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Medical Sciences - Biochemistry - Level 4 > Introduction: Biochemistry > Flashcards

Introduction: Biochemistry Flashcards

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USMLE® Step 1 flashcards
1
Q

What is entropy?

A

Going from order to disorder.

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2
Q

Entropy of Energy

A

Focus - Dispersed

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3
Q

Entropy of Information

A

High - Low

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4
Q

Entropy of Organisation

A

Complex - Simple

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5
Q

General Entropy

A

Life - Death

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6
Q

Four main classes of biological molecule

A

Proteins Lipids Carbohydrates DNA (water)

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7
Q

Percentage of Biological Molecule Proteins

A

15-20%

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8
Q

Percentage of Biological Molecule Lipids

A

10 -15%

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9
Q

Percentage of Biological Molecule Carbohydrates

A

2%

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10
Q

Percentage of Biological Molecule DNA / RNA

A

1%

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11
Q

Percentage of Biological Molecule Water

A

50-65%

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12
Q

Metabolism What is Catabolism?

A

Breakdown

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13
Q

Metabolism What is Anabolism?

A

Synthesis (combination of separate elements to form a coherent whole - creating)

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14
Q

Metabolism must be tightly regulated by

A

Health Efficiency

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15
Q

Metabolism is context dependent.

A

i.e. greater caloric intake for someone in the arctic to someone in the UK.

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16
Q

Proteins General

A

Large biomolecules Mr > 10,000 Da Most abundant organic compounds in healthy humans Formed of amino acids

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17
Q

Proteins General Roles

A

Cell structure Transport Catalysis Metabolic Regulation

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18
Q

Amino Acids General

A

Amino acids are monomers, “building blocks” that bond to form peptide / protein polymers. 20 principal amino acids Same fundamental structure differentiated by side chains: asymmetric, “left handed” Essential / Non-essential

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19
Q

alpha-Amino acid structure

A

Chain of carboyx group. Alpha carbon with hydrogen and amino group. Side chain (residue; “R”) connected to alpha-carbon.

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20
Q

Amino acids

Nonpolar

A

Glycine (Gly)

Alanine (Ala)

Valine (Val)

Leucine (Leu)

Isoleucine (Ile)

Methionine (Met)

Tryptophan (Trp)

Phenylalanine (Phe)

Proline (Pro)

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21
Q

Amino acids

Polar

A

Serine (Ser)

Theronine (Thr)

Cysteine (Cys)

Tyrosine (Tyr)

Asparagine (Asn)

Glutamine (Gln)

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22
Q

Amino Acids

Electrically Charged

Acidic

A

Aspartic Acid (Glu)

Glutamic Acid (Asp)

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23
Q

Amino Acids

Electrically Charged

Basic

A

Lysine (Lys)

Arginine (Arg)

Histidine (His)

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24
Q

Features of Amino Acids

Cysteine

A

Able to form Disulfide (S-S)

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25
Q

Features of Amino Acids

Proline

A

Imide rather than Amide

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26
Q

Features of Amino Acids

Buffering capabilities

A

Weak acid groups (COOH)

Base groups (NH2)

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27
Q

Amino Acids

Peptide

A

Amino acids linked by peptide bonds

28
Q

Amino Acids

Polypeptide

A

>50 amino acids linked by peptide bonds

29
Q

Amino Acids

Proteins

A

Formed by one or more polypeptide chains

30
Q

Residue meaning

Table

A

Generic other atoms

31
Q

Non-polar meaning

A

Electromag the same

No significant +/- charge

Hydrophobic

32
Q

Polar meaning

A

Active groups

Strong +/- charge

Repel lipids

33
Q

Acidic meaning

A

Releasing hydrogens

34
Q

Basic

A

Accepting hydrogens

35
Q

Primary structure

Amino Acids

Protein

A

Peptide bonds: link the alpha-amino group to the carbonyl group of thenext.

Trans-arrangement: side chains of bonded as in opposite directions (except prolin, wich can be cis- or trans-)

By convention, start at N-terminus and end at C-terminus

No rotation around peptide bonds

36
Q

Enzymes

General function

A

Change shape to cause chemical reactions.

37
Q

Secondary Structure

A

Local organisation polypeptide chains causedby folding.

Primary structure determines how proteins fold.

Folding assisted by chaperone proteins.

Maintained by hydrogen bonds formed between amide and carboyl elements of peptide bonds.

38
Q

Alpha helix

Structure

A

3.6 a.a. residues per helix turn, 0.54nm pitch.

Densely-packed, side chains on outside

39
Q

Beta-pleated sheet

A

Parallel or anti-parallel rows of AAs linked by H-bonds.

Pleated structure

40
Q

Tertiary Structure

A

Geometric arrangement of a singly polypetide chain

Contains multiple secondary structures

Maintained by hydrophobic interactions, ionic bonds, disulfide bonds and hydrogen bonds,

41
Q

Quaternary Structure

What are oligomers?

A

Proteins made up of multiple polypetide subunits

42
Q

Quaternary Structure

homomers

A

All the same subunit

43
Q

Quaternary Structure

Heteromers

A

Different subunits

44
Q

Quaternary Structure

Subunits

A

Subunits helf together by non-covalent forces.

Can undergo rapid conformational changes.

These conformational changes enabe to facilitate protein functions.

45
Q

Non-amino acid Protein Elements

How are they further modified?

A

Attachment ofcarbohydrate, lipid, RNA groups.

Atachment of small inorganic and organic molecules: metal ions, vitamins, methyl groups, phosphorylation, etc.

46
Q

Non-amino acid Protein Elements

How are they further modified?

Cofactors

A

Usually metal ions or small organic molecules necessaru for protein activity

47
Q

Summary of Protein Structure

A

Amino acids

Peptide Bonds

48
Q

Summary of Protein Structure

Secondary structure

A

a-helix and B-pleated sheet

49
Q

Summary of Protein Structure

Tertiary Structure

A

Folded arrangement of polypeptide chain

50
Q

Summary of Protein Structure

Quaternary Structure

A

Subunit arrangement in oligomers

51
Q

Types of Protein

A

Globular Proteins

Fibrous Proteins

Membrane Proteins

52
Q

Types of Protein

Globular proteins

A

Fold into roughly spherical shape.

Usually water soluble.

Enzymes, messengers, transporters.

Usually insoluble.

53
Q

Types of Protein

Membrane Proteins

A

Embedded in the cell membrane, transmembrane or integral monotopic.

54
Q

Globular Proteins

Blood Proteins

Albumins

A

>50% of blood protein.

Transports steriods, hormones, fatty acids, stabilises blood value.

55
Q

Types of Protein

Blood proteins

Globulins

A

Various functions (e.g. inhibitors, immune system, etc.)

56
Q

Globular proteins

Haemoglobin

General

A

4 subunits (“tetramer”) in roughtly tetrahedral arrangement.

Each subunit comprises multiple a-helices binding a heme group.

Heme groups bind O2 / CO2

O2 bound in one heme induces conformation change to enhance binding at others.

57
Q

Fibrous proteins

Collagen

General

A

Most abundant mammalian protein; >20 types

Trimer - 3 subunits wrapped in a helix, rich in glycine and proline.

High strength - connective tissues (ligaments, tendons, skin), also bone, muscle, etc.

Brittle bone disease is a mutation in collagen Type 1.

58
Q

Fibrous Proteins

Elastin

General

A

Flexible - common in tissues requiring tension, stretching or deformation (lungs, arteries, bladder, skin, connective tissue)

Covalently crosslinked polypeptides that are coiled at rest, but can stretch out

Rich in non-polar aas, especially glycine, ananine, valine, proline.

Smoking promotes elastin breakdown: emphysema, wrinkles.

59
Q

Muscle proteins

Actin & Myosin

Actin

A

Globular monomers (G-actin) polymerise to fibrous, thin filament (F-actin)

60
Q

Muscle proteins

Actin & Myosin

Myosin

A

Thick filament with globular “head”

Conformational change when ATP is hydrolysed to ADP, pulling the actin filament.

61
Q

Transmembrane Proteins

A

Transmembrane portion rich in hydrophoic alpha-helices.

Often function by undergoing conformational changes

Regulateactivity between extra- and intracellular

Ion channels, transporters, receptors, enzymes.

62
Q

Membrane proteins

Ion channels

A

Proteins form pores that allow movement of ions and small molecules across the membrane.

Gated ion channels undergo conformational changes to open or close the pore.

Pentameric ion channel.

63
Q

Cystic fibrosis transport conductance regulator

A

Gated channel

Allows movement of Cl-

Mutations prevent of impair Cl- movement leading to build-up of mucus

64
Q

Membrane Proteins

Cell adhesion Molecules

A

e.g. Integrins, Cadherins

Bind cells to surroundings - other cells and extracellular matrix. Often linked to cystoskeleton.

65
Q

Summary - Protein Function

Structure

A

Globular - Spherical, usually soluble and free-floating

Fibrous (usually involved in structural tissues)

Membrane

66
Q

Summary - Protein Function

Function

A

Structural, Enzymes, Cell Transport, Carriers, Cell Signaling, Metabolic regulation

Medical Sciences - Biochemistry - Level 4 (5 decks)

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