?

In physical appearance

What is the scientific meaning of "mutation"?

A change in the genome that can produce new traits; it has no inherent negative connotation

Give an example of a mutation that is beneficial in some contexts.

Sickle Cell Anemia allele provides malaria resistance in heterozygotes

Why should we be careful with language about genetic differences?

Terms like "mutant" or "disability" can misrepresent natural variation and influence perception negatively

How are complex traits different from simple traits?

Complex traits are influenced by many genes/loci

What is the spectrum of natural genetic variation?

It ranges from deleterious diseases to variations that make individuals unique and special

How are bipolar disorder and schizophrenia related to human traits?

They can be linked to creativity and high intelligence in some individuals

What are SNPs?

Single Nucleotide Polymorphisms; numerous and useful for mapping genes and ancestry

What are small insertions/deletions?

Rare mutations involving the addition or loss of a few nucleotides

What are simple sequence repeats (SSRs or microsatellites)?

Highly variable DNA sequences used for DNA fingerprints, paternity, and forensics

What are larger structural changes in the genome?

Copy number variation, large-scale rearrangements, insertions, and deletions

Where can mutations occur?

In germ cells (egg, sperm) or somatic cells (like in cancer)

How do we detect mutations?

Compare sequences to a reference genome using alignment and computational analysis

Why do we need multiple human genomes for comparison?

To get a consensus of alleles and account for sequence fragments

What is structural variation?

Genomic differences at all scales, from small to large chromosome portions

How are structural variants revealed?

Through de novo genome assemblies and long-read sequencing

What is the pangenome?

A reference that incorporates genomic diversity from many human populations

How much genetic variation exists among humans?

Very little overall (~0.4%), but differences matter

What is genetic essentialism?

The mistaken idea that single genes fully determine traits

Do BRCA genes cause breast cancer?

No; they help repair DNA and influence risk but do not directly cause it

Is there a single "basketball gene"?

No; many genes influence traits like athletic ability

What is genotype vs. phenotype?

Genotype = genetic makeup; Phenotype = physical traits or appearance

Simple traits vs. complex traits?

Simple traits: few genes, easy to predict (e.g., eye color); Complex traits: many genes, influenced by environment (e.g., height, diabetes)

What are complex/continuous/quantitative traits?

Traits with a continuous range of variation, not discrete categories