Human Populations Exam 1

What is a gene?

A region of DNA that codes for messenger RNA (which encodes a protein) or for a functional RNA molecule

What is the genetic code?

The set of rules by which the sequence of nucleotides in mRNA is translated into the amino acid sequence of a protein

What determines protein function?

The three-dimensional structure of a protein

What are the main levels of protein structure?

Primary (amino acid sequence), secondary (α-helices and β-sheets), tertiary (3D folding), and quaternary (multi-subunit complexes)

What are non-coding RNA products?

RNA molecules that are not translated into proteins but have functions on their own (e.g., rRNA, tRNA, miRNA, ribozymes)

What are chromosomes?

Highly compacted structures of DNA and proteins that contain genes and other DNA elements

Define ploidy

The number of sets of chromosomes in a cell (e.g., haploid = 1 set, diploid = 2 sets, polyploid = multiple sets)

What is a genome?

The complete set of genetic material in an organism, including all of its genes and non-coding DNA

What percent of the genome is composed of genes?

Only a small percentage (around 1–2% in humans)

What are the two methods of transposition?

cut-and-paste (transposon excises and reinserts elsewhere)
Copy-and-paste (transposon makes a copy that inserts elsewhere)

What is a mutation?

A change in the DNA sequence relative to a reference or ancestral sequence

Why are mutations important?

They are the ultimate source of genetic variation, drive evolution, leave records of evolutionary history, and can cause genetic disorders

What causes mutations?

DNA replication errors, meiotic errors, environmental mutagens, or transposable elements

Can mutations occur in both somatic and germline cells?

Yes. Somatic mutations affect only the individual, while germline mutations are heritable

Are DNA replication errors fixed?

Most are corrected by proofreading and repair, but some escape correction and persist

How many mutations enter the human population yearly?

About 9.5 billion new mutations (≈68 new mutations per child × 140 million births per year)

What is a substitution mutation?

A single nucleotide is replaced with another, which may alter a protein’s amino acid sequence (e.g., mc1r gene in beach mice)

What are insertion/deletion (INDEL) mutations?

Mutations where one or more nucleotides are inserted or deleted from the DNA sequence, potentially disrupting gene function

How can mutations occur in non-coding regions?

They can alter regulatory elements (e.g., promoters, enhancers, introns), affecting gene expression without changing protein coding sequence

What do gene duplications generate?

New copies of existing genes, which can evolve new functions (example: antifreeze proteins in Antarctic icefish)

What is a chromosomal inversion?

A mutation where a chromosome segment is flipped in orientation.

• Paracentric inversion: does not include the centromere

• Pericentric inversion: includes the centromere

What is a translocation?

A mutation where segments of DNA are swapped between different chromosomes

What is a chromosomal fusion?

A mutation where two separate chromosomes join together into one

What are the largest-scale mutations?

Whole chromosome duplications/deletions (aneuploidy) and whole genome duplications (polyploidy)

What is a locus?

A specific physical location of a gene (or genetic marker) on a chromosome

What is an allele?

A variant form of a gene found at a locus

What is a genotype?

The combination of alleles present in an individual at one or more loci

What is a phenotype?

The observable characteristics of an individual (e.g., color, size, shape) determined by genotype + environment

What is a haplotype?

The combination of alleles at multiple loci on the same chromosome in one individual

What is the mechanism of inheritance at the chromosomal level?

Chromosomal segregation during meiosis + recombination (crossing over) leads to inheritance patterns

What is Mendel’s Law of Segregation?

During meiosis, the two alleles for a gene separate so each gamete gets only one allele

What was Mendel’s pea flower color experiment?

He crossed purple and white flowered peas to study inheritance

What was the result and conclusion of Mendel’s pea experiment?

Traits are inherited in predictable ratios (3:1 in F2); inheritance is determined by discrete units (alleles), not blending

What is genetic linkage?

The tendency of alleles close together on the same chromosome to be inherited together

What is crossing over during meiosis?

The exchange of DNA segments between homologous chromosomes, creating new allele combinations (recombinants)

Who were T.H. Morgan and Alfred “Hot Dog” Sturtevant?

Geneticists who used Drosophila melanogaster (fruit flies) to demonstrate genetic linkage and map genes

What was the hypothesis of Morgan & Sturtevant’s experiment?

• H1: Genes for body color (b) and wing shape (vg) assort independently

• H2: They are inherited together as a single unit (linked)

What was the result of Morgan & Sturtevant’s experiment?

Offspring ratios did not match independent assortment → instead showed linkage with some recombinants

What was the conclusion of the experiment?

The b and vg loci are on the same chromosome but separated by a measurable genetic distance; recombination frequency reflects physical distance between loci

What determines the strength of genetic linkage?

Physical proximity of loci: close together → strong linkage (inherited together). Far apart → weak linkage (more recombination)

What is a recombination rate?

The average number of crossovers in a chromosomal region per generation

What are recombination hotspots?

Specific regions in genomes (like in humans) where crossing over occurs more frequently

Why does the amount of shared DNA among siblings vary?

Recombination is probabilistic → different crossover events shuffle alleles differently in each meiosis

What is a selective sweep?

When a beneficial allele increases in frequency, nearby linked loci also increase in frequency due to reduced recombination

What is genetic hitchhiking?

The rise in frequency of alleles near a beneficial mutation because they are linked to it

Why does recombination matter for evolution?

It creates new allele combinations each generation, increasing genetic diversity for natural selection to act on

Why are siblings genetically different despite having the same parents?

Independent assortment of chromosomes + recombination during meiosis remix alleles each generation

What is a gamete?

A haploid reproductive cell (sperm/egg) that carries one allele for each locus

What is the difference between haploid and diploid?

Haploid = 1 set of chromosomes (gametes). Diploid = 2 sets of chromosomes (somatic cells, parents)

How do recombination rates vary across species?

They differ massively; some species have high rates, others low, affecting how genetic variation is generated

What is a double (or multiple) crossover?

More than one recombination event between loci in a single meiosis, leading to complex recombinant haplotypes

What is the C-value paradox?

It’s the observation that genome size does not correlate with organismal complexity

Why is the C-value paradox considered paradoxical?

Because simpler organisms can have larger genomes than more complex ones

What is a transposable element (TE)?

A DNA sequence that can move or copy itself within the genome

How do TEs relate to the C-value paradox?

Variation in TE content helps explain why genome size differs among species despite similar complexity

What types of data did the authors use to study genome size evolution?

Comparative genomic data across multiple taxa, including total genome size, repetitive DNA, and TE proportions

Which groups of organisms were analyzed in the study?

Animals, fungi, land plants, and protists

According to the study on c-value enigma, what are the main contributors to genome size variation among taxa?

Transposable elements (TEs) and other repetitive DNA sequences

What result in the study was surprising?

That even within the same group, such as animals or plants, there is wide variation in genome size and TE content

Why is incorporating phylogenetic information important in this type of study?

It helps distinguish whether patterns in genome size are due to shared ancestry or independent evolutionary events

Why are TEs commonly found in introns and non-coding regions?

Because insertions there are less likely to disrupt essential genes, allowing them to persist

According to Figure 3b, why is there so much variation in TE proportion across genomes?

Differences in TE amplification, removal rates, and the effectiveness of genome defense mechanisms cause this variation

What does population genetics study?

It studies the distribution and change of genetic variation within populations over time

What is a population in genetics?

A group of interbreeding individuals of the same species within a defined area

What does “frequency” mean in population genetics?

It is the proportion of a specific genotype or allele in a population

How is frequency calculated?

Frequency = (count of a specific item) ÷ (total number of items)

How do scientists estimate genotype and allele frequencies?

By sampling individuals, genotyping or sequencing them, and calculating proportions statistically

Why are large sample sizes important in genetic studies?

They produce more accurate estimates of allele frequencies and reduce random sampling error

What is genotyping?

The process of identifying specific genetic variants (alleles) at chosen loci in the genome

What is sequencing?

Determining the exact order of nucleotides (A, T, G, C) in DNA

How does genotyping differ from sequencing?

Genotyping targets a few specific loci; sequencing can analyze entire genomes or long regions

What is PCR (Polymerase Chain Reaction)?

A technique that amplifies a specific DNA region, producing millions of identical copies for analysis

What does PCR amplification allow scientists to do?

Detect or analyze specific genetic sequences even when only small amounts of DNA are available

What is the presence/absence of a specific viral locus used to detect?

The presence of viral DNA or RNA, as in COVID-19 PCR tests

What is Sanger sequencing?

A method for determining the DNA sequence of fragments less than about 1000 base pairs in length

What is an SNP (Single Nucleotide Polymorphism)?

A variation at a single base pair position in the genome among individuals

What is a polymorphism?

The existence of multiple co-existing alleles at a genetic locus within a population

What are SNP chips used for?

They allow genotyping of thousands of SNPs at once using allele-specific probes

What is a major issue with short-read sequencing?

Short reads can miss large structural variants or repetitive regions, leaving gaps in the genome

What is a reference genome?

A high-quality, representative genome used as a standard to compare and align new DNA sequences

What is a coordinate system in genomics?

A framework that assigns positions to genes and variants along chromosomes using a reference genome

What are genetic variants or alleles?

Different DNA sequence forms that occur at the same position in a genome

How are genetic variants identified?

By aligning DNA reads to a reference genome and noting differences at specific sites

Why are some genomic sites ignored during analysis?

Sites identical across all samples and the reference do not reveal genetic variation

Why might researchers use smaller sample sizes despite lower accuracy?

Due to practical limits like cost, time, or conservation concerns

What determines how genotype affects phenotype?

The effect of genotype on phenotype is the result of development, which is coordinated by changes in gene expression across space and time

What is the formula that represents the sources of phenotypic variation?

P = G + E + G×E
Where P = phenotype, G = genotype, E = environment, and G×E = gene-environment interaction

What is a trait?

A specific measurable aspect of phenotype (e.g., height, eye color, fur color)

What is genetic architecture?

describes how a trait is controlled by genes (how many genes are involved, how strong their effects are, and how they interact with each other and the environment)

What does “polygenic” mean?

A polygenic trait is influenced by many genes/loci, often hundreds or more

What is an effect size?

Effect size refers to how strongly a particular gene or allele influences the phenotype

Why can genes differ in effect size?

Genes can differ in effect size because of their position in biochemical pathways—some control key steps while others have minor roles

What are quantitative traits?

Quantitative traits show continuous variation (like height or weight) and are typically polygenic

Why do quantitative traits show continuous variation?

Because the effects of many genes combine, creating a continuum of phenotypes rather than distinct categories

How polygenic are most traits or diseases?

Most traits are influenced by 100–500 loci with detectable effects, though some may involve thousands

What are “core genes”?

Genes that have a large, direct effect on a specific trait by directly influencing the biological processes that determine it

How does the environment influence traits?

Traits can vary depending on environmental conditions, even in genetically identical individuals

What is phenotypic plasticity?

Phenotypic plasticity is when the same genotype produces different phenotypes in different environments

What is a gene-environment interaction (G×E)?

When the effect of a gene on a trait depends on the environment, or vice versa

How do scientists determine genetic architecture?

Through crosses, pedigree studies, QTL mapping, or GWAS