Topic 1 Bio 285 (umass - Dr. Francis) 2026

Amino acid

Building block of proteins: a central carbon bonded to an amino group, carboxyl group, hydrogen, and R group

Central (alpha) carbon

The middle carbon that the four groups attach to

Amino group

Nitrogen-containing group (NH₂ / NH₃⁺)

Carboxyl group

Acid group (COOH / COO⁻)

R group (side chain)

The variable group on an amino acid

Ribosome

Large structure of protein + RNA that builds proteins

Ribosomal RNA (rRNA)

The RNA part of the ribosome

Peptide bond

Covalent bond between the carboxyl carbon of one amino acid and the amino nitrogen of the next

Covalent bond

Bond where atoms share electrons

Dehydration (condensation) reaction

Reaction that joins two molecules and releases water

Carbonyl group

C=O

Peptide group

The C=O and N–H region around the peptide bond

Dipeptide

Two amino acids joined by one peptide bond

Polypeptide

Many amino acids joined in a chain

Polymer

Long chain of repeating building blocks

Monomer

A single building block of a polymer

N-terminus (amino terminus)

End of the chain with a free amino group

C-terminus (carboxyl terminus)

End of the chain with a free carboxyl group

Polypeptide backbone

The repeating part shared by all amino acids in the chain

Resonance

Electrons shared and moving across neighboring bonds

Double-bond character

The peptide bond being short and non-rotating like a double bond

Steric strain

Stress from bulky groups being too close together

Secondary structure

Local folding patterns: alpha helices and beta sheets

Hemoglobin

Red blood cell protein that carries oxygen from lungs to cells

Backbone model

Shows only the path of the backbone

Good skeletal view; no atoms or R groups

Ribbon model

Backbone path with secondary structure as ribbons

Wireframe model

Sticks for every covalent bond

Shows overall shape and size, all atoms included

Ball-and-stick model

Balls for atoms, sticks for bonds

Shows overall shape; good for highlighting specific R groups

Space-filling model

Every atom shown at its van der Waals radius

Best view of the protein’s surface

Van der Waals radius

How much space an atom takes up

It’s the size of each sphere in a space-filling model

Levels of protein structure

Four ways of describing a protein’s structure: primary, secondary, tertiary, quaternary

They’re descriptive terms, not the order a protein folds in

Protein folding

The process of a polypeptide taking its 3D shape, driven by the chemistry of the aqueous solution

It’s complex and doesn’t go level by level

Primary structure

The amino acid sequence of a polypeptide

The most basic level; a mutation that swaps an amino acid changes it

Mutation

A change that can put a different amino acid at a position

How primary structure gets altered

Secondary Struture

Alpha helices and beta sheets

Found in essentially all folded proteins

Alpha Helicase

A coiled secondary structure

One of the two universal folds; hemoglobin has only these

Beta sheet (beta pleated sheet)

A secondary structure of strands lying side by side

The other universal fold; some proteins have only these

Tertiary structure

The overall fold of a single polypeptide, including secondary structures and the folds between them

Describes the full 3D shape of one chain

Non-covalent Bonds

Weak interactions between R groups (and backbone atoms)

Many of them together hold the protein in a stable fold

Domain

A section of one polypeptide that folds independently of the rest

Used all semester; similar domains appear across different proteins

Kinase

An enzyme that puts phosphates on other molecules

Her main example of proteins sharing a domain; key in cell signaling

Kinase Domain

The part of a kinase that does the catalytic phosphate-adding

Similar structure, function, and sequence across different kinases

Pyruvette Kinase

A single-polypeptide protein with three domains

Her real-protein example of domains

Signal transduction (cell signaling)

Cellular communication pathways

Where domains will come up again later

Quaternary structure

The interactions between multiple polypeptides in a protein whose functional unit has more than one

Not all proteins have it

Subunit

Each individual polypeptide in a multi-polypeptide protein

Each has its own tertiary structure and can have domains

Hemoglobin

Oxygen-carrying protein with four subunits: two alpha, two beta

Her main example of quaternary structure

Antibody

Protein with four subunits: two light chains, two heavy chains

Second quaternary example; shows domains within subunits

Light chain

The smaller antibody subunit (two per antibody)

Each one has two visible domains

Heavy Chain

The larger antibody subunit (two per antibody)

Pairs with light chains to make the full antibody