BSCI222- Exam #2

Linkage group

Clusters of genes located on the same chromosome that tend to be inherited together during meiosis.

The Central Dogma of Biology

Describes the flow of genetic information in a cell: DNA is transcribed into RNA, and RNA is translated into a polypeptide (protein).

RNA

When DNA is transcribed, the result is an ___ molecule.

Digital

DNA and RNA are ______.

Proteins

Do most of the work of the cell with numerous biological functions.

Polymers

Proteins are ______ consisting of amino acids linked by peptide bonds.

Analog

Proteins are _____ molecules e.g., “lock and key hypothesis.”

Complete Androgen Insensitivity Syndrome

A genetic disorder that causes XY fetuses to become impassive to androgens or male hormones. They are born appearing externally female even if they are genetically male.

At puberty when menstruating is supposed to start but it doesn’t

When is complete androgen insensitivity syndrome frequently confirmed?

Peptide bonds

Amino acids are joined together by _____ _____.

Amino group, carboxyl group, and R group (side chain)

What three fundamental groups does every amino acid contain?

R groups

The common amino acids have similar structures; they are distinguished by the __ _____ with their different functional groups.

Function

After ribosomes link all aa’s, the protein folds into shape that determines _____.

The amino acid sequence

What is the primary structure of protein organization?

AlphaFold 3

What can predict the structure and interactions of all of life’s molecules?

AlphaFold

Can predict how proteins fold into 3D shapes, a fiendishly complex process that is fundamental to understanding the biological machinery of life.

The challenge of accurately predicting a protein’s three-dimensional structure from its amino acid sequence.

What problem did DeepMind's program AlphaFold solve?

Polypeptide

Long chain of amino-acids joined by peptide bonds. Are extremally diverse. A typical one contains 150 amino acids so 20^150 possible sequences. Each sequence will have different properties.

Predicted the 3D structure of almost every protein known

What has DeepMind done?

The primary structure

What primarily determines the secondary and tertiary structures of a protein?

Thomas Hunt Morgan

A pioneering American geneticist who established the chromosomal theory of inheritance through his studies on the fruit fly Drosophila melanogaster.

Scientists knew genes were located on chromosomes, but they did not yet know the chemical nature of genes.

What was understood about genes by the time Thomas Hunt Morgan died in 1945?

DNA

By 1950, what molecule was known to be the genetic material?

Nucleotides

What are the building blocks of DNA?

A sugar, a phosphate group, and a nitrogenous base

What are the three components of a nucleotide?

Double helix structure of DNA

What major discovery in 1953 helped explain how DNA works?

They are chemically linked together to form a long chain (a polymer)

What does it mean for nucleotides to be “polymerized”?

Crick and the American

They were known in Cambridge.

Pauling

Who discovered the alpha helix structure of proteins?

Franklin

Who produced the famous photo51?

Wilkins

Who conducted X-ray diffraction studies of DNA at King’s College London?

Watson

Who co-proposed the double helix model of DNA in 1953?

Crick

Who co-developed the double helix model, helped interpret X-ray data mathematically, and later contributed to the central dogma?

Watson and Crick

Who created the double helix model of DNA?

Nucleic acids Genetic Material

• Genetic material must contain complex information.

• Must be compact

• Must be stable

• Genetic material must replicate faithfully (copied accurately).

• Genetic material must be changeable.

• Genetic information must be quickly and easily retrieved

These are all characteristics of…

Because the DNA molecule is much longer than the cell itself and must fit into a very small space.

Why must DNA be tightly packed inside a cell?

Paleogenetics

The stability of DNA allows _________.

Paleogenetics

The study of DNA from ancient remains (fossils, bones, preserved tissue).

Archeological genetics

The study of genetic (DNA) and proteomic (protein) material preserved in ancient archaeological samples.

Environmental DNA or eDNA

This is genetic material that is shed from plants and animals - for example, from skin cells or droppings - and accumulates in their surroundings.

It shows how species may adapt and coexist in warmer climates.

Why is the discovery of the 2-million-year-old Greenland ecosystem important for climate change research?

eDNA

Shows the plasticity of biological organisms in terms of where they can live and the plants or animals that can live together, is larger than what we thought. Can tally biodiversity by sampling water, soil or air for the DNA animals shed in their environments daily.

RNA and DNA

What are the two main classes of nucelotides?

RNA

_____ contains the sugar ribose.

DNA

_____ contains the sugar deoxyribose?

Chargaff’s rules

States that in DNA, the amount of adenine (A) equals thymine (T), and guanine (G) equals cytosine (C).

Thymine (T)

Adenine (A) pairs with _______.

Guanine (G)

Cytosine (C) pairs with _____.

2

How many hydrogen bonds are between A and T?

3

How many hydrogen bonds are between C and G?

C-G

______ pairs are stronger (3 hydrogen bonds) than A–T pairs (2 hydrogen bonds).

Separate

DNA regions with more C–G pairs are harder to _______.

Showed DNA had a helical structure and provided key measurements used to build the double helix model.

How did Franklin, Wilkins, and Gosling contribute to the discovery of DNA’s structure?

Right-handed B-DNA double helix

What type of double helix is DNA?

Deoxyribose sugar

What sugar does DNA consist of?

Phosphate groups and deoxyribose sugars

The backbone of DNA consists of alternating _____ _____ and _____ _____.

Purines

What are A and G?

Pyrimidines

What are C and G?

B-DNA

Which form of DNA is most common in cells?

The two strands run in opposite directions (5’→3’ and 3’→5’).

What does antiparallel mean in DNA?

B-DNA

• Most common form in cells

• Right-handed helix

• ~10 base pairs per turn

• Diameter ~2 nm

• Well-defined major and minor grooves

A-DNA

• Right-handed helix

• Shorter and wider than B-DNA

• ~11 base pairs per turn

• Bases tilted relative to helix axis

• Major groove is narrow and deep

• Minor groove is wide and shallow

Forms under:

• Dehydrated conditions

• DNA–RNA hybrids

• Double-stranded RNA

Z-DNA

• Left-handed helix (very different!)

• Occasionally present in active genes

• ~12 base pairs per turn

• Zig-zag sugar-phosphate backbone

• Narrow and elongated shape

Forms in:

• GC-rich sequences

• High salt conditions

• Regions under torsional stress

Ribose

RNA contains _____ sugar.

Uracil

Which base is unique to RNA?

Usually single stranded

Is RNA single- or double-stranded?

Because ribose has a 2’ hydroxyl group that makes it more reactive.

Why is RNA less stable than DNA?

Purines have two rings; pyrimidines have one ring.

What structural feature distinguishes purines from pyrimidines?

3’–5’ phosphodiester bonds.

What type of bond forms the DNA backbone?

Hydrogen bonds between complementary bases

What holds the two DNA strands together?

Doubleness

– Thin to allow packing

– Stability-protects nucleotide sequence

– Prevents DNA tangling up on itself by internal base pairing.

– Internal base pairing in RNA can produce complex structures

These are all advantages of ______ in DNA.

Hairpin structure

In single strands of nucleotides, when sequences of nucleotides on the same strand are inverted complement.

Loop

When the complementary sequences are contiguous, the hairpin has a stem but no _____.

Ribozymes

RNA molecules may contain numerous hairpins, allowing them to fold up into complex structures such as _______.

Supercoiling

The coiling of the DNA double helix by overwinding or underwinding of the duplex.

Topoisomerase’s

Add or remove rotations in DNA by breaking strands, rotating ends and rejoining broken ends.

Chromatin

A complex of DNA, RNA, and proteins (mainly histones) that packages long DNA molecules into dense, compact structures within the eukaryotic nucleus.

Heterochromatin is tightly packed and inactive; euchromatin is loosely packed and active.

How does heterochromatin differ from euchromatin?

Heterochromatin

A highly condensed, transcriptionally silent form of DNA found in eukaryotic cells, typically localized at the nuclear periphery, near the nucleolus, or at telomeres.

Euchromatin

A lightly packed, less condensed form of chromatin (DNA, RNA, and protein) in the cell nucleus that is rich in gene concentration and actively involved in transcription.

Inner region of the nucleus.

Where is euchromatin located?

At centromeres, telomeres, and specific regions.

Where is heterochromatin located?

Polytene chromosome

Created by repeated rounds of DNA replication with no cell division.

Histones

Help organize chromosomes. Highly basic proteins in eukaryotic cell nuclei that act as spools for DNA, organizing it into structural units called nucleosomes.

To package DNA into nucleosomes and regulate gene accessibility.

What is the role of histones?

By tightly or loosely wrapping DNA and through chemical modifications on histone tails.

how do histones control gene expression.

The Encode project

Aims to identify all functional elements in the human genome.

Unique DNA

DNA sequences that occur once or a few times, mostly coding for genes

Moderately competitive DNA

DNA repeated tens to hundreds of times, including some gene families and rRNA genes.

Highly repetitive DNA

DNA repeated thousands to millions of times, often in centromeres, telomeres, or satellite regions.

By copy number, function, and location

How do unique, moderately, and highly repetitive DNA differ?

Pseudogene

Nonfunctional genomic DNA sequences that resemble functional genes but have lost their ability to produce proteins due to accumulated mutations, such as premature stop codons or deletions.

Telomeres

To prevent the loss of genes as chromosome ends wear down, the tips of eukaryotic chromosomes have specialized DNA “caps”; non-coding DNA that can be sacrificed to replication. Consists of hundreds of tandem repeats of the same short DNA sequence.

Centromeres

Binding site of spindle fibers: large arrays of repetitive DNA (e.g. Satellite DNA) tandem repeats.

Telomeres protect ends; centromeres ensure proper chromosome separation.

What is the difference in function of telomeres and centromeres?

Satellites DNA

Repeated pattern between 1 base pair long to several thousand base pairs long.

Microsatellites

Most no known function; but inserted into gene promoters may change how genes are regulated

► tandem repeats of 2-5 base pair lengths (can be up to 8bp) in specific regions of the genome

► used in DNA fingerprinting

DNA fingerprinting

Identifying individuals by unique patterns in their DNA. Can be used to determine the

presence of a suspect at a crime scene. May be used to establish paternity.

Steps of DNA fingerprinting

DNA extraction → fragmentation → separation → visualization → comparison.

Transposable elements

Sequences that can move about the genome.